Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2562
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: 13865
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:4210 original size:32 final size:33
Alignment explanation
Indices: 4155--4216 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
4145 CAAGCCAATG
**
4155 TATCGATACAATTTTTTGTGTATCGATACATTC
1 TATCGATACAATACTTTGTGTATCGATACATTC
4188 TATCGATAC-ATACTTTGTGTATCGATACA
1 TATCGATACAATACTTTGTGTATCGATACA
4217 AGTTTGGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (33 bp):
TATCGATACAATACTTTGTGTATCGATACATTC
Found at i:5376 original size:165 final size:165
Alignment explanation
Indices: 4999--5577 Score: 547
Period size: 166 Copynumber: 3.5 Consensus size: 165
4989 TCCAAGCATC
* * ** * * * *
4999 AAAATTCTTC-AATATTATCATTTAAATCCTATTAAATCAGTTTTGAAAAATTACATTTATTTT-
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATT-CATTCATTTTC
* * * * * * ** * *
5062 TTGAGTTATTGATTTTCTT--TTAAAATTTCTTCTGTTT-TTAAATTTCGAGATTTTCTACTCTG
65 ATGAGTTTTTAATTTT-TTCCTTAAAA-TTCCTATGTTTCTAAAAAATAGAG-TTTTCTACTCCG
* ** * ** *
5124 TAAATTTTTTCGAGAAGATTTTCATGGGTTTAAAATTTTC
127 TAAATTTTTTTGAGGGGATTTTC-TTGGTTTTTAATTTTT
*
5164 AAAATTCATCAAATATTATTATTTAATTT-ATATTAAATTAGTTTTCAAAAATGCATTCATTTTC
1 AAAATTCATCAAATATTATTATTT-ATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTC
*
5228 AT-AGGTTTTTAATTTTTTTCTTAAAATTTTCCTAT-TTTC-AAAAAAT-GAAGTTTTCTACTCC
65 ATGA-GTTTTTAATTTTTTCCTTAAAA--TTCCTATGTTTCTAAAAAATAG-AGTTTTCTACTCC
* *
5289 ATAAATTTTTTTGAGGGGGTTTTCTTGGTTTTTAATTTTT
126 GTAAATTTTTTTGAGGGGATTTTCTTGGTTTTTAATTTTT
* *
5329 AAAATTTATCAAATATTATTA-TTATTTCATAATAAATTAGTTTTTC-AAAATTCATTCATTTTC
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAATTAG-TTTTCAAAAATTCATTCATTTTC
* * * *
5392 ATGATTTTTTGAATTTTTTCCTTGAAATTCCTTTGTTTCTAAAAAATAGAGATTTCTACTCCGTA
65 ATGAGTTTTT-AATTTTTTCCTTAAAATTCCTATGTTTCTAAAAAATAGAGTTTTCTACTCCGTA
* * *
5457 AATCTTTTTG-GGGGATTTTTTCTTTGTTTTTATTTTTT
129 AATTTTTTTGAGGGGA--TTTTCTTGGTTTTTAATTTTT
* * *
5495 AAAATCCATAAAATATTATTATTTATTTCACATTAAATCTA-TTTTCAAAAATTCATTCATTTTC
1 AAAATTCATCAAATATTATTATTTATTTCATATTAAAT-TAGTTTTCAAAAATTCATTCATTTTC
*
5559 ATGAGTTTTAAATTTTTTC
65 ATGAGTTTTTAATTTTTTC
5578 TTTGAAATCC
Statistics
Matches: 346, Mismatches: 47, Indels: 41
0.80 0.11 0.09
Matches are distributed among these distances:
163 10 0.03
164 44 0.13
165 103 0.30
166 125 0.36
167 56 0.16
168 8 0.02
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (165 bp):
AAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTCA
TGAGTTTTTAATTTTTTCCTTAAAATTCCTATGTTTCTAAAAAATAGAGTTTTCTACTCCGTAAA
TTTTTTTGAGGGGATTTTCTTGGTTTTTAATTTTT
Found at i:5585 original size:166 final size:164
Alignment explanation
Indices: 5157--5585 Score: 516
Period size: 165 Copynumber: 2.6 Consensus size: 164
5147 ATGGGTTTAA
* *
5157 AATTTTCAAAATTCATCAAATATTATTATTTAATTT-ATATTAAATTAGTTTTCAAAAATGCATT
1 AATTTTTAAAATTCATCAAATATTATTATTT-ATTTCATATTAAATTAGTTTTCAAAAATTCATT
* * *
5221 CATTTTCAT-AGGTTTTTAATTTTTT-TCTTAAAATTTTCCTATTTTCAAAAAATGAAGTTTTCT
65 CATTTTCATGAGGTTTTAAATTTTTTCT-TTGAAA--TTCCTATTTTCAAAAAATGAAGATTTCT
*
5284 ACTCCATAAATTTTTTTGAGGGGGTTTTCTTGGTTTTT
127 ACTCCATAAATCTTTTTGAGGGGGTTTTCTTGGTTTTT
* *
5322 AATTTTTAAAATTTATCAAATATTATTA-TTATTTCATAATAAATTAGTTTTTC-AAAATTCATT
1 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAG-TTTTCAAAAATTCATT
** * * *
5385 CATTTTCATGATTTTTTGAATTTTTTCCTTGAAATTCCTTTGTTTCTAAAAAAT-AGAGATTTCT
65 CATTTTCATGAGGTTTTAAATTTTTTCTTTGAAATTCCTAT-TTTC-AAAAAATGA-AGATTTCT
* * *
5449 ACTCCGTAAATCTTTTTG-GGGGATTTTTTCTTTGTTTTT
127 ACTCCATAAATCTTTTTGAGGGG--GTTTTCTTGGTTTTT
* * * *
5488 ATTTTTTAAAATCCATAAAATATTATTATTTATTTCACATTAAATCTA-TTTTCAAAAATTCATT
1 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAAT-TAGTTTTCAAAAATTCATT
5552 CATTTTCATGA-GTTTTAAATTTTTTCTTTGAAAT
65 CATTTTCATGAGGTTTTAAATTTTTTCTTTGAAAT
5586 CCCCCTTTTC
Statistics
Matches: 228, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
163 10 0.04
164 40 0.18
165 79 0.35
166 62 0.27
167 35 0.15
168 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (164 bp):
AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTC
ATTTTCATGAGGTTTTAAATTTTTTCTTTGAAATTCCTATTTTCAAAAAATGAAGATTTCTACTC
CATAAATCTTTTTGAGGGGGTTTTCTTGGTTTTT
Found at i:5641 original size:166 final size:166
Alignment explanation
Indices: 5157--5641 Score: 522
Period size: 166 Copynumber: 2.9 Consensus size: 166
5147 ATGGGTTTAA
* *
5157 AATTTTCAAAATTCATCAAATATTATTATTTAATTT-ATATTAAATTAGTTTTCAAAAATGCATT
1 AATTTTTAAAATTCATCAAATATTATTATTT-ATTTCATATTAAATTAGTTTTCAAAAATTCATT
* * ** *
5221 CATTTTCAT-AGGTTTTTAATTTTTT-TCTTAAAATTTTCCTATTT-TCAAAAAATGAAGTTTTC
65 CATTTTCATGAGGTTTTAAATTTTTTCT-TTGAAATTCCCCTATTTCTCAAAAATTG-AGTTTTC
**
5283 TACTCCATAAATTTTTTTGAGGG-GGTTTTCTTGGTTTTT
128 TACTCCATAAA-TTTTTTGAGGGATTTTTTCTTGGTTTTT
* *
5322 AATTTTTAAAATTTATCAAATATTATTA-TTATTTCATAATAAATTAGTTTTTC-AAAATTCATT
1 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAG-TTTTCAAAAATTCATT
** * * ** * * * *
5385 CATTTTCATGATTTTTTGAATTTTTTCCTTGAAATTCCTTTGTTTCTAAAAAATAGAGATTTCTA
65 CATTTTCATGAGGTTTTAAATTTTTTCTTTGAAATTCCCCTATTTCTCAAAAATTGAGTTTTCTA
* * *
5450 CTCCGTAAATCTTTTTGGGGGATTTTTTCTTTGTTTTT
130 CTCCATAAAT-TTTTTGAGGGATTTTTTCTTGGTTTTT
* * * *
5488 ATTTTTTAAAATCCATAAAATATTATTATTTATTTCACATTAAATCTA-TTTTCAAAAATTCATT
1 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAAT-TAGTTTTCAAAAATTCATT
* *
5552 CATTTTCATGA-GTTTTAAATTTTTTCTTTGAAATCCCCCT-TTTCTCGAAAAATTGAGTTTTTT
65 CATTTTCATGAGGTTTTAAATTTTTTCTTTGAAATTCCCCTATTTCTC-AAAAATTGAGTTTTCT
* * *
5615 ATTCCATAAATATTTCGAGAGGATTTT
129 ACTCCATAAATTTTTTGAG-GGATTTT
5642 CTTTGGTCTA
Statistics
Matches: 264, Mismatches: 44, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
163 4 0.02
164 32 0.12
165 90 0.34
166 101 0.38
167 35 0.13
168 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (166 bp):
AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTC
ATTTTCATGAGGTTTTAAATTTTTTCTTTGAAATTCCCCTATTTCTCAAAAATTGAGTTTTCTAC
TCCATAAATTTTTTGAGGGATTTTTTCTTGGTTTTT
Found at i:6257 original size:14 final size:13
Alignment explanation
Indices: 6234--6264 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
6224 ACAGCAAGTG
6234 AAAAAAAACAAAA
1 AAAAAAAACAAAA
6247 AAAACAAAACAAAA
1 AAAA-AAAACAAAA
6261 AAAA
1 AAAA
6265 GGAAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:8414 original size:20 final size:20
Alignment explanation
Indices: 8345--8416 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
8335 TGTTAATGCT
* *
8345 TGCATTTGTATCATTTTACA
1 TGCATTTGCATCATTTAACA
**
8365 TGCATTTGCATTCAGATAACA
1 TGCATTTGCA-TCATTTAACA
*
8386 TTGGCATTTGCATCATTTAATA
1 -T-GCATTTGCATCATTTAACA
8408 TGCATTTGC
1 TGCATTTGC
8417 CACTTGGCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 17 0.40
21 8 0.19
22 8 0.19
23 9 0.21
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (20 bp):
TGCATTTGCATCATTTAACA
Found at i:8583 original size:44 final size:43
Alignment explanation
Indices: 8535--8660 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 43
8525 TAACATTCGC
*
8535 ATTTGCATCATTTCCTATGCATTTGCTATTTTATTGATCCTTG-T
1 ATTTGCATCATTTCCTA-GCATTTGC-ATTTTATTGATCATTGAT
*
8579 ATTTGCATCATTTCACCTA-CATTTGCATTTTAGATGA-CATTGAT
1 ATTTGCATCATTT--CCTAGCATTTGCATTTTA-TTGATCATTGAT
* * *
8623 ATTTACATCATTTCATAGGCATTTGCCACTTTATTGAT
1 ATTTGCATCATTTCCTA-GCATTTG-CATTTTATTGAT
8661 GTTGCATTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
42 3 0.04
43 10 0.15
44 45 0.66
45 6 0.09
46 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (43 bp):
ATTTGCATCATTTCCTAGCATTTGCATTTTATTGATCATTGAT
Found at i:10357 original size:28 final size:28
Alignment explanation
Indices: 10302--10399 Score: 105
Period size: 28 Copynumber: 3.5 Consensus size: 28
10292 GGAATAAAGC
*
10302 CGGGGTT-GAGTATCTCCT--TGGAAGTAA
1 CGGGGTTGGAGTATC-CCTGAT-GAAATAA
10329 CGGGGTTGGAGTATCCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCTGATGAAATAA
* *
10357 CGAGGTTGGAAGTATCCCCGATGAAATAA
1 CGGGGTTGG-AGTATCCCTGATGAAATAA
*
10386 C-GAGTTGGAGTATC
1 CGGGGTTGGAGTATC
10400 TGATTGTGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
27 16 0.26
28 26 0.42
29 20 0.32
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.26
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCTGATGAAATAA
Found at i:10379 original size:29 final size:28
Alignment explanation
Indices: 10326--10399 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 28
10316 TCCTTGGAAG
* *
10326 TAACGGGGTTGGAGTATCCCTGATGAAA
1 TAACGAGGTTGGAGTATCCCCGATGAAA
10354 TAACGAGGTTGGAAGTATCCCCGATGAAA
1 TAACGAGGTTGG-AGTATCCCCGATGAAA
10383 TAACGA-GTTGGAGTATC
1 TAACGAGGTTGGAGTATC
10400 TGATTGTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 6 0.14
28 16 0.37
29 21 0.49
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
TAACGAGGTTGGAGTATCCCCGATGAAA
Found at i:12293 original size:11 final size:11
Alignment explanation
Indices: 12279--12318 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
12269 AATGGACTAG
12279 TGTTTTTTTGT
1 TGTTTTTTTGT
12290 TGTTTTTTTG-
1 TGTTTTTTTGT
12300 -GTTTTTTT-T
1 TGTTTTTTTGT
*
12309 TTTTTTTTTG
1 TGTTTTTTTG
12319 CTAAAGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
9 8 0.32
10 7 0.28
11 10 0.40
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TGTTTTTTTGT
Found at i:12305 original size:20 final size:19
Alignment explanation
Indices: 12280--12318 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12270 ATGGACTAGT
12280 GTTTTTTTGTTGTTTTTTTG
1 GTTTTTTT-TTGTTTTTTTG
*
12300 GTTTTTTTTTTTTTTTTTG
1 GTTTTTTTTTGTTTTTTTG
12319 CTAAAGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
GTTTTTTTTTGTTTTTTTG
Found at i:12799 original size:20 final size:22
Alignment explanation
Indices: 12774--12819 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 22
12764 AAAAATGCCT
12774 AAATGTATCGATACAT-T-GTA
1 AAATGTATCGATACATCTGGTA
12794 AAATGTATCGATACATCTGGTA
1 AAATGTATCGATACATCTGGTA
12816 AAAT
1 AAAT
12820 TTCCAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
AAATGTATCGATACATCTGGTA
Found at i:12931 original size:19 final size:18
Alignment explanation
Indices: 12907--12974 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
12897 CAGTAGCTAA
12907 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
12926 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
12941 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
12958 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
12975 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:12947 original size:13 final size:13
Alignment explanation
Indices: 12929--12953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12919 ACAATACTTA
12929 TGTATCGATACAT
1 TGTATCGATACAT
12942 TGTATCGATACA
1 TGTATCGATACA
12954 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12951 original size:32 final size:32
Alignment explanation
Indices: 12910--12972 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
12900 TAGCTAATTA
*
12910 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
12942 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
12973 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:13858 original size:55 final size:56
Alignment explanation
Indices: 13744--13865 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
13734 ATAAAGTGTA
*
13744 TCCTGCTCTTTGAGGACTAAAAACGTGGCACCAACTCATGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAACGTGCCACCAACTCATGTGGGCTTTGAAAGGCG
* ** *
13800 TCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTAAAAACGTGCCACCAACTCATGTGGGCTTTGAA-AGGCG
13855 TCCTGCTCTTT
1 TCCTGCTCTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
54 2 0.03
55 40 0.67
56 18 0.30
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTAAAAACGTGCCACCAACTCATGTGGGCTTTGAAAGGCG
Done.