Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1385
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: 1719
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Found at i:370 original size:55 final size:54
Alignment explanation
Indices: 170--999 Score: 1251
Period size: 55 Copynumber: 15.4 Consensus size: 54
160 ATAAATTGTA
* * *
170 TCCTGCTCATTGAGGAGT-AAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGG-G
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
223 TCCTGCTCTTTGAGGACTGAAAGGTGACA-CAACTTGTGTGGGCTTTGAA-A-GTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
276 TCCTGCTCTTTGGGGAATGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
330 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
385 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
440 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGT-GGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
493 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTT--GAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
545 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
599 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
654 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
709 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
763 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
818 TCCTGCTCTTTGAGGACTG-AAATGCCACCAACTTGTGTGGGCTTT-A-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
869 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
922 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
977 TCCTGCTCTTTGAGGACTAAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
1000 GCGGAAGGAG
Statistics
Matches: 726, Mismatches: 29, Indels: 43
0.91 0.04 0.05
Matches are distributed among these distances:
51 24 0.03
52 87 0.12
53 171 0.24
54 168 0.23
55 274 0.38
56 2 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:655 original size:269 final size:267
Alignment explanation
Indices: 170--994 Score: 1321
Period size: 269 Copynumber: 3.1 Consensus size: 267
160 ATAAATTGTA
* * * *
170 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGG-GTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTT
* * * *
234 GAGGACTGAAAGGTGACA-CAACTTGTGTGGGCTTTGAAAGTGTCCTGCTCTTTGGGGAATGAAA
66 GAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AGGTGTCCTGCTCTTTGAGGACTGAAA
298 GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
129 -TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGG-AAATGCCACCAA
* *
363 CTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGG
192 CTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGG
427 GCTTTAAGAGGTG
255 GCTTTAAGAGGTG
440 TCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGT-GGCTTT-AAGAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCT
502 TTGAGGACTGGAAA-TGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGAGGACTGGA
64 TTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGAGGACT-GA
566 AATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACC
127 AATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA--TGCCACC
*
630 AACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTG
190 AACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTG
695 GGCTTTAAGAGGTG
254 GGCTTTAAGAGGTG
709 TCCTGCTCTTTGAGGACTGGAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTT
773 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGA
65 TGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT--GAGGTGTCCTGCTCTTTGAGGACTGA
838 AATGCCACCAACTTGTGTGGGCTTT-A-AGGTGTCCTGCTCTTTGAGGACTGGAAATGCCACCAA
127 AATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAATGCCACCAA
901 CTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC
192 CTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGC
966 TTTAAGAGGTG
257 TTTAAGAGGTG
977 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
995 AAAAAGCGGA
Statistics
Matches: 524, Mismatches: 12, Indels: 40
0.91 0.02 0.07
Matches are distributed among these distances:
267 3 0.01
268 86 0.16
269 221 0.42
270 125 0.24
271 38 0.07
272 27 0.05
273 24 0.05
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (267 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTT
GAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGAGGACTGAAATG
CCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTG
TGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTA
AGAGGTG
Found at i:678 original size:26 final size:26
Alignment explanation
Indices: 594--679 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
584 GGGCTTTAAG
*
594 AGGTGTCCTGCTCTTTGAGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
620 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
648 GAGGTGTCCTGCTCTTTGGGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
675 AGGTG
1 AGGTG
680 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 9 0.20
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:782 original size:324 final size:323
Alignment explanation
Indices: 170--994 Score: 1373
Period size: 324 Copynumber: 2.5 Consensus size: 323
160 ATAAATTGTA
* * * *
170 TCCTGCTCATTGAGGAGTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGG-GTCCTGCTCTTT
1 TCCTGCTCTTTGAGGACTGAAA-TGCCACCAACTTGTGTGGGCTTTG--AGGTGTCCTGCTCTTT
* * *
234 GAGGACT-GAAAGGTGACA-CAACTTGTGTGGGCTTTGAAA-GTGTCCTGCTCTTTGGGGAATGA
63 GAGGACTGGAAA--TGCCACCAACTTGTGTGGGCTTT-AAAGGTGTCCTGCTCTTTGAGGACTGA
296 AA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
125 AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCAC
*
360 CAACTTGTGTGGGCTTTGAAAGGTGTCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT
190 CAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGT
425 GGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGAAAGGTGCCACCAACTTGTGT-GGCTTTAAGA
255 GGGCTTTAAGAGGTGTCCTGCTCTTTGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA
489 GGTG
320 GGTG
493 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGA
1 TCCTGCTCTTTGAGGACT-GAAATGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGA
558 GGACTGGAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
65 GGACTGGAAATGCCACCAACTTGTGTGGGCTTTAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGG
* *
623 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAA
129 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAA
687 CTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGG-AAATGCCACCAACTTGTGTGG
193 CTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGG
750 GCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA
257 GCTTT-AAGAGGTGTCCTGCTCTTTG-GGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGA
814 GGTG
320 GGTG
*
818 TCCTGCTCTTTGAGGACTGAAATGCCACCAACTTGTGTGGGCTTTAAGGTGTCCTGCTCTTTGAG
1 TCCTGCTCTTTGAGGACTGAAATGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGAG
883 GACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTG
66 GACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTG
948 CCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
131 CCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT
995 AAAAAGCGGA
Statistics
Matches: 478, Mismatches: 12, Indels: 24
0.93 0.02 0.05
Matches are distributed among these distances:
321 9 0.02
322 37 0.08
323 192 0.40
324 208 0.44
325 32 0.07
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (323 bp):
TCCTGCTCTTTGAGGACTGAAATGCCACCAACTTGTGTGGGCTTTGAGGTGTCCTGCTCTTTGAG
GACTGGAAATGCCACCAACTTGTGTGGGCTTTAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTG
CCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTT
GTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTT
TAAGAGGTGTCCTGCTCTTTGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Done.