Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1016
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: 28609
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1389 original size:15 final size:15
Alignment explanation
Indices: 1369--1416 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1359 TCAAAGATGG
1369 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
1384 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
1399 -TTTATGGATATAAA
1 GTTTATGGATATGAA
1413 GTTT
1 GTTT
1417 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:1396 original size:29 final size:29
Alignment explanation
Indices: 1363--1422 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1353 AAGGATTCAA
* *
1363 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
1392 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
1421 AG
1 AG
1423 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:2439 original size:14 final size:14
Alignment explanation
Indices: 2397--2441 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2387 TTAAAGAAGC
2397 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
2411 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
2424 AACTCATTTAATTA
1 AACTCATTAAATTA
2438 AACT
1 AACT
2442 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:4913 original size:24 final size:24
Alignment explanation
Indices: 4886--4955 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
4876 TTCACATTCT
*
4886 TTCTCTCTCTCAAACTCTTTTTCA
1 TTCTCTCTCTCAATCTCTTTTTCA
* * * *
4910 TTCTCTTTTTCAATCTCATTTTCT
1 TTCTCTCTCTCAATCTCTTTTTCA
* *
4934 TTTTCACTCTCAATCTCTTTTT
1 TTCTCTCTCTCAATCTCTTTTT
4956 TATTTCTTTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (24 bp):
TTCTCTCTCTCAATCTCTTTTTCA
Found at i:4928 original size:18 final size:18
Alignment explanation
Indices: 4907--4955 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
4897 AAACTCTTTT
4907 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
4925 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
4943 TCAATCTCTTTTT
1 TCATTCTCTTTTT
4956 TATTTCTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:5892 original size:18 final size:18
Alignment explanation
Indices: 5853--5891 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5843 TATGTTCAAA
5853 TTTTCAGATTTTGTTTTT
1 TTTTCAGATTTTGTTTTT
5871 TTTTCA-ATTTT-TTTTCT
1 TTTTCAGATTTTGTTTT-T
5888 TTTT
1 TTTT
5892 TTTTGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.10, C:0.08, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTCAGATTTTGTTTTT
Found at i:6144 original size:29 final size:29
Alignment explanation
Indices: 6111--6170 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6101 AAGGATTCAA
* * *
6111 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATAGATATAAAGTTTATGT
*
6140 AGATGGATTTATAGATATAAAGTTTTTGT
1 AGATGGATTTATAGATATAAAGTTTATGT
6169 AG
1 AG
6171 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATAGATATAAAGTTTATGT
Found at i:7189 original size:14 final size:14
Alignment explanation
Indices: 7147--7191 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
7137 TTAAAGAAGC
7147 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
7161 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
7174 AACTCATTTAATTA
1 AACTCATTAAATTA
7188 AACT
1 AACT
7192 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:8000 original size:8 final size:8
Alignment explanation
Indices: 7987--8012 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
7977 TAAGGTGAAA
7987 AGATGGAT
1 AGATGGAT
7995 AGATGGAT
1 AGATGGAT
8003 AGATGGAT
1 AGATGGAT
8011 AG
1 AG
8013 GTGAACGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (8 bp):
AGATGGAT
Found at i:10244 original size:19 final size:18
Alignment explanation
Indices: 10231--10269 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
10221 AAAAAAGAGA
10231 AGAAATTCAAAAAAAAAT
1 AGAAATTCAAAAAAAAAT
*
10249 CGAAATTCAAAAAAAAA-
1 AGAAATTCAAAAAAAAAT
10266 AGAA
1 AGAA
10270 GTGAGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.13
Consensus pattern (18 bp):
AGAAATTCAAAAAAAAAT
Found at i:10303 original size:24 final size:24
Alignment explanation
Indices: 10276--10323 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
10266 AGAAGTGAGC
10276 AAAA-AACTAAAAAAAAAGTAAAAA
1 AAAAGAAC-AAAAAAAAAGTAAAAA
*
10300 AAAAGAACAAAAAAAAAGTGAAAA
1 AAAAGAACAAAAAAAAAGTAAAAA
10324 GTCTTGCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAAGAACAAAAAAAAAGTAAAAA
Found at i:10311 original size:10 final size:11
Alignment explanation
Indices: 10276--10314 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
10266 AGAAGTGAGC
*
10276 AAAAAACTAAA
1 AAAAAAGTAAA
10287 AAAAAAGTAAA
1 AAAAAAGTAAA
10298 AAAAAAG-AACA
1 AAAAAAGTAA-A
10309 AAAAAA
1 AAAAAA
10315 AAGTGAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (11 bp):
AAAAAAGTAAA
Found at i:13222 original size:6 final size:6
Alignment explanation
Indices: 13199--13312 Score: 63
Period size: 6 Copynumber: 18.5 Consensus size: 6
13189 AAAGAAATTG
* * * *
13199 AAAG-A AAACAA AAAGAA AATGAA AAAGAA AAAGAA ATTA-CA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA
* ** * * *
13246 AAAGAA ATCA-AA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
13297 AAAGAA AAAGCAA AAA
1 AAAGAA AAAG-AA AAA
13313 AAGAAATTGA
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
5 5 0.06
6 57 0.71
7 14 0.17
8 4 0.05
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:13229 original size:18 final size:18
Alignment explanation
Indices: 13203--13311 Score: 78
Period size: 18 Copynumber: 5.8 Consensus size: 18
13193 AAATTGAAAG
*
13203 AAAACAAAAAGAAAATGA
1 AAAAGAAAAAGAAAATGA
*
13221 AAAAGAAAAAG-AAATTA
1 AAAAGAAAAAGAAAATGA
*
13238 CAAAAGAAAAAG-AAATCAA
1 -AAAAGAAAAAGAAAAT-GA
** * *
13257 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAATGA
*
13275 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-TGA
13296 AAAAGAAAAAGCAAAA
1 AAAAGAAAAAG-AAAA
13312 AAAGAAATTG
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.07
18 38 0.54
19 9 0.13
20 12 0.17
21 6 0.09
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:13286 original size:14 final size:13
Alignment explanation
Indices: 13268--13324 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
13258 AAAGTGAGAG
13268 AAAAAGAAAATGA
1 AAAAAGAAAATGA
13281 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
13295 AAAAAGAAAAAGCAA
1 AAAAAGAAAATG--A
*
13310 AAAAAGAAATTGA
1 AAAAAGAAAATGA
13323 AA
1 AA
13325 GAGAGCTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
12 1 0.03
13 13 0.36
14 10 0.28
15 12 0.33
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:13286 original size:15 final size:15
Alignment explanation
Indices: 13266--13323 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 15
13256 AAAAAGTGAG
13266 AGAAAAAGAAAATGA
1 AGAAAAAGAAAATGA
13281 AG-AAAAGAAAAT--
1 AGAAAAAGAAAATGA
* *
13293 TGAAAAAGAAAAAGCA
1 AGAAAAAGAAAATG-A
*
13309 A-AAAAAGAAATTGA
1 AGAAAAAGAAAATGA
13323 A
1 A
13324 AGAGAGCTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 12 0.35
15 12 0.35
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (15 bp):
AGAAAAAGAAAATGA
Found at i:13297 original size:27 final size:27
Alignment explanation
Indices: 13267--13324 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
13257 AAAAGTGAGA
* *
13267 GAAAAAGAAAATG-AAGAAAAGAAAATT
1 GAAAAAGAAAAAGCAAAAAAAG-AAATT
13294 GAAAAAGAAAAAGCAAAAAAAGAAATT
1 GAAAAAGAAAAAGCAAAAAAAGAAATT
13321 GAAA
1 GAAA
13325 GAGAGCTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (27 bp):
GAAAAAGAAAAAGCAAAAAAAGAAATT
Found at i:13312 original size:13 final size:12
Alignment explanation
Indices: 13185--13304 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
13175 AGAAAGAGAT
*
13185 TGAAAAAGAAAT
1 TGAAAAAGAAAA
13197 TG--AAAGAAAA
1 TGAAAAAGAAAA
*
13207 -CAAAAAGAAAA
1 TGAAAAAGAAAA
13218 TGAAAAAGAAAA
1 TGAAAAAGAAAA
* * *
13230 AGAAATTACAAAA
1 TGAAA-AAGAAAA
13243 -GAAAAAG-AAA
1 TGAAAAAGAAAA
* * *
13253 TCAAAAAAGTGAGA
1 T-GAAAAAG-AAAA
13267 -GAAAAAGAAAA
1 TGAAAAAGAAAA
13278 TGAAGAAAAGAAAA
1 TG-A-AAAAGAAAA
13292 TTGAAAAAGAAAA
1 -TGAAAAAGAAAA
13305 AGCAAAAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
10 10 0.12
11 11 0.13
12 33 0.40
13 15 0.18
14 12 0.14
15 2 0.02
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.09
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:16558 original size:13 final size:13
Alignment explanation
Indices: 16540--16568 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16530 CGGCTAACCT
16540 ACATAATTAAATA
1 ACATAATTAAATA
16553 ACATAATTAAATA
1 ACATAATTAAATA
16566 ACA
1 ACA
16569 CACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:16803 original size:21 final size:21
Alignment explanation
Indices: 16779--16818 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16769 GAAAAAGGAA
*
16779 TGAGCTGAAACGAGCTAAATT
1 TGAGCTAAAACGAGCTAAATT
16800 TGAGCTAAAACGAGCTAAA
1 TGAGCTAAAACGAGCTAAA
16819 ACGAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAGCTAAAACGAGCTAAATT
Found at i:16816 original size:10 final size:10
Alignment explanation
Indices: 16780--16825 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
16770 AAAAAGGAAT
*
16780 GAGCTGAAAC
1 GAGCTAAAAC
**
16790 GAGCTAAATTT
1 GAGCTAAA-AC
16801 GAGCTAAAAC
1 GAGCTAAAAC
16811 GAGCTAAAAC
1 GAGCTAAAAC
16821 GAGCT
1 GAGCT
16826 CAAGTAAGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 22 0.73
11 8 0.27
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (10 bp):
GAGCTAAAAC
Found at i:27597 original size:14 final size:14
Alignment explanation
Indices: 27575--27613 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
27565 AGAAGAGGTT
27575 AATTCGAAAAAAAA
1 AATTCGAAAAAAAA
*
27589 AATTTG-AAAAAAA
1 AATTCGAAAAAAAA
27602 AA-TCGAAAAAAA
1 AATTCGAAAAAAA
27614 TAGGAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 15 0.68
14 5 0.23
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (14 bp):
AATTCGAAAAAAAA
Done.