Mercurial > repos > peterjc > seq_primer_clip

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fasta	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,60 @@
+>GLZRM4E04IPVGX
+CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
+>GLZRM4E04I9EJK
+CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
+>GLZRM4E04JHW0A
+TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
+>GLZRM4E04IBNFY
+CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
+>GLZRM4E04IKCQP
+CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
+>GLZRM4E04ITXFU
+CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT
+>GLZRM4E04JAY4Z
+CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
+>GLZRM4E04H9M21
+CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
+>GLZRM4E04IQDP5
+CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG
+>GLZRM4E04I0CYE
+TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT
+>GLZRM4E04I2NA7
+CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
+>GLZRM4E04I5BWJ
+CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
+>GLZRM4E04IK8WX
+GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG
+>GLZRM4E04I22QH
+CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
+>GLZRM4E04IVVFA
+GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG
+>GLZRM4E04ILU3V
+CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
+>GLZRM4E04IDVJT
+CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG
+>GLZRM4E04I3ZJ6
+CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
+>GLZRM4E04I3UBT
+CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
+>GLZRM4E04H59S1
+CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
+>GLZRM4E04JFA38
+CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
+>GLZRM4E04J4EK3
+CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
+>GLZRM4E04IK96G
+CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
+>GLZRM4E04JVL8Q
+CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT
+>GLZRM4E04IOQ36
+CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
+>GLZRM4E04JBJJ1
+CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG
+>GLZRM4E04IEFNO
+CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
+>GLZRM4E04JOT5I
+CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
+>GLZRM4E04J4HNG
+CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT
+>GLZRM4E04JC544
+CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,120 @@
+@GLZRM4E04IPVGX
+CCGACTCGAGGGTGGGTTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
++
+FIIIIIIIIHHHIDDDIIIIIIIIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1
+@GLZRM4E04I9EJK
+CCGACTCGAGTTTTTTAAATGCTTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
++
+IIIIGCBCF=422211:882<<9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII
+@GLZRM4E04JHW0A
+TCGACTCGAGCCCCTCAAGTCCAATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
++
+IIIIIIIIIF;;;;HFDDEHHHIIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,
+@GLZRM4E04IBNFY
+CCGACTCGAGAGGAAGATGTGGGCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
++
+IIIIIIIIIIIIIIIIIIII666IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII
+@GLZRM4E04IKCQP
+CCGACTCGGAGTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
++
+IIIIIH???GDGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129
+@GLZRM4E04ITXFU
+CCGACTCGAGAGAAAATTCAGGCAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT
++
+IIIIGDD===@@3111DD@><<DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7
+@GLZRM4E04JAY4Z
+CCGACTCGAGGTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
++
+FIIIIIIIIIIHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81
+@GLZRM4E04H9M21
+CCGACTCGAGGAAGGGAAGTCCCTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
++
+IIIIIIIIIIIIIGGGIIII;;;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII
+@GLZRM4E04IQDP5
+CCGACTCGAGGGGAAGTTTACGTTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG
++
+IIHIIIIE@111177?@88<AA88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII
+@GLZRM4E04I0CYE
+TTCAGGAGGTGATCACCGGCGTTCGTGCCGCCGGCTTTAATGGCGAGGGAGACTAGGGAAGCGTTAGGGTTTGGGTTCGGT
++
+HHHIIHIIIIIIIIIIIIIIIIIIIIIIIIIHHHHHHHHHHFFFFFFFFFFFFCC666::ADDBA?888866,,,,,.,,,
+@GLZRM4E04I2NA7
+CCGACTCGAGTTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
++
+FGDBAA??==21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113,
+@GLZRM4E04I5BWJ
+CCGACTCGAGTGTGGGAAATGCTTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
++
+FIIIIIIIIIIIIHHHHHHIIIIIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,-
+@GLZRM4E04IK8WX
+GCGCAAGCTTCGCGCCCAGGGTAGAATCCATAGCTGGTACACTCCGCGCGGGATCCGCG
++
+IIIIIIIIIIIIIIH??;;;HIIICCGIIIIIIH????IIIIIIIIII?666HIIIIII
+@GLZRM4E04I22QH
+CCGACTCGAGCCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
++
+444:<:34466,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232-----
+@GLZRM4E04IVVFA
+GGATGGGGTAATATGAAGGGTCGAGATCTTTATGCTGACGGGGAACGGTGTCGTTTCAACCTGAAAAGAGGCTCGAGTCGG
++
+HHIICCBBIIIIIIIIIHHHIIIIIIIIGGGIIIIIIIH6666IIIAAIIIIH;;;IHHHHIIBBCCIIIIIIIIIIIIII
+@GLZRM4E04ILU3V
+CCGACTCGAGCTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
++
+DDDDFECADBBA>=;9674220..42>==?>8;?AEFFAA>=?9999/0
+@GLZRM4E04IDVJT
+CCGACTCGAGGTGTGGTCTGGGGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG
++
+IIIIIIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@@@ICCHHDDDDHII
+@GLZRM4E04I3ZJ6
+CCGACTCGAGGGGAGTAAATGCATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
++
+CCGIIIIIIAAAAIFH;;;IIIIIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII
+@GLZRM4E04I3UBT
+CCGACTCGAGAAAACCTTTACGAATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
++
+GGGIIIIIGG9999GGHHHIIIIIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,,
+@GLZRM4E04H59S1
+CCGACTCGAGGGAAGGTTTACGTAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
++
+IIIIIIIII???IIGG;;;HIIIIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC
+@GLZRM4E04JFA38
+CCGACTCGACGCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
++
+:8875782222..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=<////71?<<=<5566BGGGGGEEDDDDD@<;766EE??6779IIIFFFIIHHHIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIICCAAIIFFIIIIIIIIBBBIIIIIIFFFHHIHHHHHFBBBIIIIIIII>>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III<D776<<GGGGEEB6555@BBBIIIIIIIIIIIIIIIIIIIIII@@@@BDAADBAA
+@GLZRM4E04J4EK3
+CCGACTCGAGGTGGGGTCTGGTGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
++
+IIIIIIII>>>>8888DIIIIIHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH
+@GLZRM4E04IK96G
+CCGACTCGAGCCACTCTTCAGGTCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
++
+FIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12,
+@GLZRM4E04JVL8Q
+CCGACCGAGGGATGGGTTTACGGTAGTTTAATAGCTCCCATAGGGTTGATTTTGGTTTTTAAAGAGCGTATCCCGGACGTTGATTTTGGAGGTCTGTAGGTCAGTTTCGATGTATTTTGGCGAAAGTTAGAAATTGGTGGAATTTTGAAAAATTTGACCGGGAGTGGACTTTTTGATGTCGGGGCCGGATCCCGATTTTGAAAGTTGAAATATGTCCATAATGTCAATTATGATTTGTGTGCAAAGTTTGGTATCAATCGGAGTTGTTTTGGTTTGAATCGGCGTCGGTTTCAGAATTTGAAAGTTCATAAGTTCATTAGGCATGAATTGGGGTGCGATTCGTATTTTTGATGTTGTTTGATGCGATTTATGGCCTCGAGTCACTCCGTTAGGTGTTTTGAAACTTTTTGGTATATTCGGAAGGGGTCCCGAGTGTGATTCGGATCGATAACAGAACAAAATTT
++
+../42236,,,9:2116../4---3;666?>:>>44...<:9,,,--17,,,,--,,,,,116?44449@A=<<44440..672222../00998?AAAABB=5333=====<<4466AA981118>@:?444>>===>>;;0...:00000..0@<===;;?:AAAA=36333BAAAAB9;==FFFFFF666EFDDDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFGF:::DD?FIGGGGIDDFGDDD??==DD:66DDDGDDDDA???=444=>?88///?000<889?AAAD???DDDDDIDDDIIIDD====D:DBA>>??89//---88:86888==DD???>D>>>D:88888>DDDDBBBDDDD33333DD7777D>>>?33331::,:8875222220444::::/:9:99766622226::::98:5:77600..,,,
+@GLZRM4E04IOQ36
+CCGACTCGAGTTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
++
+HHHGCD@B?0-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998
+@GLZRM4E04JBJJ1
+CCGACTCGAGGGGTAGAAATGCAAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG
++
+IIIIIIH?;;;@>IIBD@@EII555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII
+@GLZRM4E04IEFNO
+CCGACTCGAGAGGAGATTCAGGGACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
++
+IIIIIIIIIIIIIIIIIIIE666EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87
+@GLZRM4E04JOT5I
+CCGACTCGAGGGGAGTTTACGGGAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
++
+IIIIIIIII=999E144445CCCIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII
+@GLZRM4E04J4HNG
+CCGACTCGAGCCGCCCACTGTGGTAGTCAAACAATCGCGAAT
++
+FFHHHHHHFF888??=A6998><44344888877=:433624
+@GLZRM4E04JC544
+CCGACTCGAGTTTTTTAAATGCATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
++
+IIIIHIHIC4------//<=IIIIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=
Binary file test-data/primers/MID4_GLZRM4E04_rnd30.sff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,50 @@
+>GLZRM4E04IPVGX
+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
+>GLZRM4E04I9EJK
+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
+>GLZRM4E04JHW0A
+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
+>GLZRM4E04IBNFY
+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
+>GLZRM4E04IKCQP
+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
+>GLZRM4E04ITXFU
+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT
+>GLZRM4E04JAY4Z
+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
+>GLZRM4E04H9M21
+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
+>GLZRM4E04IQDP5
+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG
+>GLZRM4E04I2NA7
+TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
+>GLZRM4E04I5BWJ
+TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
+>GLZRM4E04I22QH
+CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
+>GLZRM4E04ILU3V
+CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
+>GLZRM4E04IDVJT
+GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG
+>GLZRM4E04I3ZJ6
+ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
+>GLZRM4E04I3UBT
+AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
+>GLZRM4E04H59S1
+TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
+>GLZRM4E04JFA38
+GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
+>GLZRM4E04J4EK3
+TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
+>GLZRM4E04IK96G
+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
+>GLZRM4E04IOQ36
+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
+>GLZRM4E04JBJJ1
+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG
+>GLZRM4E04IEFNO
+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
+>GLZRM4E04JOT5I
+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
+>GLZRM4E04JC544
+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,100 @@
+@GLZRM4E04IPVGX
+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
++
+IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1
+@GLZRM4E04I9EJK
+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
++
+9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII
+@GLZRM4E04JHW0A
+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
++
+IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,
+@GLZRM4E04IBNFY
+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
++
+6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII
+@GLZRM4E04IKCQP
+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
++
+DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129
+@GLZRM4E04ITXFU
+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACCCCACCTCGAGT
++
+DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>888<5//<:@G<7
+@GLZRM4E04JAY4Z
+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
++
+IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81
+@GLZRM4E04H9M21
+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
++
+;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII
+@GLZRM4E04IQDP5
+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGGCAGTCTCGAGTCGG
++
+88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CCIIIIIIIIIIIIII
+@GLZRM4E04I2NA7
+TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
++
+21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113,
+@GLZRM4E04I5BWJ
+TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
++
+IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,-
+@GLZRM4E04I22QH
+CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
++
+6,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232-----
+@GLZRM4E04ILU3V
+CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
++
+BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0
+@GLZRM4E04IDVJT
+GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACCCCACCTCGAGTCGG
++
+CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@@@ICCHHDDDDHII
+@GLZRM4E04I3ZJ6
+ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
++
+IIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII
+@GLZRM4E04I3UBT
+AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
++
+IIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,,
+@GLZRM4E04H59S1
+TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
++
+IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC
+@GLZRM4E04JFA38
+GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
++
+2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=<////71?<<=<5566BGGGGGEEDDDDD@<;766EE??6779IIIFFFIIHHHIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIICCAAIIFFIIIIIIIIBBBIIIIIIFFFHHIHHHHHFBBBIIIIIIII>>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III<D776<<GGGGEEB6555@BBBIIIIIIIIIIIIIIIIIIIIII@@@@BDAADBAA
+@GLZRM4E04J4EK3
+TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
++
+IHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH
+@GLZRM4E04IK96G
+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
++
+IIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12,
+@GLZRM4E04IOQ36
+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
++
+-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998
+@GLZRM4E04JBJJ1
+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAGTCGACTCGAGTCGG
++
+555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHIIIIIIIIIIIIIII
+@GLZRM4E04IEFNO
+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
++
+6EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87
+@GLZRM4E04JOT5I
+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
++
+CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII
+@GLZRM4E04JC544
+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
++
+IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=
Binary file test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,50 @@
+>GLZRM4E04IPVGX
+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
+>GLZRM4E04I9EJK
+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
+>GLZRM4E04JHW0A
+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
+>GLZRM4E04IBNFY
+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
+>GLZRM4E04IKCQP
+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
+>GLZRM4E04ITXFU
+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC
+>GLZRM4E04JAY4Z
+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
+>GLZRM4E04H9M21
+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
+>GLZRM4E04IQDP5
+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG
+>GLZRM4E04I2NA7
+TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
+>GLZRM4E04I5BWJ
+TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
+>GLZRM4E04I22QH
+CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
+>GLZRM4E04ILU3V
+CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
+>GLZRM4E04IDVJT
+GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC
+>GLZRM4E04I3ZJ6
+ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
+>GLZRM4E04I3UBT
+AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
+>GLZRM4E04H59S1
+TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
+>GLZRM4E04JFA38
+GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
+>GLZRM4E04J4EK3
+TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
+>GLZRM4E04IK96G
+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
+>GLZRM4E04IOQ36
+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
+>GLZRM4E04JBJJ1
+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG
+>GLZRM4E04IEFNO
+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
+>GLZRM4E04JOT5I
+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
+>GLZRM4E04JC544
+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,100 @@
+@GLZRM4E04IPVGX
+AGGTGATCACCGGCGTTCGTGCCGCCGGTTTTAATGGCGAGGGAGACTAGGGCGGCGTTAGGGTTTGGGTTCGGT
++
+IIIIIIIIIIIHHHHHHFHHFFFFFFFF===;AA;BDDDD333:9BBBA336?>ABBA?=68800.--,,,73.1
+@GLZRM4E04I9EJK
+TTGATTTGGGCCGGAAAACTGATCTAGGGGGGTTTCGGTAGACTCGTGGGGGTAGATAGGCATTTTGTGGAGCTGGGTACTGGGAGAGTGATGTACGACTTTGGGGGTTCTGTGGAGAGAAGTGGCATTTGGAGAACTCGAGTCGG
++
+9992/..//399662444<A@@9979112222AAAG:6<D?@DA@@>/////:A9EDEEGGIAB@@F=HHGFDD555:A;6/11;4BB@AABBIIIIIIHHH:::::HHIIIIIIIIIIIIIIIIGB666IIIHHHIIIIIIIIII
+@GLZRM4E04JHW0A
+AATCCCCAAAAAATTCCGTATGCCCGAAATTCCCAAATATAATGGTACGACCGATCCTAACGAACACGTCACCTCCCACACATGTGCCATCAAAGGCAACGATTTGGAGGATGATGAGATCGAATCCGTGTTGTTGAAAAAGTTCGGAGAGACCCTCGCAAAGGGAGCAATGATCTGGTATCACAACTTACCACCAAATTCCGTTGATTCTTTCGCCATGTTAGCAGATTCGTTCATAAAAGCACATGCTGGTGCCATAAAGGTTGCAACAAGGAAATCGGACCTCTTCAAAGTAAACAAAGGGGTAACGAAATACTGAGGGAATTCGTATCCCGATTTTAAATGGAGCGTATGGACTTCCCCC
++
+IIIAA??9998665333DEA<<///:;;;<<:::??;<6;;?GDD@@@@GGGGGEGDD798=889BHIIIIIIIHHHIIIIIIIIIIIIII@@@IIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII>>>>>IIIIIIIIIIIHHHIIIIHHHBBBIIIIIIIIIIIIIIIIIIIIIIFFFIIIII@@@IIIIIIIIIIIIHHHIIIIIIIFFDIIIIIIIIIIIIIICCCCIIIIIIIIIIIIIIIIIHHHDDDDIHDDDIIGH555IIIIIIIIIIIIHHHID---@::99976:44:////5055DD;??EGBBBBBBBBBBDD9988444/==DDIEHHHHHEBAA533,,
+@GLZRM4E04IBNFY
+GCTATGTGTGGTTGTGGTATTGGGATTGTTGTTTAGGGAATGTTGTGGTATATGGGAACATGTGGTGCGAGTTGTTATATTGCGTTGTTATGTTTTTTGGCACATGTGGGATTGTTTAGAGGAATTGTCATGGTGTTTGCATGGTGTTCGCTATGACTTTGATTTATGAGATGATAATATTATTGTTGTGCACTTGTGAGATTTATGCACTGATCATGTTATTAGCGAGTATCGTTAATAATTATTGTCTCTATTACCTCACGAGGTAATAGAG
++
+6IIIIIIIIIIIIIICCGIIIHHHIIIIIIIHHHIGGGHHIIIIIIHHHHIIH666HHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;;;;IIIIIIIIICCCIIIIHHHIIIIIIIIIIIIIIIIII???IIIICCDIIIIIIIIIIII???IIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIC???IIDCAEIIGGGE;5559BCIGCHBGEEGE1122@44111:@EEGIIIEHHHIIIIIIIIIIIIIIIIII
+@GLZRM4E04IKCQP
+GTCTTTTTTCAGGTATTGACACTAACAGAATAGGGAGTCTCGACCAGCGAGCTTCTCCCCGGAGGTAAGAAAAGAAGGGTTTCGGCACAGTTTATATACAGTTAAGATAATATCAAAAGCGGAAAAAGACAACATTTAGCACTTTTATGCAAAACATGTAATAAAGATCAGATAGTAAAGCCAAATATAACAATTATTCTAAGCTCGAATTCTTGGACCCTGAACCAGTGGTTCCGGGTCACACTTCCCCAGCAGAGTCGCCAGAGCTGTCACACCTCCTTTTTGCGCGCCCACCCCGAAGGGTTAAATGCGCGGGTGGAGTTTTTCCAATTTAAGTGACAATATTCGAAAATGGGATTATTTATTTAATTCAGAGTCGCCACTTGGGAAAGGTTTGGCTTTTGGTGTCCCAAGTCACCGGTTTATCCTGAACCCCA
++
+DGG6699;8HHCCGHIIIIIIIIIIIIIIIIICCCHIIIIIIIIIIIIIIIHHHII@@@@IIIIIIIIICCCCIIIHHHHHHIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIICCCCIIII?????IIIIIIICCCIIIEC4444;:II===@IIIIIIIIHHHIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHGGHIIIIIIIIIIIIIHHGGGIIIIIDCC@@AAIIIIIIIIIIIIIIIIIIIIIIIIIIIHH77775GGEB@<<DE3333B=???BGIBGGIIIIIHHHIIIII?????IIIIHHHIIIII?;;;IIIIIIBBBBIHHHIIIICDDI777IIAAIIIIDDDHHHHIIIFFFFCC77??HIII<<<@EE;9<<?DEEEEE<7799CCCC4<<=@7721129
+@GLZRM4E04ITXFU
+CAACTAGTGCCTCAACCAAGTTTAGATAGAACACTTACCTCAAACAAGCCAAAACAAAATACCGAGAAAGCCAAACGACACTCTAGAAGTGCCATCCTACGCGTAACAACCTCTGAACGGCTCGAAACTAGCTAAAAGCAACCCAAATACATCAAATAATGCCTAAGGGAAACAACCCCAAATGATAAAGGTCGAATCTTTAATCAAAAACTCAAAGTCAACCAAAAAGTCAAACCTGAACC
++
+DDEIGDDDI>>?BGGGGIIIHHHIIIGGGIIIIIIIIIIIIHHHGFFIIIBBCCI@@@=I?GGIIGGGHIIIHHHIIIIIGGGIIIIIIII@@@DDIIIIIIIIIII>>??IIIGGFFHIIIIIBBBEH<H@73333<DDDBBB@BCB>BGII;;:I??EHGGH;;1//213<00--,,,,,7773,,,44;=:<<=@@35557@55:::E=8531AA=6611,,,,,777,,,11?@>>88
+@GLZRM4E04JAY4Z
+GTTTGGTCTGGTATGAAGCTGGGGTTGTTTGGTGTAGATCGAGTTTTGACTCGAATCTTCAAATGAAGATTCGAGGACCTGGGGGTGGATTCGAAGTGTGTGGTTGGTAGATTTAGGTTCAGGTGGCATGGGGTTC
++
+IHHHIIIIIIIIIIIIIIIIFFFFIIIHHHBB@FFFFFFFFFF@@@@FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;7777A..488411189<<??>>>>332766,,,2--,,./../8>==?5555A81
+@GLZRM4E04H9M21
+CTAACTTGATTGGACATGTTTTGTCGAAAGCTAGTAACTTGAAGGTATTAATATTTCTTAGGTTTGACCGTAGGTTGACGTTATAGCTACCGGGCGATTTTAGTTTCGGGACTTTGGAGGCTCGAGTCGG
++
+;IIIIIIIIIIIIIIIIH;;;;IIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIGGGIII;;;;IIFFIIHHHIIHHHIIIIIIIIIIIIIII
+@GLZRM4E04IQDP5
+TTTTTCCAGCGAGCTGGTGAGATCGGGTGAAAGGGAAAGGTTGTTGCTGCTGTTGAGTGCTATCGTGAGGAGGAAGACGGGTGGAGGTTGTTTTTGTTGGTGAAGGTTTAGGGTCTCTGGTTATTGTGTCCTACGTGAGGGGTGGTCGTTTTCCGACGATGGTGAGCTGAAGGGTGGTCGTCGATGGAGCTCGTGGATGTTGGTCCGGCATGCATGGGTCGTGTATGGCTGCTCAGGGTGTAGGCTGGCGTTTGGACAGCACAGCATCGCCGGCAGCGTAGGGTCGTTTGGACAGGAACAACGATGCGTAAAGG
++
+88888IIIIIIIIIICCGIIIIII???II???HHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIII:66666I=BIIIIIIIIHHHIHHHIIIIIIIIIIIIIIIIIIIIIIIIICCCCIIIIIICCCCIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIHH===?=IIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIHHHIIIIIIIIIIIIIH=??DII;;;CC
+@GLZRM4E04I2NA7
+TTAAAACGCTTACGTATCTAGTCGGTAACCTGCATTAACCGGTAGTATCAATTTGGGAACATCGACTAAGTTTGCGATCTTCGAATA
++
+21,,,,///--4//,/2427:2/--/----577:9911111111,//24--,,,,,,--75/...-722424634444:<;34113,
+@GLZRM4E04I5BWJ
+TTGCGAAACTGGAGGCATTGATTGGGGATGTTCCTGAAGGTGAGGAATTTTAGACTCTTGTGACAAGGCTTGCCTACCTTGAGGTAGAATTGGCAAGGTTAAGTCAAGAGAATGCATATCTGAACAGCGAGATAGTGGTGCTGCGATGTGCTGTGGGCGAGGATGCTCCTCAACGTGGTGCTGATCGTCTCAAGGTAAAATTCCTGAACCTAAGGCATTTGGGGGC
++
+IIIHHHHFFFFFFFFFFFFFFFF??A=FFFFF<<<<<D:::@@>@>>44458:::A?AABBDDB==:::>A?444989::==ABDDFFFFFFFFFFFFFFFFFFF<::9=BBBBA:::DDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFFFFFFFFFFDDDFFFFFFFFFFFDBAAA>>4400008886?=<??@444<<>:111----,-
+@GLZRM4E04I22QH
+CCCTTCTCTGGTTTTTCTCATCTCACCTTGGCAGTAATTTTTTTGAGAATGGTAACATTATATAAATATAAAACAGCGACAAAGTTTGTGCTGCTAAAAGTGATCCTTGTAAGTTTTTGTAGTGGCGGGATTCTTTTCTTTTTGGGGATGTATTCTATGATATCAAGTATGGAGTTACTATCATTTACAGGGCATTCTTTACACCAAAAAAGAAAAAGCAACTAAACAGTTCATTTTGATTTTCTGAATGGAGTTGCTAAACATCCTCAAAAACATCTAGAGTTCCTCTCGTTCCAGACTGACCACCAAATGCAGGCTGGGATCTTCTGCCGCCATTTCTTCTGTCTGACTCCACCTGTCACACCAGACCCCC
++
+6,,--1585--,,,,,/,57:7524--..22?><<<</16661133355448??>9344?=862222.2,,,,3/33-.-,,,31112.2777:>4444@BBBBBDDDFCCCF;;;;7D;DDDDDD:::?><=22558/////4476AABDFFFFFFFFFFFFFFFFFFFFFFFFFFDDDFFD???DD?666;DDDB===A?666622222@-----<<544<888?:A<<<?11119<6666>5@BB@>=?888?9110037=<<<;--///4.97<=>444:==DAAABBDDDD???BBBBBBAA000?ADBBBAB=??:5000BBA544>AA544>7/3288@@=333==D>>?B@@><<88232-----
+@GLZRM4E04ILU3V
+CTTCCAAGTCCAAAGATGGAGAAATGAATCAAGCCCTCG
++
+BA>=;9674220..42>==?>8;?AEFFAA>=?9999/0
+@GLZRM4E04IDVJT
+GGCGGTAGTTATTCTGCGGGGGTCGTGGGTTATAGTGGTTGCGGTAAGGAGGCTGATTTCTGGGAGGTTGAGCTGGGCCTCGGTTGGCTTGTTGTGGTGGATGGTTATAAGGTTGGGCATTCATGACCATATAAGGTTGATGAGCATATGCCAAATTTGAGTGGGGGTAGTAGTGTTGTGGGGCTCTTTTCGGAAAATGGGGCCTGGGATGACGATACTCCCTTGCTTCAGAGGCTGCCATAGCCGTTTCTTCCTTCTTCTTTCCCCTTGTCGTTCCTCCAGACC
++
+CCIIIIIIIIIIIIIIG11111CI:I???HHIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIGGGIIIIIIIIII???IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIHHHHIIIIIIIIIIIIIIHHEBB@HEA?111117@;BBBBFEEC<5555CC?<<=>IIICCCCICCCCIII???IIIIIIIIIIIHHHIIIIIIIIHHHHIIIIIHHHIIIIFFI<77EEE????E???999<??EEEEEII?????DIB@
+@GLZRM4E04I3ZJ6
+ATTAAGCAGCATGACAACCCGTGTTATCAAAGGCGATAAGCGCAAAAAACTCTAAGGTCTGTTGAGGCTTTAAGCGCAAAACGCAAATAAAGCGTGGGCTTTAATGAAGAAAGGCGCAAATGCAGAAAAACAATCAAGGATTCGAGGTATTGGGCATTTGATGGGCTCGAGTCGG
++
+IIIIIIIIIIIIIII;;665CIEEEIIICCCHHHIIIIIIIII9<<<<<IHHHIIIIIIIIIIIIIH?;;;HHIIIIBB@BIIIHHGD<<<IIIIHEEIHHHHHI???IHHHIIIIIHHHIIIII=====I@@IIIIIHHCCDIIIIIIHHDDFIH666?DHHFFIIIIIIIIII
+@GLZRM4E04I3UBT
+AATCCCTAACTCTTATCCCTCGAATCCCAGCCGTGTGCTTCAAATCTTAGATCGAAAATCAGGTCGGAACCTTATCTCGTCCAATAGCCTCCAATTTCACACCACAGCTTCCCCAAGACTTCCCCGCTCCAGTCCCACGCTCAGTTTCCTTCGAATCACCCCCGAGCTCCTCAAATCTTAGGTCAAAAGAATCGACCCAAACCCTAATCCATTCATATACCACTAAACTCACACCCTGCCACCCCCGACTCTCCCTCGTTCGTAAA
++
+IIIHHHIIIIIIIIIIGGGIIIGGCBBHIIIIIIIIIIIIIHHHIIIIIIIIIICCCAGGGIIIIIIIIIIGBBBCHHIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIII>>>>IIIIIIICCCCIIIIIIIIGGGIIIIIIIIHHHIIIIIIIIIII==?<;GGGIIIIIHDDDGGHHIBAAF@@A@>33BBIIEB@??A;;;;5265;AAAAADB?677?B?;=;???CEB<:6554;6/////5;4ABB>><515455511,,
+@GLZRM4E04H59S1
+TAGTAGACAAAACTAAACATACAAACTAGGAAACATAATAAATCAAACACAAGTAAGGAAAGAGGAGCATGTAGAACCGACTAAGAACCAAATTAGGAGAAAAATCAGGCAAACCCTAATTTTGCCTGGAATCACAAATTGGCCGAAGAATCTTGGTGAATTTGAACCTCATAGCCTTGCTATGAACGTATAACGATGAAATATCGTCCAAATCTTGGAGATTAAAGCCGATCTCCTTTGATTCAAAGATTGATATTTGCCAAAAGTGAGACAAACACTAAGTAACACCACAATCTTGTAATTAGCAATGAGATAACCCCGTAAAGGGGGCTCGAGTCGG
++
+IIIIIIIICCCCIIIIIIIIIIHHHIIIIIHHHIIHHHIHHHII;;;IIIIIIIIIIIHHHIIIIIIIIIIIII????IIIIIIIIIIIHHBEE?GGE?11133CCIIIIFHHHHHIIICCBBIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIICCCIIIIIICC666?HIIIIIII?????IIIIIIIIIIGGGIIIIIGGGIIIIIIIICCCIII5554BEEEEEI9;;?CIIIIIIIIIIIIHHHHHHIHHHIIIIIIIIGDDA?A3------.-,,,...11@@>IIFIIEC
+@GLZRM4E04JFA38
+GCCTCTCAAGTCCAAAAATGAAGGAAAGTGGAATCAAACCCACGATTTGGCTCATTTTCTGCCAGTTAAACCGCACCTACGGTCCATTAACCGCTTCTGCGGCTAAAGCTCCGCACCTTCACACTTATATCCGCATCTGCGGATGCGCTTTTGCGCTCAATCGTCCGCTTCTGCAGAACCTTGGGTCCTTCTCATCTCCGTATCTGCGACTGCCCTTCCACAGAAGCGGCTCCACTCCTGCGGCTCACTCGTCGCATCTGCGACCACTGACTCCCCGGTCTAAAGGCGCACCTGCGATCCCAGCCTCGCTTCTGCGGAGCCGCACCTGCGGACTT
++
+2..23883377..,,,,,22..336668<44/127===:::9?@<311AADD=<////71?<<=<5566BGGGGGEEDDDDD@<;766EE??6779IIIFFFIIHHHIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIICCAAIIFFIIIIIIIIBBBIIIIIIFFFHHIHHHHHFBBBIIIIIIII>>>IIIIIIIIIIIII;;;DD@@DFGG<==IIIIFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII??==III<D776<<GGGGEEB6555@BBBIIIIIIIIIIIIIIIIIIIIII@@@@BDAADBAA
+@GLZRM4E04J4EK3
+TGCTACCTTTGATGAGGTTGTCGACATTGCTCGACAGATTGAGATGGTTCGTGGTCAGGAAAGGGTTGAGAGGGAGGCCAAGAGGCCTCGTGGTCAGGGTGGATTTAGCAGTGCTCATTTTGGGGGTCAGTTTCAGCACGGTAGAGGTCGTCATTTCAGACAGGCTCAGACAGCTTGGCCATTTCACCGTGGTGCATCATCTGGCCATGGTTCTCATAGTCATCAACATGGTCAGTCATCATTTAGTGCACTACCAGCGCAGAGTTCTCATCATGTCCCACCACTCAGGTATCCTTGGGTAGTTCTTTGGGCATCAGGAGCACTAATTTCGCCAGAGGGGGCTCGAGTCGG
++
+IHIIIIIHHHGGGIIIIGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGC9944488?HEEBCBIIIIIIIIIIIBBDDDCIIIIIHHHIIIIHHHIIIBBBGIIIB444453822/DDB566BIIIIIIIIIIIIIIIIII?666BIIIIIIIIIIIIIIIIIIIIIIIBBBBIIIFGG>>>GIIIIIIHEEE====4411;9BEGCDCIIIBBBIIIIIIIGGGGI999BBBAICIIDFGFFFGGGEEGDA<44479IDDDGDCBBB:11HFGEGDDEBB4444,,,57,--3,//449EE@@=A>><D:8544///5544??C24446<BIIIIIIHH
+@GLZRM4E04IK96G
+TCCAAACGCCATTAACAAACAGCTCGTCACACTCATACACACATGCACCAACACACCCAGCTGCGTCTTCATCGAGTTTCATCGAGTCTTCATCTTCTTCGTCGAAGGCAACACCTCACCACCCTCGAACCCGA
++
+IIIHHHIIIIIIIIIIHHHIFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFDCCFFFA?666?=ADDDA??????FFDFFFFFFFFFFFFFF???DBAAA::888444?=<;;96667,.--,,12,
+@GLZRM4E04IOQ36
+TTTTTAAATGCATAATAATACAAATTTGTTGCTTAATAGTATTAGAGAGAGGCATAAAATGATGTTCCCTGTATATGAGTTGATTTACGCAAATGTCCCTCTTTTAGGCTATTATTCAAATTTTGTTAATATTTTTAAAAAAATTATTTAGTCCTAAAGAAATTACCCCTTCAGGGTAACGTTAGACCTTTTGTTCATATAGTTTTCAGTTTGCTCAATCGTACATATAAAATATTAGAATGTGATCTAACGTTATAATAAAGTATCAAATTTAAACCATACTCTATTTTCACGTAAGATTTTCAGTTTGCTCAAGAGTGGAAGAGAAAATAAAAGGGTACATTTACTAAGCAGCTATGCCAAACTGGGAAAAATTTCT
++
+-,,,,.../<<<733856=;?////001//<ADDDDGEIDDDDDDDDG@899HHHABBBHG@@@@ECAAB666BBB?=688EGHHHHHHH<<;GE@444;:2222DGGHHHEEEHHHHCC6442D66B=::00000//////1772BBBGGHIGE664@444BB>9599EE=D999>BEHAGECGG@@6666<89DDDEGGH9999EHHHHHHHHEEEHHHHHHHHHH====E<@@;;;;EGGED?;666B;664BBBB=9998289441,,,---88/42;BBBB9999BBBBBEGGG::::EB666@@>BE;9:8<?8888663////;////8669/9=9443>:@9333=BBB?AAA>>=899=>55;55=9998
+@GLZRM4E04JBJJ1
+AAAGGAGGTAAGGGACATAAGGGTGCCTATAGGTTGAGAATTGGGTCATGGAACATAGTTACATTGATGGGTAAGTCTATAGAGCTGGCGAAGATCCTACAAAAGAGGAAAGTCAATATAATGTATGTCCAAGAGACTCGGTGGATAGGGTCGAGGGCGAAGAATACAGACGAGTATAAGCTATGGTACTTTGGAGTCCTGAAGGGTAAGAATGGTGTAGGCATTTAG
++
+555;;A??GIIBBCIIIIIIHHHIIIIIIIIIIIIIIIIIHH;;;<IIICCCCIIIIIIIIIIIIIIIGGGIIIIIHHHHHIIIIIIIIIIIIIIIIIIIBBBBIIHHCCCIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII;;;IIIIGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIIIIIIIIIIIHHG???=BBIIIIIIIIIIIGGGHI
+@GLZRM4E04IEFNO
+GACAAAGAAGAGGAGCTCGAGGTGAGCAGTGGGGTCGAGGCACAATGTGCCAACCCAAGCCCAAGTGGTTTCATTGTGTGCCGAGCTCGGGGAGTGTCAACCCAAAATGGTCGCTCTGAGTGGCGAGGTCACTGAGAAGGCAGTGGGTTTAGAGAAGGCAGAGTTGGCCCAGCTATCAACTGCAAGGAGAACATGGGCTTTAGAGATCATGATCCGCGTTCTCAGTTCTGAGTGGGAGGGTGATTTGGACACGGCCAAGCTCAGAGAAGAGCAGCTTGATGAGCGGATAGGGGAGCTGGAAAAAGAGACTTTGGGCCTTAGTGATCGAGTTGCTGCTCTCGAGGCCGAAAAGGCACAGTTATTGGCTCAACCGTCCTCCTCCCGCGCTTCTGCTTTCCTGATGTTGCACGATATTGTATGAGGAATGGATTCACGCTGAAGCTCAGCTAGA
++
+6EI666IIIIIIIIIIIIIIGGGIIIIIEE55666CAIIIIIIIIIIIIIICC:::IIIGGGIIIIIIHHHIIIIIIIIICCCIIIIG6666C>IIIIIIDGG>>>>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG666;:DGIIIIIIIIIIIIIIIIHHHIIIIIIIGGGIIIIIIIIIIIIIIGGGIHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHHIHHHIIIHHHIIIIICCCIIIIIIIIIIIGGGIIICCCCCGGIIIIIIIIIIICC@=I8GGED...--2+88=::=BBCEEIIIIIIIIIIIIIIIIIIIICCCIG????I@@@>EAB>=;@@771144>BEGGEEIIIB?;;E;;;<7==<=9155...22.87852228<<=9522286<<55....89784488<<9883325<9<888<87
+@GLZRM4E04JOT5I
+GAGTACTTCTCATGAGGTATTGTGTATAAGTGATATATTAGTCATTTGAGGGGGAGAGTTTGAGATCAGATAAGAGATTCCTGTATTATTGAGGTTTAGAGACTGGATGTTCTCAAAGGCAAACTATTCCTTGGTTGCGGATCGTAAAGGGAGGCTCGAGTCGG
++
+CIFIIIIIIIIIIIIHCGGHHHH???DHHIIIIIIIIIIIIIIIHFFID33333C4EEBBBIIIIIIIIIIHHHIIIIIIIIIIIHHHHHIIIIHHHHHHHIIICCDHIIIIIIHHHIIIHHHIIIII????HHHHHIIIIIIIIHHHGGGIIIIIIIIIIIII
+@GLZRM4E04JC544
+ATATTCGGGGTACAACCAAATTAAAATGGACCCCAGTGACGAAGAAAAACTTACTTTCATCACAGACAGGGGGACGTTACAGTTATAAAGTAATGCCCTTTGGTTCTCAAAAATAGCTGGAGCAACCTATCAAAGGTTGGTCACCAAAATATTCCAAGAATATTTAGAAAAATACATAGAGGTATATATAGACGATATGCTCGTCAAAACCAAACATTCTCATGATCATATTTCTCATTTATCTGTTACATTTGAAATTTTACGAAATTTAATATGAAACTCAATCCAGAAAATGTGCATTTAGGGGGC
++
+IIIIIG6666FII=<<<@@@==6699A==>====GGGBAA@C>>/////@AD6B;;<FGGIIIIIIII=====II>IIIGGGIIIIHHHGGFDIIFFFEB?//..:52,,,,,5-=AFFDGGIIIIIGFDD555BBBB??EGGEG9999B:FFIIGGGIIIIHHEIG99999B1==BBIIIIIIIIIIIIIIIIIIIIIIIIGGGACCCIIFFFIIIIIIIIIIIIIIIIHHHIIIIHHHIIIIIIIIIIHHHIBBB::7773.,,////.-269=;;;E=;=954455,,,,::9A?:446<47777=
Binary file test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/primers/dop_primers.fasta	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,16 @@
+>DOP_start
+CCGACTCGAG
+>DOP1
+CCGACTCGAGNNNNNNATGTGG
+>DOP2
+CCGACTCGAGATGNNNNNNTG
+>DOP3
+CCGACTCGAGNNNNNNAAATGC
+>DOP4
+CCGACTCGAGNNNNNNTTTACG
+>DOP5
+CCGACTCGAGNNNNNNTTCAGG
+>DOP6
+CCGACTCGAGNNNNNNAAGTCC
+>DOP7
+CCGACTCGAGANNNNNNTCTGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/primers/seq_primer_clip.py	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,358 @@
+#!/usr/bin/env python
+"""Looks for the given primer sequences and clips matching SFF reads.
+
+Takes eight command line options, input read filename, input read format,
+input primer FASTA filename, type of primers (forward, reverse or reverse-
+complement), number of mismatches (currently only 0, 1 and 2 are supported),
+minimum length to keep a read (after primer trimming), should primer-less
+reads be kept (boolean), and finally the output sequence filename.
+
+Both the primer and read sequences can contain IUPAC ambiguity codes like N.
+
+This supports FASTA, FASTQ and SFF sequence files. Colorspace reads are not
+supported.
+
+The mismatch parameter does not consider gapped alignemnts, however the
+special case of missing bases at the very start or end of the read is handled.
+e.g. a primer sequence CCGACTCGAG will match a read starting CGACTCGAG...
+if one or more mismatches are allowed.
+
+This can also be used for stripping off (and optionally filtering on) barcodes.
+
+Note that only the trim/clip values in the SFF file are changed, not the flow
+information of the full read sequence.
+
+This script is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.8 of the script. Currently it uses Python's regular
+expression engine for finding the primers, which for my needs is fast enough.
+"""
+import sys
+import re
+from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
+from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    print "v0.0.5"
+    sys.exit(0)
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg)
+    sys.exit(err)
+
+try:
+    from Bio.Seq import reverse_complement
+    from Bio.SeqIO.SffIO import SffIterator, SffWriter
+except ImportError:
+    stop_err("Requires Biopython 1.54 or later")
+try:
+    from Bio.SeqIO.SffIO import ReadRocheXmlManifest
+except ImportError:
+    #Prior to Biopython 1.56 this was a private function
+    from Bio.SeqIO.SffIO import _sff_read_roche_index_xml as ReadRocheXmlManifest
+
+#Parse Command Line
+try:
+    in_file, seq_format, primer_fasta, primer_type, mm, min_len, keep_negatives, out_file = sys.argv[1:]
+except ValueError:
+    stop_err("Expected 8 arguments, got %i:\n%s" % (len(sys.argv)-1, " ".join(sys.argv)))
+
+if in_file == primer_fasta:
+    stop_err("Same file given as both primer sequences and sequences to clip!")
+if in_file == out_file:
+    stop_err("Same file given as both sequences to clip and output!")
+if primer_fasta == out_file:
+    stop_err("Same file given as both primer sequences and output!")
+
+try:
+    mm = int(mm)
+except ValueError:
+    stop_err("Expected non-negative integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+if mm < 0:
+    stop_err("Expected non-negtive integer number of mismatches (e.g. 0 or 1), not %r" % mm)
+if mm not in [0,1,2]:
+    raise NotImplementedError
+
+try:
+    min_len = int(min_len)
+except ValueError:
+    stop_err("Expected non-negative integer min_len (e.g. 0 or 1), not %r" % min_len)
+if min_len < 0:
+    stop_err("Expected non-negtive integer min_len (e.g. 0 or 1), not %r" % min_len)
+
+
+if keep_negatives.lower() in ["true", "yes", "on"]:
+    keep_negatives = True
+elif keep_negatives.lower() in ["false", "no", "off"]:
+    keep_negatives = False
+else:
+    stop_err("Expected boolean for keep_negatives (e.g. true or false), not %r" % keep_negatives)
+
+
+if primer_type.lower() == "forward":
+    forward = True
+    rc = False
+elif primer_type.lower() == "reverse":
+    forward = False
+    rc = False
+elif primer_type.lower() == "reverse-complement":
+    forward = False
+    rc = True
+else:
+    stop_err("Expected foward, reverse or reverse-complement not %r" % primer_type)
+
+
+ambiguous_dna_values = {
+    "A": "A",
+    "C": "C",
+    "G": "G",
+    "T": "T",
+    "M": "ACM",
+    "R": "AGR",
+    "W": "ATW",
+    "S": "CGS",
+    "Y": "CTY",
+    "K": "GTK",
+    "V": "ACGMRSV",
+    "H": "ACTMWYH",
+    "D": "AGTRWKD",
+    "B": "CGTSYKB",
+    "X": ".", #faster than [GATCMRWSYKVVHDBXN] or even [GATC]
+    "N": ".",
+    }
+
+ambiguous_dna_re = {}
+for letter, values in ambiguous_dna_values.iteritems():
+    if len(values) == 1:
+        ambiguous_dna_re[letter] = values
+    else:
+        ambiguous_dna_re[letter] = "[%s]" % values
+
+
+def make_reg_ex(seq):
+    return "".join(ambiguous_dna_re[letter] for letter in seq)
+
+def make_reg_ex_mm(seq, mm):
+    if mm > 2:
+        raise NotImplementedError("At most 2 mismatches allowed!")
+    seq = seq.upper()
+    yield make_reg_ex(seq)
+    for i in range(1,mm+1):
+        #Missing first/last i bases at very start/end of sequence
+        for reg in make_reg_ex_mm(seq[i:],  mm-i):
+            yield "^" + reg
+        for reg in make_reg_ex_mm(seq[:-i], mm-i):
+            yield "$" + reg
+    if mm >= 1:
+        for i,letter in enumerate(seq):
+            #We'll use a set to remove any duplicate patterns
+            #if letter not in "NX":
+            pattern = seq[:i] + "N" + seq[i+1:]
+            assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
+                   % (pattern, len(pattern), seq, len(seq))
+            yield make_reg_ex(pattern)
+    if mm >=2:
+        for i,letter in enumerate(seq):
+            #We'll use a set to remove any duplicate patterns
+            #if letter not in "NX":
+            for k,letter in enumerate(seq[i+1:]):
+                #We'll use a set to remove any duplicate patterns
+                #if letter not in "NX":
+                pattern = seq[:i] + "N" + seq[i+1:i+1+k] + "N" + seq[i+k+2:]
+                assert len(pattern) == len(seq), "Len %s is %i, len %s is %i" \
+                       % (pattern, len(pattern), seq, len(seq))
+                yield make_reg_ex(pattern)
+
+def load_primers_as_re(primer_fasta, mm, rc=False):
+    #Read primer file and record all specified sequences
+    primers = set()
+    in_handle = open(primer_fasta, "rU")
+    reader = fastaReader(in_handle)
+    count = 0
+    for record in reader:
+        if rc:
+            seq = reverse_complement(record.sequence)
+        else:
+            seq = record.sequence
+        #primers.add(re.compile(make_reg_ex(seq)))
+        count += 1
+        for pattern in make_reg_ex_mm(seq, mm):
+            primers.add(pattern)
+    in_handle.close()
+    #Use set to avoid duplicates, sort to have longest first
+    #(so more specific primers found before less specific ones)
+    primers = sorted(set(primers), key=lambda p: -len(p))
+    return count, re.compile("|".join(primers)) #make one monster re!
+
+
+
+#Read primer file and record all specified sequences
+count, primer = load_primers_as_re(primer_fasta, mm, rc)
+print "%i primer sequences" % count
+
+short_neg = 0
+short_clipped = 0
+clipped = 0
+negs = 0
+
+if seq_format.lower()=="sff":
+    #SFF is different because we just change the trim points
+    if forward:
+        def process(records):
+            global short_clipped, short_neg, clipped, negs
+            for record in records:
+                left_clip = record.annotations["clip_qual_left"]
+                right_clip = record.annotations["clip_qual_right"]
+                seq = str(record.seq)[left_clip:right_clip].upper()
+                result = primer.search(seq)
+                if result:
+                    #Forward primer, take everything after it
+                    #so move the left clip along
+                    if len(seq) - result.end() >= min_len:
+                        record.annotations["clip_qual_left"] = left_clip + result.end()
+                        clipped += 1
+                        yield record
+                    else:
+                        short_clipped += 1
+                elif keep_negatives:
+                    if len(seq) >= min_len:
+                        negs += 1
+                        yield record
+                    else:
+                        short_neg += 1
+    else:
+        def process(records):
+            global short_clipped, short_neg, clipped, negs
+            for record in records:
+                left_clip = record.annotations["clip_qual_left"]
+                right_clip = record.annotations["clip_qual_right"]
+                seq = str(record.seq)[left_clip:right_clip].upper()
+                result = primer.search(seq)
+                if result:
+                    #Reverse primer, take everything before it
+                    #so move the right clip back
+                    new_len = result.start()
+                    if new_len >= min_len:
+                        record.annotations["clip_qual_right"] = left_clip + new_len
+                        clipped += 1
+                        yield record
+                    else:
+                        short_clipped += 1
+                elif keep_negatives:
+                    if len(seq) >= min_len:
+                        negs += 1
+                        yield record
+                    else:
+                        short_neg += 1
+
+    in_handle = open(in_file, "rb")
+    try:
+        manifest = ReadRocheXmlManifest(in_handle)
+    except ValueError:
+        manifest = None
+    in_handle.seek(0)
+    out_handle = open(out_file, "wb")
+    writer = SffWriter(out_handle, xml=manifest)
+    writer.write_file(process(SffIterator(in_handle)))
+    #End of SFF code
+elif seq_format.lower().startswith("fastq"):
+    in_handle = open(in_file, "rU")
+    out_handle = open(out_file, "w")
+    reader = fastqReader(in_handle)
+    writer = fastqWriter(out_handle)
+    if forward:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Forward primer, take everything after it
+                cut = result.end()
+                record.sequence = seq[cut:]
+                if len(record.sequence) >= min_len:
+                    record.quality = record.quality[cut:]
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+    else:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Reverse primer, take everything before it
+                cut = result.start()
+                record.sequence = seq[:cut]
+                if len(record.sequence) >= min_len:
+                    record.quality = record.quality[:cut]
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+elif seq_format.lower()=="fasta":
+    in_handle = open(in_file, "rU")
+    out_handle = open(out_file, "w")
+    reader = fastaReader(in_handle)
+    writer = fastaWriter(out_handle)
+    #Following code is identical to that for FASTQ but without editing qualities
+    if forward:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Forward primer, take everything after it
+                cut = result.end()
+                record.sequence = seq[cut:]
+                if len(record.sequence) >= min_len:
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+    else:
+        for record in reader:
+            seq = record.sequence.upper()
+            result = primer.search(seq)
+            if result:
+                #Reverse primer, take everything before it
+                cut = result.start()
+                record.sequence = seq[:cut]
+                if len(record.sequence) >= min_len:
+                    clipped += 1
+                    writer.write(record)
+                else:
+                    short_clipped += 1
+            elif keep_negatives:
+                if len(record) >= min_len:
+                    negs += 1
+                    writer.write(record)
+                else:
+                    short_negs += 1
+else:
+    stop_err("Unsupported file type %r" % seq_format)
+in_handle.close()
+out_handle.close()
+
+print "Kept %i clipped reads," % clipped
+print "discarded %i short." % short_clipped
+if keep_negatives:
+    print "Kept %i non-matching reads," % negs
+    print "discarded %i short." % short_neg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/primers/seq_primer_clip.txt	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,103 @@
+Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
+===========================================================
+
+This tool is copyright 2011 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (using the Galaxy library functions and
+Biopython). There are just two files to install:
+
+* seq_primer_clip.py (the Python script)
+* seq_primer_clip.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/primers folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
+this to tools_conf.xml.sample in order to run the tests:
+
+<tool file="primers/seq_primer_clip.xml" />
+
+There are optionally some example files required to run the functional tests,
+put these in the test-data/primers folder.
+
+test-data/primers/dop_primers.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
+test-data/primers/MID4_GLZRM4E04_rnd30.sff
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
+
+You should then be able to run the tests with:
+
+sh run_functional_tests.sh -id seq_primer_clip
+
+You will also need to install Biopython 1.54 or later. That's it.
+
+
+History
+=======
+
+v0.0.1 - Initial version (not publicly released)
+v0.0.2 - Sort primers by length (longest and therefore most specific first)
+v0.0.3 - Consider missing bases at start/end of read as mismatches
+v0.0.4 - Apply minimum length to sequences with no match too
+v0.0.5 - Count clipped & non-matched short reads separately, length bug fixes
+v0.0.6 - Added some functional tests
+v0.0.7 - Added error check for bad filename arguments
+v0.0.8 - Record version of Python script when run from Galaxy.
+       - Check for errors using Python script's return code.
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+This incorporates the previously used hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/fasta_filter
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ tar -czf seq_primer_clip.tar.gz tools/primers/seq_primer_clip.* test-data/primers/*
+
+Check this worked:
+
+$ tar -tzf seq_primer_clip.tar.gz
+tools/primers/seq_primer_clip.py
+tools/primers/seq_primer_clip.txt
+tools/primers/seq_primer_clip.xml
+test-data/primers/dop_primers.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30.fastqsanger
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger
+test-data/primers/MID4_GLZRM4E04_rnd30_fclip.sff
+test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fasta
+test-data/primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger
+test-data/primers/MID4_GLZRM4E04_rnd30_frclip.sff
+test-data/primers/MID4_GLZRM4E04_rnd30.sff
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/primers/seq_primer_clip.xml	Mon Apr 29 06:11:00 2013 -0400
@@ -0,0 +1,137 @@
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.8">
+    <description>Trim off 5' or 3' primers</description>
+    <version_command interpreter="python">seq_primer_clip.py --version</version_command>
+    <command interpreter="python">
+seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/>
+        <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/>
+        <param name="primer_type" type="select" label="Type of primers">
+            <option value="Forward">Forward (5') primers</option>
+            <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option>
+            <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option>
+        </param>
+        <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)">
+            <validator type="in_range" min="0" max="2" />
+        </param>
+        <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/>
+        <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data" label="$primer_type primer clipped">
+            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
+            <change_format>
+                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
+                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
+                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
+                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
+                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
+                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30.sff" ftype="sff" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Forward" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="false" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+        </test>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" />
+        </test>
+        <test>
+            <param name="input_file" value="primers/MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" />
+            <param name="primer_fasta" value="primers/dop_primers.fasta" />
+            <param name="primer_type" value="Reverse" />
+            <param name="mm" value="2" />
+            <param name="keep_negatives" value="true" />
+            <param name="min_len" value="35" />
+            <output name="output_file" file="primers/MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" />
+        </test>
+    </tests>
+    <requirements>
+        <requirement type="python-module">Bio</requirement>
+    </requirements>
+    <help>
+
+**What it does**
+
+Looks for the given primer sequences (within the existing clipped sequence) and
+further clips the reads to remove the primers and any preceding/trailing sequence.
+
+Reads containing a forward primer are reduced to just the sequence after (and
+excluding) the forward primer.
+
+Reads containing a reverse primer are reduced to just the sequence before (and
+excluding) the reverse primer.
+
+Degenerate primers can be specified using the standard IUPAC ambiguity codes,
+thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity
+codes) and so on.
+
+Note that for SFF files only the clip/trim positions are edited - you will still
+be able to extract the original full read (with any adapter sequence and poor
+quality sequence) if you need to.
+
+.. class:: warningmark
+
+**Note**. This tool was initially written for Roche 454 data, and should also
+work fine on Sanger or Ion Torrent as well. However, it is probably too slow
+for use on large Illumina datasets.
+
+
+**Citation**
+
+This tool uses Biopython. If you use this tool in scientific work leading to a
+publication, please cite:
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+    </help>
+</tool>