+Processed file: input.pir
+Number of sequences: 17
Alignment assumed to be: Protein
+New number of positions: 56 (selected positions are underlined in blue)
+
+ 10 20 30 40 50 60 + =========+=========+=========+=========+=========+=========+ +nad3_parde ------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF +nad3_acaca ---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF +nad3_allma --------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL +nad3_apec -----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL +nad3_arath ---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS +nad3_balca -------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ +nad3_chocr ------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF +nad3_drome -------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK +nad3_human -------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM +nad3_ktun -------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK +nad3_lter -------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK +nad3_marpo -----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF +nad3_metse ---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF +nad3_picca MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF +nad3_podan -------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF +nad3_prowi ----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF +nad3_recam -----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF + ############# + + + 70 80 90 100 110 120 + =========+=========+=========+=========+=========+=========+ +nad3_parde D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA +nad3_acaca E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI +nad3_allma G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI +nad3_apec N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI +nad3_arath G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL +nad3_balca A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI +nad3_chocr D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI +nad3_drome S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY +nad3_human S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA +nad3_ktun S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL +nad3_lter S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI +nad3_marpo D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV +nad3_metse G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV +nad3_picca R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI +nad3_podan LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV +nad3_prowi D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI +nad3_recam D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI + ############################ ####### + + + 130 140 150 + =========+=========+=========+=== +nad3_parde YEWKKGALEWA---------------------- +nad3_acaca YEWQKGALEWD---------------------- +nad3_allma YEFVSGAITDSF--------------------- +nad3_apec FEWVQGGLDWAE--------------------- +nad3_arath YEWKRGASDRE---------------------- +nad3_balca YEWMEGGLEWAE--------------------- +nad3_chocr YEWYKGALEWE---------------------- +nad3_drome HEWNQGMLNWSN--------------------- +nad3_human YEWLQKGLDWTE--------------------- +nad3_ktun HEWSEGSLEWFSSSN------------------ +nad3_lter HEWKEGSLDWSS--------------------- +nad3_marpo YEWKKGALDWE---------------------- +nad3_metse YEWLKGGLEWE---------------------- +nad3_picca IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI-- +nad3_podan YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI +nad3_prowi YEWRKGALDWS---------------------- +nad3_recam YEWKKGALDWE---------------------- + ######## + + + ++
+ + +
Parameters used +Minimum Number Of Sequences For A Conserved Position: 9 +Minimum Number Of Sequences For A Flanking Position: 14 +Maximum Number Of Contiguous Nonconserved Positions: 8 +Minimum Length Of A Block: 10 +Allowed Gap Positions: None +Use Similarity Matrices: Yes + +
Flank positions of the 3 selected block(s) +Flanks: [48 60] [64 91] [114 128] + +New number of positions in input.pir-gb: 56 (36% of the original 153 positions) + + + + diff -r 000000000000 -r daf61c79c8b4 test-data/Gblocks_Selected_Blocks_on_data_95.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Gblocks_Selected_Blocks_on_data_95.txt Thu Apr 12 06:59:23 2018 -0400 @@ -0,0 +1,68 @@ +>P1;nad3_parde + +EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL* + +>P1;nad3_acaca + +EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL* + +>P1;nad3_allma + +EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI* + +>P1;nad3_apec + +EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL* + +>P1;nad3_arath + +EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS* + +>P1;nad3_balca + +EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL* + +>P1;nad3_chocr + +EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL* + +>P1;nad3_drome + +EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML* + +>P1;nad3_human + +EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL* + +>P1;nad3_ktun + +EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL* + +>P1;nad3_lter + +EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL* + +>P1;nad3_marpo + +EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL* + +>P1;nad3_metse + +EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL* + +>P1;nad3_picca + +NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI* + +>P1;nad3_podan + +EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL* + +>P1;nad3_prowi + +EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL* + +>P1;nad3_recam + +EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL* + diff -r 000000000000 -r daf61c79c8b4 test-data/Gblocks_on_data_95.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Gblocks_on_data_95.txt Thu Apr 12 06:59:23 2018 -0400 @@ -0,0 +1,8 @@ + +17 sequences and 153 positions in the first alignment file: +input.pir + +input.pir +Original alignment: 153 positions +Gblocks alignment: 56 positions (36 %) in 3 selected block(s) + diff -r 000000000000 -r daf61c79c8b4 test-data/nad3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nad3.fasta Thu Apr 12 06:59:23 2018 -0400 @@ -0,0 +1,101 @@ +>P1;nad3_parde + +------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF +D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA +YEWKKGALEWA----------------------* + +>P1;nad3_acaca + +---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF +E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI +YEWQKGALEWD----------------------* + +>P1;nad3_allma + +--------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL +G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI +YEFVSGAITDSF---------------------* + +>P1;nad3_apec + +-----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL +N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI +FEWVQGGLDWAE---------------------* + +>P1;nad3_arath + +---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS +G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL +YEWKRGASDRE----------------------* + +>P1;nad3_balca + +-------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ +A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI +YEWMEGGLEWAE---------------------* + +>P1;nad3_chocr + +------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF +D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI +YEWYKGALEWE----------------------* + +>P1;nad3_drome + +-------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK +S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY +HEWNQGMLNWSN---------------------* + +>P1;nad3_human + +-------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM +S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA +YEWLQKGLDWTE---------------------* + +>P1;nad3_ktun + +-------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK +S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL +HEWSEGSLEWFSSSN------------------* + +>P1;nad3_lter + +-------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK +S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI +HEWKEGSLDWSS---------------------* + +>P1;nad3_marpo + +-----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF +D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV +YEWKKGALDWE----------------------* + +>P1;nad3_metse + +---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF +G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV +YEWLKGGLEWE----------------------* + +>P1;nad3_picca + +MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF +R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI +IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--* + +>P1;nad3_podan + +-------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF +LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV +YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI* + +>P1;nad3_prowi + +----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF +D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI +YEWRKGALDWS----------------------* + +>P1;nad3_recam + +-----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF +D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI +YEWKKGALDWE----------------------*