Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold683
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, 839
Length: 1399
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Found at i:251 original size:13 final size:13
Alignment explanation
Indices: 233--258 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223 ACAAAGATCC
233 ATGTATCGATACA
1 ATGTATCGATACA
246 ATGTATCGATACA
1 ATGTATCGATACA
259 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:253 original size:33 final size:33
Alignment explanation
Indices: 212--278 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
202 AAAATTTCCA
***
212 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
245 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
278 A
1 A
279 TTTCCTGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:350 original size:30 final size:31
Alignment explanation
Indices: 300--359 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
290 TAGCTAATTA
*
300 TGTATCGATACAATACTTATGTATCGATACT
1 TGTATCAATACAATACTTATGTATCGATACT
331 TGTATCAATACAA-ACTTATGTATCGATAC
1 TGTATCAATACAATACTTATGTATCGATAC
360 AAATTGTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (31 bp):
TGTATCAATACAATACTTATGTATCGATACT
Found at i:423 original size:21 final size:22
Alignment explanation
Indices: 397--454 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
387 GTTGGGACCC
*
397 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACATTTGTACAAA
*
418 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
439 TGTATCGATACATTTG
1 TGTATCGATACATTTG
455 GAAATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 26 0.81
22 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:1218 original size:55 final size:55
Alignment explanation
Indices: 1129--1396 Score: 307
Period size: 55 Copynumber: 5.1 Consensus size: 55
1119 GTGTATCCTA
* *
1129 TCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGC
1 TCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGC
* *
1184 TCTTTGAGGACTGGAAAATGGCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGC
1239 TC-TT---GA--GG---ATGCCACC-ACTTGTGTGGGCTTTGAAAGGTGTCCTGC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGC
* *
1284 TCTTTGAGGACTGGAAAAATGCCACCAA-TTGTGTGGGCTTCGAAAGGGGT-CTGC
1 TCTTTGAGGACTGG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGC
* * * *
1338 TCTTTGGGGACT-GAAAATGCCACCAACTTATGTAGGCTTTG--AGCGTGTCCTAC
1 TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG-GTGTCCTGC
1391 TCTTTG
1 TCTTTG
1397 GGG
Statistics
Matches: 184, Mismatches: 14, Indels: 32
0.80 0.06 0.14
Matches are distributed among these distances:
45 30 0.16
46 9 0.05
49 4 0.02
51 6 0.03
52 16 0.09
53 21 0.11
54 17 0.09
55 76 0.41
56 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (55 bp):
TCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGC
Found at i:1270 original size:45 final size:47
Alignment explanation
Indices: 1205--1293 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
1195 TGGAAAATGG
*
1205 CACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTC-TTGAGGATGC
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGATGC
1251 CACC-ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
1 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGA
1294 CTGGAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 30 0.73
46 11 0.27
ACGTcount: A:0.16, C:0.21, G:0.31, T:0.31
Consensus pattern (47 bp):
CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGATGC
Found at i:1275 original size:100 final size:100
Alignment explanation
Indices: 1147--1341 Score: 313
Period size: 100 Copynumber: 1.9 Consensus size: 100
1137 GACTAAAAAG
*
1147 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGG-AAAATGGCACCAA
1 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAATGCCACCAA
* * *
1211 CTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTGAGGA
66 -TTGTGTGGGCTTCGAAAGGGGT-CTGCTCTTGAGGA
*
1248 TGCCACC-ACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAATGCCACCAA
1 TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAATGCCACCAA
1312 TTGTGTGGGCTTCGAAAGGGGTCTGCTCTT
66 TTGTGTGGGCTTCGAAAGGGGTCTGCTCTT
1342 TGGGGACTGA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
99 8 0.09
100 61 0.69
101 19 0.22
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (100 bp):
TGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAAATGCCACCAA
TTGTGTGGGCTTCGAAAGGGGTCTGCTCTTGAGGA
Done.