Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga06g01862.M3
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: 5341
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Found at i:546 original size:127 final size:127
Alignment explanation
Indices: 393--897 Score: 879
Period size: 127 Copynumber: 4.0 Consensus size: 127
383 GGTGGAAGTT
393 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
*
458 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGACTGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* * *
520 AGAGAGAAACGCTGATTTTGTGTTTGTTGAATTATATTTGTTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* *
585 TTTCTAGTTCAATTTAAACAGTCTTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
* *
647 AGAGAGAAACACTGATTTTGTGTTTGTTGAATTATATTTGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
* * * *
712 TTTCTAGTTCAGTTAAAACAGTCTTATTTTATTTGTTTGAATGCAGGAAACAAAGATTTCTA
66 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
774 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
1 AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
*
839 TTTCTAGTTCAATTGAAACAATCCTA--TTATGTGTTTGAATGCAGGAAACAAAGATTTCT
66 TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCT
898 TTATGTGATT
Statistics
Matches: 360, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
125 32 0.09
127 328 0.91
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (127 bp):
AGAGAGAAACCCTGATTTTGTGTTTGTTGAATTATATTAGGTGAGATTTAGATTGGGACTTCAAA
TTTCTAGTTCAATTGAAACAGTCCTATTTTATGTGTTTGAATGCAGGAAACAAAGATTTCTA
Found at i:1647 original size:369 final size:366
Alignment explanation
Indices: 885--1765 Score: 1446
Period size: 369 Copynumber: 2.4 Consensus size: 366
875 GAATGCAGGA
885 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
* * * *
950 ATGGTACTTCACAAAGTGGTTGTAAAGAGGCTGGGGATTCATGCCTTCCCTTTCCCAAAATTGGT
66 ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT
* *
1015 TCTCAACAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTTAGTTTACAGGAGGAA
131 TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA
* * *
1080 GAAACGGTGGGGCTGCAGCAGCAGTGCTAGTGCTGTTGTTGCCAACTTTTGTGCACAGGAGCTGG
196 GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG
* * *
1145 TTAATTCAAAGAGAAGTGTGGATTGTTTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
261 TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
*
1210 ATGGAGCAAAAGGGAGTTTCTCGAGTTGAACATGAAACTGC
326 ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
* *
1251 AACAAAGACTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGATTCCTAAATGTG
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
1316 ATGGTACTTCAC-AAGCTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
66 ATGGTACTTCACAAAG-TGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
* * * * *
1380 TTCTCAGCAGCCATCTGTGAGTGTGATGTTTGAAAGTCCTATGCCGATTTCAGTTTACAGTAGGG
130 TTCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTAC---AGGA
*
1445 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAGCT-CTGTTGTTGCCAACTTTTATGCACGGGA
192 GGAAGAAACGGTGGGGCAGCAGCAGCAGCGCTAG-TGCTGTTGTTGCCAACTTTTATGCACAGGA
* * *
1509 GCAT-GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAG
256 GC-TGGTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAG
*
1573 GCAGTTATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
320 GCAGTTATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
1620 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTT-GCAAGATGACTCCTAAATGT
1 AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGC-AGATGACTCCTAAATGT
1684 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
65 GATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGG
1749 TTCTCAGCAGTCATCTG
130 TTCTCAGCAGTCATCTG
1766 AGCTGGTTAA
Statistics
Matches: 479, Mismatches: 28, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
365 3 0.01
366 171 0.36
368 2 0.00
369 298 0.62
370 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (366 bp):
AACAAAGATTTCTTTATGTGATTGGATGTCTGGTAATGAAACTTGGCAGATGACTCCTAAATGTG
ATGGTACTTCACAAAGTGGATGTAAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGT
TCTCAGCAGTCATCTGTGAGTATGATGTTTGAAAGTCCAACGCCGATTTCAGTTTACAGGAGGAA
GAAACGGTGGGGCAGCAGCAGCAGCGCTAGTGCTGTTGTTGCCAACTTTTATGCACAGGAGCTGG
TTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTCTTAGTTCTAATGCACTTTCAGAGGCAGTT
ATGGAGCAAAAGGGAGTTTCTCAAGTTGAACATGAAACTGC
Found at i:1970 original size:258 final size:258
Alignment explanation
Indices: 1513--2023 Score: 869
Period size: 258 Copynumber: 2.0 Consensus size: 258
1503 ACGGGAGCAT
* * *
1513 GTTAATTCAAAGAGAAGGGCGGATTGTCTTTCTGTTGTTAGTTCTGATGCACTTTCGGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
1578 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* * * *
1643 GGATGTCTGGTAATGAAACTTGCAAGATGACTCCTAAATGTGATGGTACTTCACAAAGTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
*
1708 AAAGAGGCTGAGGATTCATGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
*
1771 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCGCTTTCAGAGGCAGT
1 GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
*
1836 TATGGAGCGAAAGGGAGTTTCTCAAGTTGATCATGAAACTGCAACAAAGATTTCTTTATGTGATT
66 TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
* ** *
1901 GGATATCTGATAATGAAACTTTCCGGATGACTCCTAAATGTGATAGTACTTCACAACCTGGATGT
131 GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
* * *
1966 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCGAAACTGGTTCTCAGCGGTTATCTG
196 AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTG
2024 TGAGTGTGAT
Statistics
Matches: 236, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
258 236 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (258 bp):
GTTAATTCAAAGAGAAGCGCGGATTGTCTTTCTGTCGTTAGTTCTGATGCACTTTCAGAGGCAGT
TATGGAGCGAAAGGGAGTTTCTCAAGTTGAACATGAAACTGCAACAAAGATTTCTTTATGTGATT
GGATATCTGATAATGAAACTTGCAAGATGACTCCTAAATGTGATAGTACTTCACAAACTGGATGT
AAAGAGGCTGAGGATTCACGCCTTCCCTTACCCAAAACTGGTTCTCAGCAGTCATCTGAGCTG
Done.