Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3640
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: 31085
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:6094 original size:40 final size:40
Alignment explanation
Indices: 6050--6234 Score: 162
Period size: 40 Copynumber: 4.7 Consensus size: 40
6040 GCTCCTCGTT
* *
6050 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAGCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCACA
* *
6090 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
* * * * * *
6130 CCAATGCCTTCGGG-CTTAGCCCAGAATTATTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
* * * * * * *
6169 CAAATACCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCA-CA
6210 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6235 CATCATTCAA
Statistics
Matches: 114, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
38 2 0.02
39 29 0.25
40 72 0.63
41 11 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
Found at i:8585 original size:24 final size:25
Alignment explanation
Indices: 8558--8628 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
8548 AGAAAAGGAG
8558 AAAGAGATTGAAAAAGAAATCAA-A
1 AAAGAGATTGAAAAAGAAATCAAGA
* ** *
8582 AAAGTGAGAGAAAAAGAAAATGAAGA
1 AAAGAGATTGAAAAAG-AAATCAAGA
*
8608 AAAGAAAATTGAAAAAGAAAT
1 AAAG-AGATTGAAAAAGAAAT
8629 TGAGAATGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 13 0.36
25 6 0.17
26 9 0.25
27 8 0.22
ACGTcount: A:0.68, C:0.01, G:0.20, T:0.11
Consensus pattern (25 bp):
AAAGAGATTGAAAAAGAAATCAAGA
Found at i:8628 original size:12 final size:12
Alignment explanation
Indices: 8558--8656 Score: 50
Period size: 12 Copynumber: 8.6 Consensus size: 12
8548 AGAAAAGGAG
*
8558 AAAGAGATTGAA
1 AAAGAAATTGAA
**
8570 AAAGAAATCAAA
1 AAAGAAATTGAA
** **
8582 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
8594 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
8608 AAAGAAAATTGAA
1 AAAG-AAATTGAA
8621 AAAGAAATTG--
1 AAAGAAATTGAA
8631 --AG-AA-TGAA
1 AAAGAAATTGAA
8639 AAA-AAATTGAA
1 AAAGAAATTGAA
8650 AAAGAAA
1 AAAGAAA
8657 AAGCGAAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 2 0.03
10 3 0.05
11 7 0.11
12 31 0.48
13 6 0.09
14 6 0.09
15 5 0.08
ACGTcount: A:0.68, C:0.01, G:0.19, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:8645 original size:17 final size:18
Alignment explanation
Indices: 8611--8659 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
8601 ATGAAGAAAA
8611 GAAAATTGAAAAAGAAATT
1 GAAAA-TGAAAAAGAAATT
*
8630 GAGAATGAAAAA-AAATT
1 GAAAATGAAAAAGAAATT
*
8647 GAAAAAGAAAAAG
1 GAAAATGAAAAAG
8660 CGAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 15 0.58
18 7 0.27
19 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
GAAAATGAAAAAGAAATT
Found at i:8654 original size:29 final size:27
Alignment explanation
Indices: 8591--8657 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 27
8581 AAAAGTGAGA
8591 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAGAAAATT
*
8618 GAAAAAGAAATTGAGAATGAAAA-AAAATT
1 GAAAAAGAAAAT--GAA-GAAAAGAAAATT
8647 GAAAAAGAAAA
1 GAAAAAGAAAA
8658 AGCGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.31
29 19 0.54
30 5 0.14
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAGAAAATT
Found at i:8711 original size:33 final size:33
Alignment explanation
Indices: 8674--8736 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
8664 AAAAGAAATT
8674 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
8707 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
8737 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:10537 original size:20 final size:20
Alignment explanation
Indices: 10514--10567 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
10504 AGTTTTTCCC
*
10514 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
10534 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
10554 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
10568 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:10549 original size:30 final size:30
Alignment explanation
Indices: 10514--10587 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
10504 AGTTTTTCCC
10514 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
10544 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
10574 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
10588 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:10577 original size:20 final size:20
Alignment explanation
Indices: 10514--10578 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
10504 AGTTTTTCCC
* * * *
10514 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
10534 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
10553 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
10574 AGCTC
1 AGCTC
10579 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:14043 original size:24 final size:25
Alignment explanation
Indices: 14003--14059 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
13993 GTTGGGACAT
* *
14003 ATTAAAT-TCGTCCACCAGCAGTTC
1 ATTAAATCTCGTCAACCAGCAGCTC
*
14027 ATTAAATCT-GTCAACCAGTAGCTC
1 ATTAAATCTCGTCAACCAGCAGCTC
14051 ATTAAATCT
1 ATTAAATCT
14060 ATCCAGGCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.32
Consensus pattern (25 bp):
ATTAAATCTCGTCAACCAGCAGCTC
Found at i:14151 original size:17 final size:18
Alignment explanation
Indices: 14131--14169 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
14121 TGCACACACA
14131 AATTAATTCAG-CACATT
1 AATTAATTCAGACACATT
*
14148 AATTAATTTAGACACATT
1 AATTAATTCAGACACATT
14166 AATT
1 AATT
14170 TTTGGCTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AATTAATTCAGACACATT
Found at i:24234 original size:21 final size:20
Alignment explanation
Indices: 24210--24252 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
24200 GAATGAGCCA
24210 AAACGAGCTAAAATCAAGCTC
1 AAACGAGCTAAAA-CAAGCTC
* *
24231 AAACGAGCTGAAACGAGCTC
1 AAACGAGCTAAAACAAGCTC
24251 AA
1 AA
24253 GTGAGCTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.12
Consensus pattern (20 bp):
AAACGAGCTAAAACAAGCTC
Found at i:27361 original size:23 final size:22
Alignment explanation
Indices: 27309--27361 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27299 TCCACGTCTT
*
27309 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27331 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27354 TTTCTTTT
1 TTTCTTTT
27362 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:30675 original size:11 final size:11
Alignment explanation
Indices: 30637--30675 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
30627 TTAGTGAAAG
*
30637 AAAAAATTCTA
1 AAAAAATTCAA
*
30648 AAAAAATTCGA
1 AAAAAATTCAA
30659 AAAAAATTCAA
1 AAAAAATTCAA
30670 AAAAAA
1 AAAAAA
30676 GTGTGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAATTCAA
Done.