📄 megamerger.txt
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catggaggca aagggatcag agaaggtacc agcacctgtg gagcttgtat tccagtgagg 181920 ccagacggaa aagaaagaaa ctgaagaaga aattggtact atgagaaaat aagacaggct 181980 gatgttgtaa gagtggcagg gagctacttt taaatacagt agtcagcaaa atcctctttg 182040 agtgtttggg tggcactgga gctgagaccc aaatgacaaa aaatagtgac caggtaaaag 182100 tttgggagca aagcatttca ggtaaaggga gcagctactg caaaggctgg aaggcggaac 182160 caagctgggg gtgttgacga caaacagaag gccagtgtgg ctggagcaga gagagagact 182220 gggaggcggg tgggagatga ggtcagagag gagggcaggg gccaggtcat gcagggccat 182280 gcaagaaggg taaagcctct agatttcatc cagccacagg aagcctttaa aggtcgtcag 182340 agtgtgtggt gcgtgcgtgt gtgtgtgtgt gtgtgtgtgt gttgcagggg agagaggggg 182400 agggagagag agagagagag agagaagagg gaggtgagca gaggtgattg gatttttttt 182460 tcttttgaca tggtgtcttg ctctgtggcc taggctggag tgcagtggca ccatcatagc 182520 ccactgcaac ctcaaaacca tgggctcaag tcatccttcc acctcagctt cccaagtatc 182580 taggactaca ggtgtgtgcc actgtgcctg gctaatttta aaaaatattt taaaattttt 182640 gttgagacag ggtctatgct gctcaggctg gtctcgaact cctggtttca agtgatctgc 182700 ccatcttggc ctcccaaagt ttttttttgt tagtttgaga ggcggtttcg ctcgttgccc 182760 aggctggagt gcaatgactg atctcatctc actgcaacct ctgcctcctg ggttcaagcg 182820 attctcctgc ttcagcctcc caagtagctg ggattacagg tgcatgccac cattcccggc 182880 taattttttg tatttagtag agatggggtt tcaccatgtt agtcaggctg atctcaaact 182940 cctgacctca ggtgatccgc ctgcctcagc ctcccaaagt tttgggatta caggtgtgag 183000 ccaccatgct gggccagcct cccaaagttt tgggattaca ggcatgagtc accacactgg 183060 ccctggattt tttttctttc ttttttttgg agacggagtc tcactctgtt gcccaggctg 183120 gagtgcaatg gcgtaatctc agctcactgc aacctctgct gcccgggttc aaacgattct 183180 cctgtcttag cctcctgagt agctgggatt ataggtgcat gccaccatgc ctggctaatt 183240 tttgtacttt tagtagagaa agtacaccat cttggccagg ctggtctcga actcctgacc 183300 tcaggtgatc cacttgcgtc ggcctcccaa agtgctggga ttacaggcgt gagacaccgc 183360 acccagcctt tttttttttt tttcttttaa gacagaatcg ctctgtcacc caggctggag 183420 tgcagtggca caatctcggc tcactgcaac ctctgcctcc caggtttaag caatccacct 183480 atgtcagtct cccaagtagc tgggattata ggtgcatgtc accatgcctg gctaattttt 183540 gtacttttag tatagaaagt acaccatgtt ggccaggctg gtcttgaact cctgacctca 183600 agtgatccgc ctgcctcagc ctcccgaagt gctggaatta cagacatgtg ccactgcacc 183660 cggcctggtt ttttttttct aagagatgga gtctcacttt tctgcccagg ttggagtgca 183720 atggcaccat catagctcac tgcagccttc aactcttggc ctcaggcaat ccttgcacct 183780 tagcctcgca gtgttgggat tacaggcatg agccactgag ccttgcctgg actttttttt 183840 ttttttgaga tggcgtctcg ctctgttgcc caggttggag tgctacggca tgatcttggc 183900 tcactgcaac ttccacctcc caggttcaag cgattctctt gcctcggccc cccgagtagc 183960 tgggattaca ggcatgcgcc accgtgcctg gctaattttg gtatttttag tagagatagg 184020 gtttcatcat gttgggcagg ctggtcttga actcctgacc tcgtgatcca cccacctcgg 184080 cctcccaaag tgctgggatt ataggcatag ccaacgcgcc cagcctggac ttgtttttaa 184140 aagatcactg tggctcctgt gtttaggctg gctggtagga gacaggtggc agtggcattg 184200 atggtgaaga gaaaatagtg gcagccatgg agatggagag aagtagacaa gtttgggata 184260 tattatacat tccaggggta gaaacaacag gactagatga tggattgatg ggtgggagat 184320 gtagatactg ggagagaagc aggattctga tggatggaaa aactaaaaaa ttctattttg 184380 ggtgtggtaa gtctaagtct attagacatg caagtagaga tgtcactggg cagatacaca 184440 tctggatttc aggggcaagg tccaagctag agaaagaaac ctgggcatgg tcagcatgag 184500 gatggtgttt aaagccatgg aacttatctt gtgcatccct ataagacccc tttgaggcac 184560 ttgtttcccc tcacaatgga tgcagtgcat cttccattct gaattccaga ggcaacaacc 184620 tcctgctcct agaagctaaa ctctccagac ttagtcttct gaattc 184666//Output file format Output files for usage example File: report# Report of megamerger of: AP000504 and AF129756AP000504 overlap starts at 1AF129756 overlap starts at 6036Using AF129756 1-6035 as the initial sequenceMatching region AP000504 1-846 : AF129756 6036-6881Length of match: 846WARNING!Mismatch region found:Mismatch AP000504 847-847Mismatch AF129756 6882-6882Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 848-1794 : AF129756 6883-7829Length of match: 947WARNING!Mismatch region found:Mismatch AP000504 1795-1795Mismatch AF129756 7830-7830Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 1796-2272 : AF129756 7831-8307Length of match: 477WARNING!Mismatch region found:Mismatch AP000504 2273-2273Mismatch AF129756 8307Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 2274-2465 : AF129756 8308-8499Length of match: 192WARNING!Mismatch region found:Mismatch AP000504 2466-2466Mismatch AF129756 8500-8500Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 2467-2654 : AF129756 8501-8688Length of match: 188WARNING!Mismatch region found:Mismatch AP000504 2655-2658Mismatch AF129756 8688 [Part of this file has been deleted for brevity]WARNING!Mismatch region found:Mismatch AP000504 95451-95451Mismatch AF129756 101481-101481Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 95452-96649 : AF129756 101482-102679Length of match: 1198WARNING!Mismatch region found:Mismatch AP000504 96650-96650Mismatch AF129756 102680-102680Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 96651-97272 : AF129756 102681-103302Length of match: 622WARNING!Mismatch region found:Mismatch AP000504 97273-97274Mismatch AF129756 103302Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 97275-97715 : AF129756 103303-103743Length of match: 441WARNING!Mismatch region found:Mismatch AP000504 97716-97716Mismatch AF129756 103744-103744Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 97717-97826 : AF129756 103745-103854Length of match: 110WARNING!Mismatch region found:Mismatch AP000504 97827-97827Mismatch AF129756 103855-103855Mismatch is closer to the ends of AP000504, so use AF129756 in the merged sequenceMatching region AP000504 97828-100000 : AF129756 103856-106028Length of match: 2173AP000504 overlap ends at 100000AF129756 overlap ends at 106028Using AF129756 106029-184666 as the final sequence File: ap000504.merged>AP000504 AP000504.1 Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.gaattctctccctcccatctgtggctgagattaaagatctgcacctgaagcactgaagaatgtgtgggtaattaaattaccctgccgattcctggagatgctgattacctggagatgacctcagagattatcctaaattaactcctacaagacacacattgcagcgggaggtgaggtaggggaaggattgtgcacctgaggctagcaaaggtttccactctgtttagagatgatgtcaccagtgcgtttacatttgcgttgtgttcacacattgagtgctactatgtacaagaccatgtgtcagacactgaggtaacaggtatagctactagatagagttcatagctatggaggcaagcagattcactgactgctaattctaacatgatgtgacagtgcaactagaaaaacataaacaagcactatgtgagcacaaagaaggtgcacatcaactccttacaggtacctgtaaaagccaaagggtaacagttggattgcaccttgaagaggatgcacttttttttttttttaagacagaatctcactctgttgcccaggctggagtgcagtggggcaatctgggctcacttcaacctctacctcccgagttcaagcaattctcctgcctcagcctcctgagtagctggtactagaggcatgcgccatgatgctgggctaatttttgtattttcggtagacgtgaagtttcaccaagttggccaggctggtcttgaactcctgacctcaaatcatccacccacctcagcctcccaaaatgctgagactacaggcgtgagccaccgcgcctgacctggatgtaagattttgataggtacagaacaaggaaaagactttccaggccgggcacagtggcttatgcctgtaatcccagcactttgggaggccgaggtgggcagatcacgaggtcagcagttcaagaccagcgtggccaacatggtgaaatcccatctctactaaaaatacaaaaattagccaggcatggtggtgggtccctgtaatcccagctactccggaggctgaggcaggagaattgcttgaacctgggaggtggaggttgcagtgagcaaagaccgcgccactgcactccagcctgggtgacagagggagactccgtctcaaaaaaaaaaaaaaaagactttccagaaggagcagcataaacacaggcatgacatgtttccataatggcaagtggccctaaatgactagaatataaggtagatccagtaggaaaggacttagaaggggctttggaaggtgagtctggaaattaaaactggggtaaacgtgatggaccctgaacatcattatactgcttaagatgctaatcttaatcctgaaggtaatgggaaaacctcctaaggtttatgttattttctttctacttaggctatttaaaaagtggagtgacggccaggcgcagtgactcatgcctgtaatcccagcactttgggaggccgaggtgggcggatcaccaggagttcgagaccagcctgaccaacatggtgaaaccccgcctctactgaaaatacaaaaattagccaggtgtggtggtgggcgcctgtaatcccagctacttgggaggctgaggcagaagaattgcttgaacccgggaagtggaggttgcagtgagcagagatcgtgccattgtactccagcctgggcaacaagagcgaaactcagtcacaaaaaaaaaaaaaaaaaaaaaggagtgacatgcttagatctctgttttggaatgacaggttttttgtttctagcatcaatccaaggttcatggcttgagaaggtgtactgccagcaatgccattaaccagcaaagggaatgcaggaagaggaacagatctggtgggcatcagtttggatgctctgagtttgagctgcctgtgaaaactgcaggtggtgatatgcaattaacattcacatacggagttcaaaactagagacacaaatttgagagtcatcacagaaatgtgaagtgtgttttctataactaaagataaccatgctaacatagccatgtgttacattagcattttttttttttttgagacggagtctcactctgttgcccaggctgaagtgcagtgcacaatcttggctcactgcaacctccacctcctgggttcaagcgattctcctgccttagtctcctgagtagctggaattacaggcacctaccaacacgcttggctaatttttgcattttagtagagatggggctttaccatgttggccagctggtctcaaactcctgacctcaagtgattcacccaccttggccccccaaagtgctgggattacaggtgtgagccactgtgcccggccttacattttgtgttttttcctgctgcttgtatgtgtgcaagtctgtgtatcatcaatgggtatatgtgtacctgcgctgacaacaaaaaatgagatgcatatcagctactacacaaagctgttataaggatgaaatgcagttagccagtgctcagtaaagggcagttgctttactactactaggtggggtggtgtatgtgagaatctgtatactgccattagtaggctttagtatgtagtgtgcatatggaattcatgcattagtgtgtagtatgtgtgggacccactcacctgagcagcttctctccccacttacagtggcatctgttgaggattcctgtgagggataaggcagggagtgaacttgttacaaggcagggacagggaatggaatgtgtttatgtgtctaagctgaggcatccaggtcagaggtgctggttgttgaggaagctggcctgggagggcacaaaggcagccaaagctggtgcctggccacaaatatgagctgggattaccgtacatggagatgggggaagggatggacactcacagggacacttagccagaaaaatacacaaagcagacctagttaaa [Part of this file has been deleted for brevity]accccctaaataaaacttctcctctaccccaacccaaccctgtttctagggctaatcttgaaaccagtttaccaccactcctaacactaaacttaaatctgactctaaatgtaagtccaatctgagccacaagcctaaagttgaactttatcctgctttatgaattattcatccattcctccatttagtgagtatctgcgtgcctaacacatgctgggcattgtcctaaggcaggagggacatggaggcaaagggatcagagaaggtaccagcacctgtggagcttgtattccagtgaggccagacggaaaagaaagaaactgaagaagaaattggtactatgagaaaataagacaggctgatgttgtaagagtggcagggagctacttttaaatacagtagtcagcaaaatcctctttgagtgtttgggtggcactggagctgagacccaaatgacaaaaaatagtgaccaggtaaaagtttgggagcaaagcatttcaggtaaagggagcagctactgcaaaggctggaaggcggaaccaagctgggggtgttgacgacaaacagaaggccagtgtggctggagcagagagagagactgggaggcgggtgggagatgaggtcagagaggagggcaggggccaggtcatgcagggccatgcaagaagggtaaagcctctagatttcatccagccacaggaagcctttaaaggtcgtcagagtgtgtggtgcgtgcgtgtgtgtgtgtgtgtgtgtgtgtgttgcaggggagagagggggagggagagagagagagagagagagaagagggaggtgagcagaggtgattggatttttttttcttttgacatggtgtcttgctctgtggcctaggctggagtgcagtggcaccatcatagcccactgcaacctcaaaaccatgggctcaagtcatccttccacctcagcttcccaagtatctaggactacaggtgtgtgccactgtgcctggctaattttaaaaaatattttaaaatttttgttgagacagggtctatgctgctcaggctggtctcgaactcctggtttcaagtgatctgcccatcttggcctcccaaagtttttttttgttagtttgagaggcggtttcgctcgttgcccaggctggagtgcaatgactgatctcatctcactgcaacctctgcctcctgggttcaagcgattctcctgcttcagcctcccaagtagctgggattacaggtgcatgccaccattcccggctaattttttgtatttagtagagatggggtttcaccatgttagtcaggctgatctcaaactcctgacctcaggtgatccgcctgcctcagcctcccaaagttttgggattacaggtgtgagccaccatgctgggccagcctcccaaagttttgggattacaggcatgagtcaccacactggccctggattttttttctttcttttttttggagacggagtctcactctgttgcccaggctggagtgcaatggcgtaatctcagctcactgcaacctctgctgcccgggttcaaacgattctcctgtcttagcctcctgagtagctgggattataggtgcatgccaccatgcctggctaatttttgtacttttagtagagaaagtacaccatcttggccaggctggtctcgaactcctgacctcaggtgatccacttgcgtcggcctcccaaagtgctgggattacaggcgtgagacaccgcacccagcctttttttttttttttcttttaagacagaatcgctctgtcacccaggctggagtgcagtggcacaatctcggctcactgcaacctctgcctcccaggtttaagcaatccacctatgtcagtctcccaagtagctgggattataggtgcatgtcaccatgcctggctaatttttgtacttttagtatagaaagtacaccatgttggccaggctggtcttgaactcctgacctcaagtgatccgcctgcctcagcctcccgaagtgctggaattacagacatgtgccactgcacccggcctggttttttttttctaagagatggagtctcacttttctgcccaggttggagtgcaatggcaccatcatagctcactgcagccttcaactcttggcctcaggcaatccttgcaccttagcctcgcagtgttgggattacaggcatgagccactgagccttgcctggacttttttttttttttgagatggcgtctcgctctgttgcccaggttggagtgctacggcatgatcttggctcactgcaacttccacctcccaggttcaagcgattctcttgcctcggccccccgagtagctgggattacaggcatgcgccaccgtgcctggctaattttggtatttttagtagagatagggtttcatcatgttgggcaggctggtcttgaactcctgacctcgtgatccacccacctcggcctcccaaagtgctgggattataggcatagccaacgcgcccagcctggacttgtttttaaaagatcactgtggctcctgtgtttaggctggctggtaggagacaggtggcagtggcattgatggtgaagagaaaatagtggcagccatggagatggagagaagtagacaagtttgggatatattatacattccaggggtagaaacaacaggactagatgatggattgatgggtgggagatgtagatactgggagagaagcaggattctgatggatggaaaaactaaaaaattctattttgggtgtggtaagtctaagtctattagacatgcaagtagagatgtcactgggcagatacacatctggatttcaggggcaaggtccaagctagagaaagaaacctgggcatggtcagcatgaggatggtgtttaaagccatggaacttatcttgtgcatccctataagacccctttgaggcacttgtttcccctcacaatggatgcagtgcatcttccattctgaattccagaggcaacaacctcctgctcctagaagctaaactctccagacttagtcttctgaattc A merged sequence is written out. Where there has been a mismatch between the two sequences, the merged sequence is written out in uppercase and the sequence whose mismatch region is furthest from the edges of the sequence is used in the merged sequence. The name and description of the first input sequence is used for the name and description of the output sequence. A report of the merger is written out.Data files None.Notes If you run out of memory, use a larger wordsize.References None.Warnings None.Diagnostic Error Messages None.Exit status It always exits with status 0.Known bugs None.See also Program name Description cons Creates a consensus from multiple alignments merger Merge two overlapping sequences Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory. A graphical dotplot of the matches used in this merge can be displayed using the program dotpath.Author(s) Gary Williams (gwilliam ⌨️ 快捷键说明
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