Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga09g00047.F1
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: 4280
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:1049 original size:210 final size:210
Alignment explanation
Indices: 777--1168 Score: 608
Period size: 210 Copynumber: 1.9 Consensus size: 210
767 GATTGAAAAG
* *
777 ATTGTCCTAATTTAAGTTGGATTCCGGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
1 ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
* ** * * * *
842 GATAGCTGCAAGGAATTGGAAGTTCTTCCTATAACCGGAGGTTGTTCATCTCTTGAAAAGCTTAG
66 AATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAG
* ** * *
907 GATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGATTATTTAGCTCCACTTGTCTCAAAG
131 CATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCCACTTGTCTCAAAG
972 AATTATATCTATGTC
196 AATTATATCTATGTC
*
987 ATTGTTCTAATTTAAGTTCGATTCCAGATTTGGAAGGATGTTT-CTCTCTT-AAAATTCTGTCAA
1 ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGAT-TTTCCTCTCTTCAAAA-TCTGTCAA
*
1050 TTAATAGCTGCAACAAATTGGAAGTTCTTCCGGTAACAGGAAGATGTTCATCTCTTGAAAAGCTT
64 TTAATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTT
1115 AGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCC
129 AGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCC
1169 TCTCTTCAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
209 4 0.02
210 157 0.96
211 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (210 bp):
ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
AATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAG
CATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCCACTTGTCTCAAAG
AATTATATCTATGTC
Found at i:1246 original size:138 final size:138
Alignment explanation
Indices: 1030--1298 Score: 396
Period size: 138 Copynumber: 1.9 Consensus size: 138
1020 AAGGATGTTT
* *
1030 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCTTCCGGTAACAGGAAGAT
1 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
1095 GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
66 GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
1160 TTTACCTC
131 TTTACCTC
* * * * * * * *
1168 CTCTCTTCAAAA-TCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCCGGAAGG
1 CTCTCTT-AAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGA
* ** *
1232 TGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGATT
65 TGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATT
1297 AT
130 AT
1299 CTGCCTGCGC
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 112 0.97
139 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (138 bp):
CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
TTTACCTC
Found at i:1458 original size:348 final size:348
Alignment explanation
Indices: 818--1516 Score: 1012
Period size: 348 Copynumber: 2.0 Consensus size: 348
808 GGAAGGATTT
* * *
818 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGGAAGTTCTTCCTATAACCGGAGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCATATAACCGGAGG
* *
883 TTGTTCATCTCTTGAAAAGCTTAGGATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGAT
66 TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
* * * * *
948 TATTTAGCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTTCTAATTTAAGTTCGATTCCA
131 TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
* **
1013 GATTTGGAAGGATGTTTCTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
196 AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
** * * *
1078 TCCGGTAACAGGAAGATGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAAT-TAAGC
261 TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAAGC
*
1142 AAGATCGGAGACGGATTATTTACC
325 AAGATCGGAGACGGATTATCTACC
* *
1166 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCAT-TACCCGGAA
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTC-TTCATATAACCGG-A
* * *
1230 GG-TGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGG
64 GGTTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGG
* * * *
1294 ATTATCT-GCCTGCGCTTGTCTCAATGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATT
129 ATTATCTAG-CTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATT
* * * **
1358 CCAAATTTGGAAGGAT-TTTCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAG
193 CCAAATTTGGAAGGATGTTT-CTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAG
*
1422 TTCTTCCAATAACTGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
257 TTCTTCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
1487 AGCAAGATCGGAGACGGATTATCTACC
322 AGCAAGATCGGAGACGGATTATCTACC
1514 TCC
1 TCC
1517 ACTTGTCTCA
Statistics
Matches: 312, Mismatches: 34, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
347 10 0.03
348 295 0.95
349 7 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (348 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCATATAACCGGAGG
TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCA
AGATCGGAGACGGATTATCTACC
Found at i:1543 original size:210 final size:210
Alignment explanation
Indices: 1166--2048 Score: 1336
Period size: 210 Copynumber: 4.2 Consensus size: 210
1156 ATTATTTACC
* * * * * *
1166 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCCGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
* * * *** * *
1231 GTGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAAT-TAAGCAAGATTGGAGACGGA
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAACCAAGATCGGAGACGGA
* * * * * * ** * *
1295 TTATCTGCCTGCGCTTGTCTCAATGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTCC
130 TTATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCC
*
1360 AAATTTGGAAGGATTT
195 AGATTTGGAAGGATTT
* ** * * * *
1376 TCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
* *
1441 ATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
* *
1506 TATCTACCTCCACTTGTCTCAAAGAATTATATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1571 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
* *
1586 TCCTCTCTTCAAAATCTATCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCCATAACAGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
*
1651 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATGACCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
*
1716 TATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1781 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
* *
1796 TCCTCTCTTCAAAATCTATCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCCATAACAGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
*
1861 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATGACCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
* *
1926 TATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTGGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1991 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
*
2006 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGG
2049 CGAGTTTTCC
Statistics
Matches: 624, Mismatches: 48, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
209 6 0.01
210 618 0.99
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (210 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
GATTTGGAAGGATTT
Found at i:2667 original size:144 final size:144
Alignment explanation
Indices: 2416--2680 Score: 343
Period size: 144 Copynumber: 1.8 Consensus size: 144
2406 CTGGTTGGGA
* * * * * *
2416 AAAGCTTAAGAGTCTTCCTCCGCAACTTCAATTCCTCTCTGCCCTTGAAGAATTGACGATATTAG
1 AAAGCTAAAGAGTCTTCCTCCGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGAG
* * * * ** *
2481 AGTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGAAATCTCTCTTCTTTAAGGCATCTATAT
66 AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATAT
2546 TTAAGTGGTTTTGG
131 TTAAGTGGTTTTGG
* * * *
2560 AAAGCTAAAGAGTCTTCCTCAC-CAACTCCAACTCCCCACTGCCCTTGAAGATTTGACTATGTGG
1 AAAGCTAAAGAGTCTTCCTC-CGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGA
* *
2624 GGGTTTCATGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
65 GAGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
2681 TGTCTGCGTA
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
144 100 0.99
145 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (144 bp):
AAAGCTAAAGAGTCTTCCTCCGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGAG
AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATAT
TTAAGTGGTTTTGG
Done.