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diff test-data/out1.align2.fasta @ 1:d6ef5937ded6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3
author iuc
date Thu, 20 Mar 2025 07:18:12 +0000
parents 6ec40b104f9d
children
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--- a/test-data/out1.align2.fasta	Tue Oct 12 14:21:06 2021 +0000
+++ b/test-data/out1.align2.fasta	Thu Mar 20 07:18:12 2025 +0000
@@ -1,104 +1,114 @@
->Alt2 (Estimated allelic Fraction: 0.28)
-TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTTGTTTGGGATTTCCC
-TCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC
-ACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC
-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCAT
-GCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCG
-GAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCG
-AACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAA
-AATAAACAGGATACCGCGTAGACAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTG
-ATGGTGGGAAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAGTCCCGC
-TGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGCCACGTCCTGTGTGGGTGAGC
-TCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGNNACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAG
-AACNGGTGCGGTTTCAAAAAAGGGACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAG
-TAAAAAACACGGGGGACGCAGATGGGAGGNTNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTATTCTNNA
-AGGNNNGCGCAAGNCNNTTC
->Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-714 forward
-TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT
-CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA
-CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC
-AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT
-GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT
-CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT
-TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC
-GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT
-TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC
-CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTC
+>Alt2 (Estimated allelic Fraction: 0.34)
+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT
+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG
+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT
+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC
+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC
+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG
+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC
+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG
+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGC
+TAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATAT
+TAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGA
+GGTCCGTTTGTGGCTATGTAAATGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGC
+CACACCTTCTTCATGTTTAAGTAAACATTAGCTGCATTTACAACTACTGTGGTTTCACCTGTT
+>Ref MT121216.12501-5000 Pangolin coronavirus isolate MP789 complete genome:720-1846 reversecomplement
+CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC
+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT
+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT
+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA
+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA
+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT
+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA
+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC
+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA
+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTT
+AAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAA
+ATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAAT
+TTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTG
+TCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGGTA
+AACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGA
+AAACATTGTTAGTGAGT
 
-Alignment score: -1120
+Alignment score: 2999
 #-------------------------------------------------------------------------
 
-Alt         1 TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTT
-              |                                                           
-Ref         1 T-----------------------------------------------------------
+Alt         1 --------------------------------------------------ACAGGCATTA
+                                                                ||||||||||
+Ref      1846 CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTA
 
-Alt        61 GTTTGGGATTTCCCTCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGA
-                        |||                                               
-Ref         2 ----------TCC-----------------------------------------------
+Alt        11 ATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1786 ATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAA
 
-Alt       121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCACTCAGGCT
-                                                                          
-Ref         5 ------------------------------------------------------------
+Alt        71 GAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1726 GAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACT
 
-Alt       181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA
-                          ||||||||                       ||||||| |  | | ||
-Ref         5 ------------ACAACATT-----------------------CCACCAAGCT-CTG-CA
+Alt       131 TTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGG
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1666 TTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGG
 
-Alt       241 GGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG
-              |||          |||| | ||           ||||              |||      
-Ref        28 GGAT---------CCCAGAGTA-----------AGAG--------------GCC------
+Alt       191 TGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTAC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1606 TGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTAC
 
-Alt       301 TGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGC
-              || | ||                                        |||||||||||||
-Ref        48 TGTATTT----------------------------------------TCCTGCTGGTGGC
+Alt       251 CACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCAC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1546 CACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCAC
 
-Alt       361 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTC
-              ||||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||
-Ref        68 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTC
+Alt       311 CTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1486 CTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
 
-Alt       421 TCGAGGATTGGGGACCCTGCACCGAACATGGACAGCATCACATCAGGATTCCGATGACCC
-              |||||||||||||||||||||||||||||||| ||||||||||||||||||| | |||||
-Ref       128 TCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCC
+Alt       371 CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1426 CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAA
 
-Alt       481 CCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAAAATAAACAGGATACCGCGTAGA
-              | |||| ||||||| ||||||||||||||||||||||||||   ||  |||||||  || 
-Ref       188 CTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGT
+Alt       431 ACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1366 ACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTT
 
-Alt       541 CAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTGATGGTGGG
-              | | |  |||||||||||||||||  ||||  | ||||||  ||  |||||  |||    
-Ref       248 CTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAA
+Alt       491 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1306 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA
 
-Alt       601 AAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAG
-              || ||  ||||||   |||||| |||||| ||| ||||||||   || | |||   ||  
-Ref       308 AATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGC
+Alt       551 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1246 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC
 
-Alt       661 TCCCGCTGAAAGAAGTGGCAGCGGGGT---ATCACATACCTCTTCATCTTGCGGGAGAGC
-              |  |||||   || ||| | |||| ||   ||||  | |||||||||| ||| |    ||
-Ref       368 TATCGCTG---GATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGC
+Alt       611 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1186 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA
 
-Alt       718 CGCCACGTCCTGTGTGGGTGAGCTCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGN
-              | |  | || ||| ||| |   || |   |  |  || |  ||||||  |   |      
-Ref       425 CTCATCTTCTTGT-TGGTT---CTTCTGGACTATCAAGGTATGTTGCCCGTTTGT-----
+Alt       671 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1126 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA
+
+Alt       731 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1066 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT
 
-Alt       778 NACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAGAACNGGTGCGGTTTCAAAAAAGG
-                    || |       ||||    | | || |  || || ||  |   | |  ||   |
-Ref       476 ------CCTCTAATTCCAGGATC--ATCAACCACCAGTACGGGACCC--TGCCGAACCTG
+Alt       791 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1006 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT
 
-Alt       838 GACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAGTAAAAAACA
-               || |  |  |    || |  |    || ||||     |  ||| | ||  |  ||||| 
-Ref       526 CAC-GACTCTTGCTCAAGGAACCTCTATGTTTCCC---TCATGTTGCTG--TTCAAAAC-
+Alt       851 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 
+Ref       946 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT
 
-Alt       898 CGGGGGACGCAGATGGGAGGN-TNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTAT
-              |   ||||| | || | |    |  ||| | | |   |  | | |     || || ||  
-Ref       579 CTTCGGACGGAAATTGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCC
+Alt       911 TGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCCACACCTT
+              ||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| 
+Ref       886 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC
 
-Alt       957 TCTNNAAGGNNNGCGCAAGNCNNTTC----------------------------------
-              | |   ||     | ||   |  |||                                  
-Ref       639 TATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGT
+Alt       971 CTTCATGTTTAAG-TAAACATTAGCTGCATTTACAACTACTGT-GGTTTCACCTGTT---
+              || |||||||||| ||||||||||||||||| ||||||||||| |||||||||||||   
+Ref       826 CTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAG
 
-Alt       983 ----------------
-                              
-Ref       699 GGTTCGCCGGGCTTTC
+Alt      1026 -----------------------------------------------
+                                                             
+Ref       766 CTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGT
 
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