Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_33121
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1848
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Found at i:1168 original size:612 final size:611
Alignment explanation
Indices: 1--1831 Score: 2809
Period size: 612 Copynumber: 3.0 Consensus size: 611
* * * * * *
1 ATGACACCAGCTGTAATTGCTAGCGTTGAAACACTGCTAGAGAAA-TGGAAAGGCCAAGAAGGTA
1 ATGACACCAGCTGTAATTGCTAGTGTTGAAACAATGCTAGA-AAAGTGGAAAGGCTATGTAGGCA
* *
65 AAGAGATTGAAGTGT-TCAATGAATTTAGATTATTGACTTCAGAAGTGATATCAAGAACAGCTTT
65 AAGAGATAGAAGTGTATC-ATGAATTTAGATTATTGACTTCAGAAGTGATATCCAGAACAGCTTT
* * * * * *
129 TGGTAGCAGTTACTTGGAAGGAGAGAAGGTTTTTGCCATGTTGAACAAGCTGTCAATAATTATGA
129 CGGTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGA
* * * * * * ** *
194 GTCGAAATCTTTAT--AATACTAGAATTCCTTTAATCAACAAGTTATGGAAACCTGCCGATATGC
194 GCCGAAAT-TTTTTCGAA-ACTCGAATTCCTCTGATCAACAAGTTATGGAAATCTGGTGATGTGC
* *
257 TAGAGTCTGAAGAACTTGCAAAAGAAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAA
257 TAGAGTCTGAAGAACTTTCAAAAGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAA
*
322 GACAAAGTTGTGAATGGAGAAGCTGATAGCTTTGGCAATGATTTTCTAGGATTACTTGTAAATGC
322 GACAAAGTTGTGAATGGAGAAGCTGATAGCTTCGGCAATGATTTTCTAGGATTACTTGTAAATGC
** * * * *
387 CTATCATGATTCGGACAAAAATAACAAGCTTTCAATGGAAGA-TCTGGTAGATGAATGCAAAACA
387 CTATCATGATTCGGATGAAAATAACAGGCTTTCAACGGAAGACT-TGGTGGATGAGTGCAAAACA
* * * * * * * *
451 TTCTATTTTGCAGGACAAGATACAGTTAATGCCTTGCTTGCCTGGACAGTCTTGCTTTTAGCAAT
451 TTCTACTTTGCTGGACAAGATACTGTTAATTCCTTACTTGCATGGATAGTCTTCCTTTTAGCAAT
* * * * * *
516 CCATGGGGATTGGCAAGATAAAGCAAGAAGGGAGGTGATTG-GCATATTTGGTAACCAAAATCCA
516 TCATGGAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAG-ATATTTGGTAACCAAATTCCA
580 CAACCGGAAG-GCAT-TGCAAAACTCAAAA-CTAAC
580 -AACCGGAAGAG-ATGT-CAAAACTCAAAATC-AAC
*
613 ATGACACCAGCTGTTATTGCTAGTGTTGAAACAATGCTAGAAAAGTGGAAAGGCTATGTAGGCAA
1 ATGACACCAGCTGTAATTGCTAGTGTTGAAACAATGCTAGAAAAGTGGAAAGGCTATGTAGGCAA
* *
678 AGAGATAGAAGTGTATCATGAATTTAGATTATTGACTTCGGAAGTAATATCCAGAACAGCTTTCG
66 AGAGATAGAAGTGTATCATGAATTTAGATTATTGACTTCAGAAGTGATATCCAGAACAGCTTTCG
743 GTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGAGC
131 GTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGAGC
*
808 CGAAATTTTTTCGAAACTCGAATTCCTCTGATCAACAAGTTTTGGAAATCTGGTGATGTGCTAGA
196 CGAAATTTTTTCGAAACTCGAATTCCTCTGATCAACAAGTTATGGAAATCTGGTGATGTGCTAGA
873 GTCTGAAGAACTTTCAAAAGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAAGACA
261 GTCTGAAGAACTTTCAAAAGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAAGACA
* *
938 AAGTTGTGAATGGAGAAGTTGATAGCTTCGGCAATGACTTTCTAGGATTACTTGTAAATGCCTAT
326 AAGTTGTGAATGGAGAAGCTGATAGCTTCGGCAATGATTTTCTAGGATTACTTGTAAATGCCTAT
1003 CATGATTCGGATGAAAATAACAGGCTTTCAACGGAAGACTTGGTGGATGAGTGCAAAACATTCTA
391 CATGATTCGGATGAAAATAACAGGCTTTCAACGGAAGACTTGGTGGATGAGTGCAAAACATTCTA
*
1068 CTTTGCTGGACAAGATACTGTTAATTCCTTAATTGCATGGATAGTCTTCCTTTTAGCAATTCATG
456 CTTTGCTGGACAAGATACTGTTAATTCCTTACTTGCATGGATAGTCTTCCTTTTAGCAATTCATG
** *
1133 GAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAGATATTTGGTAACCAAATTCCGAATTCT
521 GAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAGATATTTGGTAACCAAATTCC-AAACCG
*
1198 GAAGAGATGTCTAAACTCAAAATCAAC
585 GAAGAGATGTCAAAACTCAAAATCAAC
* *
1225 ATGACACCAGCTGTAATTGCTAGTATTAAAACAATGCTAGAAAAGTGGAAAGGCTATGTAGGCAA
1 ATGACACCAGCTGTAATTGCTAGTGTTGAAACAATGCTAGAAAAGTGGAAAGGCTATGTAGGCAA
* * *
1290 AGAGATGGAAGTGTATCATGAATTTAGATTATTGACCTCAGAAGTGATATCCAGAACAGCTTTCA
66 AGAGATAGAAGTGTATCATGAATTTAGATTATTGACTTCAGAAGTGATATCCAGAACAGCTTTCG
1355 GTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGAGC
131 GTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGAGC
* * *
1420 AGAAATCTCTTCGAAACTCGAATTCCTCTGATCAACAAGTTATGGAAATCTGGTGATGTGCTAGA
196 CGAAATTTTTTCGAAACTCGAATTCCTCTGATCAACAAGTTATGGAAATCTGGTGATGTGCTAGA
* *
1485 GTCTGAAGAACTTTCAAAGGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAAGACG
261 GTCTGAAGAACTTTCAAAAGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAAGACA
**
1550 AAGTTGTGAATGGAGAAGCCAATAGCTTCGGCAATGATTTTCTAGGATTACTTGTAAATGCCTAT
326 AAGTTGTGAATGGAGAAGCTGATAGCTTCGGCAATGATTTTCTAGGATTACTTGTAAATGCCTAT
*
1615 CATGATTCGGATGAAAATAACAGACTTTCAACGGAAGACTTGGTGGATGAGTGCAAAACATTCTA
391 CATGATTCGGATGAAAATAACAGGCTTTCAACGGAAGACTTGGTGGATGAGTGCAAAACATTCTA
1680 CTTTGCTGGACAAGATACTGTTAATTCCTTACTTGCATGGATAGTCTTCCTTTTAGCAATTCATG
456 CTTTGCTGGACAAGATACTGTTAATTCCTTACTTGCATGGATAGTCTTCCTTTTAGCAATTCATG
* * *
1745 GAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAGATATTCGGTAACCAAATTCCAAATTCT
521 GAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAGATATTTGGTAACCAAATTCCAAA-CCG
*
1810 GAAG-GCATGTCTAAACTCAAAA
585 GAAGAG-ATGTCAAAACTCAAAA
1832 CCGTAAGTAA
Statistics
Matches: 1128, Mismatches: 79, Indels: 24
0.92 0.06 0.02
Matches are distributed among these distances:
611 10 0.01
612 1108 0.98
613 10 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (611 bp):
ATGACACCAGCTGTAATTGCTAGTGTTGAAACAATGCTAGAAAAGTGGAAAGGCTATGTAGGCAA
AGAGATAGAAGTGTATCATGAATTTAGATTATTGACTTCAGAAGTGATATCCAGAACAGCTTTCG
GTAGCAGTTACTTGGAAGGGGAGAAGATTTTTGACATGTTGAACAAGTTGTCAATAATTAGGAGC
CGAAATTTTTTCGAAACTCGAATTCCTCTGATCAACAAGTTATGGAAATCTGGTGATGTGCTAGA
GTCTGAAGAACTTTCAAAAGGAATACAAGATTGTGTGATGAAGATTGTTAAGAAAAGAGAAGACA
AAGTTGTGAATGGAGAAGCTGATAGCTTCGGCAATGATTTTCTAGGATTACTTGTAAATGCCTAT
CATGATTCGGATGAAAATAACAGGCTTTCAACGGAAGACTTGGTGGATGAGTGCAAAACATTCTA
CTTTGCTGGACAAGATACTGTTAATTCCTTACTTGCATGGATAGTCTTCCTTTTAGCAATTCATG
GAGATTGGCAAGAGAAAGCAAGAAGAGAAGTGATTGAGATATTTGGTAACCAAATTCCAAACCGG
AAGAGATGTCAAAACTCAAAATCAAC
Done.