Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1974
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, 707
Length: 1179
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Found at i:286 original size:169 final size:168
Alignment explanation
Indices: 1--1179 Score: 1196
Period size: 169 Copynumber: 7.0 Consensus size: 168
* * ** * * * * *
1 CTAAAGGCAGTGAATCTTGTTTCCCTAGTC-TTGCAGTGGAGCAGATTAGAGTTGAGTGCAGCGA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAG-CATTGCAACGGAGCAGATTAAAGCTAAGGGTAGCGA
* * * * * * * *
65 ATCTTATCTCCCTGTCGTTAAGACTTGAAATAGCTGAAATGAAGCGGATTAAAGCTATGGGAAGT
65 ATC-TGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAGC
* * *
130 GAATCCTATCTCTTTGGCATTATAGAGGAACAGATAAAAG
129 GAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
* * * *
170 CTAAAGGTAGCAAATCTTCTTTCCCTAGTATTGCAACGGAGCAGATTAGAGCTAAGGGTAGCGAA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTAAGGGTAGCGAA
* * * * **
235 TCTGCTCTCCCTGTCGTTAAGACTTGAAATAACTTAAGTGGAGCAGATTAAAGCTATCAGCAGCG
66 TCTG-TCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCG
* * * *
300 AACCCTATCTCTTTGGCTTTATATTGCAACAGATTAATG
130 AATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
* *
339 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGC-AGAGGATAGCGA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTA-AGGGTAGCGA
* ** * *
403 ATCTTATCTCCCTGGCGTTAAGACTTGAAATAGA-TGAAGTACAGCGGATTAAAACTGTGGGCAA
65 ATC-TGTCTCCCTGGCGTTAAGACTTGAAATA-ACTGAAGTGGAGCGGATTAAAGCTGTGGGCAG
* *
467 TGAATCCTATCTCTTTGG-TATTATAGTGGAATAGATTAAAG
128 CGAATCCTATCTCTTTGGCT-TTATAGTGGAACAGATTAAAG
* * * * *
508 CTAAAGGTAGCGAATCTT-TATCCTCTAGCATTGCAGA-GGAGCAGATTAAAGCTGATGGCAGCA
1 CTAAAGGTAGCGAATCTTGTTTCC-CTAGCATTGCA-ACGGAGCAGATTAAAGCTAAGGGTAGCG
* * * * * *
571 AATCTTATCTCCCTTGCGTTAAGACTTGAAATAACCGAAGTGGAGCAGATTAAGGCTGTGGGTAG
64 AATC-TGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAG
* * * *
636 AGAATCCTATTTCTTTGGGTTTATGGTGGAACAGATTAAAG
128 CGAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
** * * * * ** *
677 CTAAAGGTAGTAAATCTTCTTTCCCTAGCATTGGAGCGGAGCAGATTAAATCTGTGGGCAGCGAA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTAAGGGTAGCGAA
* * * * ** *
742 TATTGTCTCTCTAGCATTAAGACTTGAAATAGTTGAAGTGAAGCGGATTAAAGCTGTGGGGCAGC
66 T-CTGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGT-GGGCAGC
* *
807 GGAT-CTATCTCTTTGGCTTTATAGTGGAACATATTAAAG
129 GAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
* * * * * *
846 CTAAAGGTAGCGAATCTTGTCTCCCTCGCATTGCAATGTAGTAGATTATAG-TAGAGGGCT-GCG
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTA-AGGG-TAGCG
* * * *
909 AATCTTGTCTCCCTGGAGCTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAAGCTGTGGGCAG
64 AATC-TGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAG
* *
974 CGGAT-CTATCTCTTTGGCTTTATAGTGGAACATATTAAAG
128 CGAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
* * * * * *
1014 CTAAAGGTAGCGAATCTTGTCTCCCTCGCATTGCAATGTAGTAGATTATAG-TAGAGGGCT-GCG
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTA-AGGG-TAGCG
* * * * *
1077 AATCTTGTCTCCCTGGAGCTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAA-TTGTGGGCAG
64 AATC-TGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAG
* *
1141 TGAATCCTATCTCTTTGGCTTTATAGTGGAACATATTAA
128 CGAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAA
Statistics
Matches: 866, Mismatches: 125, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
167 12 0.01
168 205 0.24
169 634 0.73
170 15 0.02
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (168 bp):
CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAACGGAGCAGATTAAAGCTAAGGGTAGCGAA
TCTGTCTCCCTGGCGTTAAGACTTGAAATAACTGAAGTGGAGCGGATTAAAGCTGTGGGCAGCGA
ATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
Found at i:617 original size:338 final size:336
Alignment explanation
Indices: 1--1179 Score: 1316
Period size: 338 Copynumber: 3.5 Consensus size: 336
* * * * **
1 CTAAAGGCAGTGAATCTTGTTTCCCTAGTC-TTGCAGTGGAGCAGATTAGAGTTGAGTGCAGCGA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAG-CATTGCAGCGGAGCAGATTAAAGCAGAG-GCAGCGA
* * * *
65 ATCTTATCTCCCTGTCGTTAAGACTTGAAATAGCTGAAATGAAGCGGATTAAAGCTATGGG-AAG
64 ATCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGAAGCGGATTAAAACTGTGGGCAA-
* * * * *
129 TGAATCCTATCTCTTTGGCATTATAGAGGAACAGATAAAAGCTAAAGGTAGCAAATCTTCTTTCC
128 TGAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTCTATCC
* * * * **
194 CTAGTATTGCAACGGAGCAGATTAGAGCTAAGGGTAGCGAATCTGCTCTCCC-TGTCGTTAAGAC
193 CTAGCATTGCAACGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTG-CGTTAAGAC
* * **
258 TTGAAATAACTTAAGTGGAGCAGATTAAAGCTATCAGCAGCGAACCCTATCTCTTTGGCTTTATA
257 TTGAAATAACTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAA-CCTATCTCTTTGGCTTTATA
* * *
323 TTGCAACAGATTAATG
321 GTGGAACAGATTAAAG
*
339 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCAGAGGATAGCGAA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCAGAGG-CAGCGAA
*
404 TCTTATCTCCCTGGCGTTAAGACTTGAAATAGATGAAGT-ACAGCGGATTAAAACTGTGGGCAAT
65 TCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGA-AGCGGATTAAAACTGTGGGCAAT
*
468 GAATCCTATCTCTTTGG-TATTATAGTGGAATAGATTAAAGCTAAAGGTAGCGAATCTT-TATCC
129 GAATCCTATCTCTTTGGCT-TTATAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTCTATCC
* *
531 TCTAGCATTGCAGA-GGAGCAGATTAAAGCTGATGGCAGCAAATCTTATCTCCCTTGCGTTAAGA
193 -CTAGCATTGCA-ACGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGCGTTAAGA
* * * * * *
595 CTTGAAATAACCGAAGTGGAGCAGATTAAGGCTGTGGGTAGAGAATCCTATTTCTTTGGGTTTAT
256 CTTGAAATAACTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAA-CCTATCTCTTTGGCTTTAT
*
660 GGTGGAACAGATTAAAG
320 AGTGGAACAGATTAAAG
** * * * * *
677 CTAAAGGTAGTAAATCTTCTTTCCCTAGCATTGGAGCGGAGCAGATTAAATCTGTGGGCAGCGAA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCAG-AGGCAGCGAA
* * * * * * * **
742 TATTGTCTCTCTAGCATTAAGACTTGAAATAGTTGAAGTGAAGCGGATTAAAGCTGTGGGGCAGC
65 TCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGAAGCGGATTAAAACTGT-GGGCAAT
* * * *
807 GGAT-CTATCTCTTTGGCTTTATAGTGGAACATATTAAAGCTAAAGGTAGCGAATCTTGTCTCCC
129 GAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTCTATCCC
* * * * * * * * * *
871 TCGCATTGCAATGTAGTAGATTATAG-TAGAGGGCTGCGAATCTTGTCTCCCTGGAGCTAAGACT
194 TAGCATTGCAACGGAGCAGATTAAAGCT-GAGGGCAGCGAATCTTATCTCCCTTGCGTTAAGACT
* ** * *
935 TGAAATAGCTGAAGTGGAGTGGATTAAAGCTGTGGGCAGCGGATCTATCTCTTTGGCTTTATAGT
258 TGAAATAACTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAACCTATCTCTTTGGCTTTATAGT
*
1000 GGAACATATTAAAG
323 GGAACAGATTAAAG
* * ** * * * * *
1014 CTAAAGGTAGCGAATCTTGTCTCCCTCGCATTGCAATGTAGTAGATTATAGTAGAGGGCTGCGAA
1 CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCAGA-GGCAGCGAA
* * * * * * *
1079 TCTTGTCTCCCTGGAGCTAAGACTTGAAATAGCTGAAGTGGAGTGGATT-AAATTGTGGGCAGTG
65 TCTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGAAGCGGATTAAAACTGTGGGCAATG
*
1143 AATCCTATCTCTTTGGCTTTATAGTGGAACATATTAA
130 AATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAA
Statistics
Matches: 709, Mismatches: 115, Indels: 36
0.82 0.13 0.04
Matches are distributed among these distances:
335 9 0.01
336 38 0.05
337 128 0.18
338 513 0.72
339 21 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (336 bp):
CTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCAGAGGCAGCGAAT
CTTATCTCCCTGGCGTTAAGACTTGAAATAGCTGAAGTGAAGCGGATTAAAACTGTGGGCAATGA
ATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTCTATCCCTA
GCATTGCAACGGAGCAGATTAAAGCTGAGGGCAGCGAATCTTATCTCCCTTGCGTTAAGACTTGA
AATAACTGAAGTGGAGCAGATTAAAGCTGTGGGCAGCGAACCTATCTCTTTGGCTTTATAGTGGA
ACAGATTAAAG
Found at i:961 original size:507 final size:503
Alignment explanation
Indices: 1--1179 Score: 1388
Period size: 507 Copynumber: 2.3 Consensus size: 503
* * * * *
1 CTAAAGGCAGTGAATCTTGTTTCCCTAGTC-TTGCAGTGGAGCAGATTAGAGTTGAGTGCAGCGA
1 CTAAAGGTAGCGAATCTTGTATCCCTAG-CATTGCAGAGGAGCAGATTAAAG-TGAG-GCAGCGA
* * *
65 ATCTTATCTCCC-TGTCGTTAAGACTTGAAATAGCTGAAATGAAGCGGATTAAAGCTATGGGAAG
63 ATCTTATCTCCCTTG-CGTTAAGACTTGAAATAGCTGAAGTGGAGCGGATT-AAGCTGTGGGAAG
* * *
129 TGAATCCTATCTCTTTGGCATTATAGAGGAACAGATAAAAGCTAAAGGTAGCAAATCTTCTTTCC
126 TGAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTCTTTCC
* * * *
194 CTAGTATTGCAACGGAGCAGATTAGAGCTAAGGGTAGCGAATCTGCTCTCCCTGTCGTTAAGACT
191 CTAGCATTGCAACGGAGCAGATTAAAGCTAAGGGCAGCGAATCTGCTCTCCCTGTCATTAAGACT
* *
259 TGAAATAACTTAAGTGGAGCAGATTAAAGCTATCAGCAGCGAACCCTATCTCTTTGGCTTTATAT
256 TGAAATAACTTAAGTGAAGCAGATTAAAGCTATCAGCAGCGAACCCTATCTCTTTGGCTTTATAG
* * *
324 TGCAACAGATTAATGCTAAAGGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAA
321 TGCAACAGATTAAAGCTAAAGGTAGCGAATCTTGTCTCCCTAGCATTGCAACGGAGCAGATTAAA
* *
389 GCAGAGGATAGCGAATCTTATCTCCCTGGCGTTAAGACTTGAAATAGATGAAGTACAGCGGATTA
386 GCAGAGGATAGCGAATCTTATCTCCCTGGAGCTAAGACTTGAAATAGATGAAGTACAGCGGATTA
* *
454 AAACTGTGGGCAATGAATCCTATCTCTTTGG-TATTATAGTGGAATAGATTAAAG
451 AAACTGTGGGCAACGAAT-CTATCTCTTTGGCT-TTATAGTGGAACAGATTAAAG
*
508 CTAAAGGTAGCGAATCTT-TATCCTCTAGCATTGCAGAGGAGCAGATTAAAGCTGATGGCAGCAA
1 CTAAAGGTAGCGAATCTTGTATCC-CTAGCATTGCAGAGGAGCAGATTAAAG-TGA-GGCAGCGA
* * * * *
572 ATCTTATCTCCCTTGCGTTAAGACTTGAAATAACCGAAGTGGAGCAGATTAAGGCTGTGGGTAGA
63 ATCTTATCTCCCTTGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGATTAA-GCTGTGGGAAGT
* * * *
637 GAATCCTATTTCTTTGGGTTTATGGTGGAACAGATTAAAGCTAAAGGTAGTAAATCTTCTTTCCC
127 GAATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTCTTTCCC
* * * ** * *
702 TAGCATTGGAGCGGAGCAGATTAAATCTGTGGGCAGCGAATATTG-TCTCTCTAG-CATTAAGAC
192 TAGCATTGCAACGGAGCAGATTAAAGCTAAGGGCAGCGAAT-CTGCTCTCCCT-GTCATTAAGAC
* * * ** * *
765 TTGAAAT-AGTTGAAGTGAAGCGGATTAAAGCTGTGGGGCAGCGGA-TCTATCTCTTTGGCTTTA
255 TTGAAATAACTT-AAGTGAAGCAGATTAAAGCTAT-CAGCAGCGAACCCTATCTCTTTGGCTTTA
* * * * * *
828 TAGTGGAACATATTAAAGCTAAAGGTAGCGAATCTTGTCTCCCTCGCATTGCAATGTAGTAGATT
318 TAGTGCAACAGATTAAAGCTAAAGGTAGCGAATCTTGTCTCCCTAGCATTGCAACGGAGCAGATT
* * * * * ** *
893 ATAGTAGAGGGCT-GCGAATCTTGTCTCCCTGGAGCTAAGACTTGAAATAGCTGAAGTGGAGTGG
383 AAAGCAGA-GGATAGCGAATCTTATCTCCCTGGAGCTAAGACTTGAAATAGATGAAGTACAGCGG
* * * *
957 ATTAAAGCTGTGGGCAGCGGATCTATCTCTTTGGCTTTATAGTGGAACATATTAAAG
447 ATTAAAACTGTGGGCAACGAATCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
* * * * * *
1014 CTAAAGGTAGCGAATCTTGTCTCCCTCGCATTGCA-ATGTAGTAGATTATAGTAGAGGGCTGCGA
1 CTAAAGGTAGCGAATCTTGTATCCCTAGCATTGCAGA-GGAGCAGATTAAAGT-GA-GGCAGCGA
* * * * * ** *
1078 ATCTTGTCTCCCTGGAGCTAAGACTTGAAATAGCTGAAGTGGAGTGGATTAAATTGTGGGCAGTG
63 ATCTTATCTCCCTTGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGATTAAGCTGTGGGAAGTG
*
1143 AATCCTATCTCTTTGGCTTTATAGTGGAACATATTAA
128 AATCCTATCTCTTTGGCTTTATAGTGGAACAGATTAA
Statistics
Matches: 567, Mismatches: 91, Indels: 30
0.82 0.13 0.04
Matches are distributed among these distances:
505 44 0.08
506 132 0.23
507 375 0.66
508 16 0.03
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (503 bp):
CTAAAGGTAGCGAATCTTGTATCCCTAGCATTGCAGAGGAGCAGATTAAAGTGAGGCAGCGAATC
TTATCTCCCTTGCGTTAAGACTTGAAATAGCTGAAGTGGAGCGGATTAAGCTGTGGGAAGTGAAT
CCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAGCAAATCTTCTTTCCCTAGC
ATTGCAACGGAGCAGATTAAAGCTAAGGGCAGCGAATCTGCTCTCCCTGTCATTAAGACTTGAAA
TAACTTAAGTGAAGCAGATTAAAGCTATCAGCAGCGAACCCTATCTCTTTGGCTTTATAGTGCAA
CAGATTAAAGCTAAAGGTAGCGAATCTTGTCTCCCTAGCATTGCAACGGAGCAGATTAAAGCAGA
GGATAGCGAATCTTATCTCCCTGGAGCTAAGACTTGAAATAGATGAAGTACAGCGGATTAAAACT
GTGGGCAACGAATCTATCTCTTTGGCTTTATAGTGGAACAGATTAAAG
Done.