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diff test-data/out1.align1.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 (3 days ago)
parents 6ec40b104f9d
children
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--- a/test-data/out1.align1.fasta	Tue Oct 12 14:21:06 2021 +0000
+++ b/test-data/out1.align1.fasta	Thu Mar 20 07:18:12 2025 +0000
@@ -1,104 +1,114 @@
->Alt1 (Estimated allelic Fraction: 0.52)
-TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAA
-TCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC
-ACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC
-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCAT
-GCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCG
-GAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCG
-AACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAA
-AATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTC
-TTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGC
-TGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTC
-TGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGA
-ACCNTTGCCGCAAGCTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA
-GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAATNCCATATGGTANNG
-GGCNNNAGCCCGCNTNNCCT
->Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-718 forward
-TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT
-CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA
-CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC
-AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT
-GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT
-CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT
-TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC
-GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT
-TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC
-CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC
+>Alt1 (Estimated allelic Fraction: 0.63)
+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT
+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG
+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT
+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC
+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC
+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG
+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC
+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG
+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGC
+TAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATAT
+TAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGA
+GGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGC
+AACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTTGTTTCCCCTGTT
+>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: 118
+Alignment score: 3039
 #-------------------------------------------------------------------------
 
-Alt         1 TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCA
-              |                                                           
-Ref         1 T-----------------------------------------------------------
+Alt         1 --------------------------------------------------ACAGGCATTA
+                                                                ||||||||||
+Ref      1846 CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTA
 
-Alt        61 TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGA
-                                                                          
-Ref         2 ------------------------------------------------------------
+Alt        11 ATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1786 ATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAA
 
-Alt       121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCT
-                                                                          
-Ref         2 ------------------------------------------------------------
+Alt        71 GAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1726 GAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACT
 
-Alt       181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA
-                                                                          
-Ref         2 ------------------------------------------------------------
+Alt       131 TTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGG
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1666 TTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGG
 
-Alt       241 GGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG
-                                                                          
-Ref         2 ------------------------------------------------------------
+Alt       191 TGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTAC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1606 TGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTAC
 
-Alt       301 TGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------T
-                    ||||||||||||||||||||||||||||||||||||||||             |
-Ref         2 ------TCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTT
+Alt       251 CACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCAC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1546 CACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCAC
 
-Alt       349 CCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATC
+Alt       311 CTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Ref        56 CCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATC
+Ref      1486 CTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG
 
-Alt       409 TCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA
+Alt       371 CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAA
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Ref       116 TCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA
+Ref      1426 CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAA
 
-Alt       469 TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACA
+Alt       431 ACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTT
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Ref       176 TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACA
+Ref      1366 ACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTT
 
-Alt       529 ATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTG
+Alt       491 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA
               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Ref       236 ATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTG
+Ref      1306 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA
 
-Alt       589 TGTCTTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA
-              ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
-Ref       296 TGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA
+Alt       551 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1246 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC
 
-Alt       649 ATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTG
-              |||||||||| |||||||||||||||||||||||| ||||||||||||||||||||| ||
-Ref       356 ATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTG
+Alt       611 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1186 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA
 
-Alt       709 CTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACTATCAAAGGTATGTTGCCCCGGT
-              ||||||||||||||| || |||||| ||| |||| |||||||| ||||||||||||  ||
-Ref       416 CTGCTATGCCTCATCTTCTTGTTGG-TTCTTCTGGACTATCAA-GGTATGTTGCCC--GT
+Alt       671 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1126 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA
+
+Alt       731 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1066 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT
 
-Alt       769 TTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGAACCNTTGCCGCAAG
-              ||||| |   |||||||| ||||||| ||  ||||| | ||||||| ||  ||||| || 
-Ref       472 TTGTCCTC--TAATTCCA-GGATCATCAA--CCACC-AGTACGGGACCC--TGCCG-AAC
+Alt       791 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref      1006 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT
 
-Alt       829 CTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA
-              ||||||||||| || ||||| ||||  || | |  |||||||||| ||||||||||||||
-Ref       523 CTGCACGACTC-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAA
+Alt       851 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref       946 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT
 
-Alt       889 GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAAT
-               ||||||||||||| ||||| ||||| |  |  |||||||||||||||| ||| ||||| 
-Ref       578 CCTTCGGACGGAAATTGCAC-TTGTATTCCC--ATCCCATCATCATGGGCTTTCGGAAAA
+Alt       911 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC
+              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+Ref       886 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC
 
-Alt       949 NCCATATGGTANNGGGCNNNAGCCCGCNTNNCCT--------------------------
-                | ||||| |  ||||   ||||||  |  |||                          
-Ref       635 TTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTT
+Alt       971 CTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGTTG-TTTCCCCTGTT---
+              ||||||||||||| ||||||||||||||||||||||||||||||| |||| ||||||   
+Ref       826 CTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAG
 
-Alt       983 ------------------------
-                                      
-Ref       695 CAGTGGTTCGCCGGGCTTTCCCCC
+Alt      1026 -----------------------------------------------
+                                                             
+Ref       766 CTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGT
 
 #-------------------------------------------------------------------------
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