Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00651.M1
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: 4462
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:2633 original size:213 final size:212
Alignment explanation
Indices: 2288--3335 Score: 1275
Period size: 213 Copynumber: 4.9 Consensus size: 212
2278 TCAAGTATTC
* * * * * * *
2288 ATAAACTGAAATCTCTCG-AGTATTTCGATCTTCAAGGTTGCTCCAGATTGGAGATTTTCCCTGA
1 ATAAATTGAAATCTCTTGAAATA-TTCAATCTT-AAAGTTGCTCAAGATTGGAGATTTTCCCAGA
* * **** * **
2352 AATCATGGACACTATGGAGAGGTTG-AGGGTTCTTGATTTAAGTGGAACGGCTTTGAAGGGCTTA
64 AATCATGGACACCATGGAGAGGATGTA-TAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTA
* * * * *
2416 CCATCCTCAATTGATAATCTTATTGGTCTTGAGGATTTGAGATTGAACTACTGTGAAGATCTTGT
128 CCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGT
*
2481 TTGCCTTCCTAAAAGCTTTT
193 TTGCCTTCCTAACAGCTTTT
* * *
2501 ATAAATTGGAATCTCTTGAAA-ATTTCAATCTTGGAAA-TTGCTCAATATTGGAGACTTTCCCAG
1 ATAAATTGAAATCTCTTGAAATA-TTCAATCTT--AAAGTTGCTCAAGATTGGAGATTTTCCCAG
* * *
2564 AAATCTTGGACGCCATGGAG-GAGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAAGAATT
63 AAATCATGGACACCATGGAGAG-GATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATT
* * *
2628 ACCATCCTCAATTGCCAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTCAAAACCTTA
127 ACCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTG
*
2693 TTTGCCTTCCTAATAGCTTTT
192 TTTGCCTTCCTAACAGCTTTT
** *
2714 ATAAATTGAAATCTCTTGAGTTATTCAATCTTGAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
1 ATAAATTGAAATCTCTTGAAATATTCAATCTT-AAAGTTGCTCAAGATTGGAGATTTTCCCAGAA
* *
2779 ATCATGGACACCATGGAGAGGCTGTATGAAA-TTGATTTAAGCGGGACGGCTTTGAAGGAATTAC
65 ATCATGGACACCATGGAGAGGATGTAT-AAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC
* ** * *
2843 CATCCTCAATTGCCAATCTTATTGGTCTTAAATATTTGGGATTGAACAACTGTGAAAATCTTGTT
129 CATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTT
* *
2908 TGCCTTCCTGACAGTTTTT
194 TGCCTTCCTAACAGCTTTT
* * * *
2927 ATAAATTGAAATCTCTTGAGATATTCAATGTTAAAGGTTGCTCGAGATTGGAGATTTTCCCTGAA
1 ATAAATTGAAATCTCTTGAAATATTCAATCTTAAA-GTTGCTCAAGATTGGAGATTTTCCCAGAA
* * * * * *
2992 ATTATGGACACCATGGAAAGGTTGTATGAACTTGATTTAAGTGGAACAGCTTTGAAGGAATTACC
65 ATCATGGACACCATGGAGAGGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACC
* * * *
3057 ATCCTCAATTGGCAATCTTATTAGTCTTAAGGATTTCAGATTGAACAACTGTGAAAACCTTATTT
130 ATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTTT
** *
3122 ATCTTCCTAACAGTTTTT
195 GCCTTCCTAACAGCTTTT
* * *
3140 ATAAATTGCAATCTCTTGAGAA-ATTCAATCTTAAAGGTTGCTCAAGATTGGAAATTTTTCCAGA
1 ATAAATTGAAATCTCTTGA-AATATTCAATCTTAAA-GTTGCTCAAGATTGGAGATTTTCCCAGA
* * * * *
3204 AATCATGGACACCATGGAG-GGATTGTATGAACTTGATTTAAGCAGAACAGTTTTAAAGGAATTA
64 AATCATGGACACCATGGAGAGGA-TGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTA
* * *
3268 CCATCCTCAATTGATAATTTTATTGGTCTTAAGGATTTGAGATTGAACGACTGTGAAAACCTTGT
128 CCATCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGT
3333 TTG
193 TTG
3336 TAGTAATTCA
Statistics
Matches: 726, Mismatches: 97, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
212 10 0.01
213 706 0.97
214 10 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (212 bp):
ATAAATTGAAATCTCTTGAAATATTCAATCTTAAAGTTGCTCAAGATTGGAGATTTTCCCAGAAA
TCATGGACACCATGGAGAGGATGTATAAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
TCCTCAATTGACAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAACCTTGTTTG
CCTTCCTAACAGCTTTT
Found at i:3008 original size:426 final size:424
Alignment explanation
Indices: 2288--3335 Score: 1406
Period size: 426 Copynumber: 2.5 Consensus size: 424
2278 TCAAGTATTC
* * * * * *
2288 ATAAACTGAAATCTCTCGAGTATTTCGATCTTCAAGGTTGCTCCAGATTGGAGATTTTCCCTGAA
1 ATAAATTGAAATCTCTTGAGTA-TTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
* * ** * **
2353 ATCATGGACACTATGGAGAGGTTG-AGGGTTCTTGATTTAAGTGGAACGGCTTTGAAGGGCTTAC
65 ATCATGGACACCATGGAGAGGTTGTA-TGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC
* * *
2417 CATCCTCAATTGATAATCTTATTGGTCTTGAGGATTTGAGATTGAACTACTGTGAAGATCTTGTT
129 CATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTT
* *
2482 TGCCTTCCTAAAAGCTTTTATAAATTGGAATCTCTTGAAAATTTCAATCTTGGAAATTGCTCAAT
194 TGCCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAATTTCAATCTT-GAAATTGCTCAAG
* *
2547 ATTGGAGACTTTCCCAGAAATCTTGGACGCCATGG-AGGAGATGTATAAACTTGATTTAAGCGGA
258 ATTGGAGACTTTCCCAGAAATCTTGGACACCATGGAAAG-GATGTATAAACTTGATTTAAGCGGA
* * *
2611 ACGGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTGGTCTTAAGGATTTGAGATTGAA
322 ACAGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGAA
* *
2676 CAACTGTCAAAACCTTATTTGCCTTCCTAATAGCTTTT
387 CAACTGTCAAAACCTTATTTACCTTCCTAACAGCTTTT
*
2714 ATAAATTGAAATCTCTTGAGTTATTCAATCTTGAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
1 ATAAATTGAAATCTCTTGAG-TATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
* * *
2779 ATCATGGACACCATGGAGAGGCTGTATGAAATTGATTTAAGCGGGACGGCTTTGAAGGAATTACC
65 ATCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACC
** ** *
2844 ATCCTCAATTGCCAATCTTATTGGTCTTAAATATTTGGGATTGAACAACTGTGAAAATCTTGTTT
130 ATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTTT
* * * * * *
2909 GCCTTCCTGACAGTTTTTATAAATTGAAATCTCTTG-AGATATTCAATGTT-AAAGGTTGCTCGA
195 GCCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAAT-TTCAATCTTGAAA--TTGCTCAA
* * * * *
2972 GATTGGAGATTTTCCCTGAAAT-TATGGACACCATGGAAAGGTTGTATGAACTTGATTTAAGTGG
257 GATTGGAGACTTTCCCAGAAATCT-TGGACACCATGGAAAGGATGTATAAACTTGATTTAAGCGG
* *
3036 AACAGCTTTGAAGGAATTACCATCCTCAATTGGCAATCTTATTAGTCTTAAGGATTTCAGATTGA
321 AACAGCTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGA
* * *
3101 ACAACTGTGAAAACCTTATTTATCTTCCTAACAGTTTTT
386 ACAACTGTCAAAACCTTATTTACCTTCCTAACAGCTTTT
* * * *
3140 ATAAATTGCAATCTCTTGAGAAATTCAATCTTAAAGGTTGCTCAAGATTGGAAATTTTTCCAGAA
1 ATAAATTGAAATCTCTTGAG-TATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAA
* * * *
3205 ATCATGGACACCATGGAG-GGATTGTATGAACTTGATTTAAGCAGAACAGTTTTAAAGGAATTAC
65 ATCATGGACACCATGGAGAGG-TTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTAC
* * *
3269 CATCCTCAATTGATAATTTTATTGGTCTTAAGGATTTGAGATTGAACGACTGTGAAAACCTTGTT
129 CATCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTT
3334 TG
194 TG
3336 TAGTAATTCA
Statistics
Matches: 544, Mismatches: 70, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
424 3 0.01
425 6 0.01
426 530 0.97
427 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (424 bp):
ATAAATTGAAATCTCTTGAGTATTCAATCTTAAAGGTTGCTCAAGATTGGAGATTTTCCCAGAAA
TCATGGACACCATGGAGAGGTTGTATGAACTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
TCCTCAATTGATAATCTTATTGGTCTTAAGGATTTGAGATTGAACAACTGTGAAAATCTTGTTTG
CCTTCCTAAAAGCTTTTATAAATTGAAATCTCTTGAAAATTTCAATCTTGAAATTGCTCAAGATT
GGAGACTTTCCCAGAAATCTTGGACACCATGGAAAGGATGTATAAACTTGATTTAAGCGGAACAG
CTTTGAAAGAATTACCATCCTCAATTGCCAATCTTATTAGTCTTAAGGATTTCAGATTGAACAAC
TGTCAAAACCTTATTTACCTTCCTAACAGCTTTT
Done.