Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3018
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: 57260
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:5432 original size:40 final size:40
Alignment explanation
Indices: 5371--5478 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
5361 TGTGAGTTAT
* *
5371 TAATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATAC
1 TAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATAC
*
5411 TAATTCCCGGGTTAAGT-CCGAAGGCATTCGTGCGAGTTTTA-
1 TAATT-CCGGGTTAAGTCCCGAAGGCATTCGTGCGAG--ATAC
* *
5452 AAAATCCGGGTTAAGTCCCGAAGGCAT
1 TAATTCCGGGTTAAGTCCCGAAGGCAT
5479 GATGAAGTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 33 0.56
41 24 0.41
42 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TAATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATAC
Found at i:7420 original size:20 final size:20
Alignment explanation
Indices: 7395--7435 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
7385 CCATGAATTT
*
7395 TATAAACATAATTAAAAACA
1 TATAAACATAACTAAAAACA
* *
7415 TATAAACTTTACTAAAAACA
1 TATAAACATAACTAAAAACA
7435 T
1 T
7436 TTGGAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAACATAACTAAAAACA
Found at i:15720 original size:39 final size:40
Alignment explanation
Indices: 15643--15749 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
15633 TAGCTCCTCG
* * *
15643 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
15683 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
15722 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
15750 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:15738 original size:40 final size:40
Alignment explanation
Indices: 15686--15869 Score: 162
Period size: 40 Copynumber: 4.6 Consensus size: 40
15676 TAACTCATTC
* *
15686 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGAAACTCGCACA
* *
15726 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
* **
15766 AAGGCCTTCGGGACTTAACCCGGAATTA-ATAACTTACACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGA-AACTCGCACA
* ** ** *
15806 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGAAAC-TCGCACA
*
15847 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
15870 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
39 8 0.07
40 99 0.85
41 10 0.09
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGAAACTCGCACA
Found at i:15814 original size:80 final size:80
Alignment explanation
Indices: 15689--15869 Score: 201
Period size: 80 Copynumber: 2.3 Consensus size: 80
15679 CTCATTCAAT
* * * *
15689 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATACCTTC-GGATCTTAACCCGGATA-
*
15752 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
* **
15768 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTTACACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCACACAAATACCTTCGGATCTTAACCCGGATA
15832 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
15849 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
15870 CAGCATTCAA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
79 7 0.08
80 69 0.79
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:19539 original size:33 final size:33
Alignment explanation
Indices: 19502--19573 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
19492 TCTAAGAAGT
19502 TGTGAAGTTCATACATAAGATTATGATTGAAAA
1 TGTGAAGTTCATACATAAGATTATGATTGAAAA
19535 TGTGAAGTTCATACATAAGATTATGATTGAAAA
1 TGTGAAGTTCATACATAAGATTATGATTGAAAA
19568 TGTGAA
1 TGTGAA
19574 CTGTTAGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (33 bp):
TGTGAAGTTCATACATAAGATTATGATTGAAAA
Found at i:28710 original size:27 final size:26
Alignment explanation
Indices: 28585--28721 Score: 96
Period size: 27 Copynumber: 5.1 Consensus size: 26
28575 GGTCGTTAAG
*
28585 ACCCCTAATTTGTAAAATTACTAAAAT
1 ACCCCCAATTTGTAAAATTAC-AAAAT
*** * *
28612 ACCCCCGGGTTGTAAAAATATCGAAAT
1 ACCCCCAATTTGTAAAATTA-CAAAAT
* *
28639 ACCCCTAATTTG-AAAATTACCGAAAT
1 ACCCCCAATTTGTAAAATTA-CAAAAT
* * **
28665 ACCCTCAATTTTTGCAATTATCAAAAT
1 ACCCCCAATTTGTAAAATTA-CAAAAT
* *
28692 ACCCCCGACTTGTAAAATTACTAAAAT
1 ACCCCCAATTTGTAAAATTAC-AAAAT
28719 ACC
1 ACC
28722 TTTGGTTTGT
Statistics
Matches: 82, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
26 22 0.27
27 59 0.72
28 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.28
Consensus pattern (26 bp):
ACCCCCAATTTGTAAAATTACAAAAT
Found at i:28789 original size:27 final size:27
Alignment explanation
Indices: 28729--28790 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
28719 ACCTTTGGTT
* *
28729 TGTAAAATTACCGAAATACCCTTTTAG
1 TGTAAAATTACCGAAATACCCTATAAG
* *
28756 TGCAAAATTATCGAAATACCCCTATAAG
1 TGTAAAATTACCGAAATA-CCCTATAAG
28784 -GTAAAAT
1 TGTAAAAT
28791 GATTGTTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCCTATAAG
Found at i:33067 original size:27 final size:28
Alignment explanation
Indices: 33037--33106 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 28
33027 TAGGGAAAAA
**
33037 CGGTCATTTTACCCTA-CAAGGGTATTT
1 CGGTCATTTTACCAAATCAAGGGTATTT
* * *
33064 CGGTAATTTTA-CAAATTAGGGGTATTT
1 CGGTCATTTTACCAAATCAAGGGTATTT
33091 CGGTCATTTTA-CAAAT
1 CGGTCATTTTACCAAAT
33107 TAGAGGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (28 bp):
CGGTCATTTTACCAAATCAAGGGTATTT
Found at i:33107 original size:27 final size:27
Alignment explanation
Indices: 33056--33109 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
33046 TACCCTACAA
33056 GGGTATTTCGGTAATTTTACAAATTAG
1 GGGTATTTCGGTAATTTTACAAATTAG
*
33083 GGGTATTTCGGTCATTTTACAAATTAG
1 GGGTATTTCGGTAATTTTACAAATTAG
33110 AGGTCTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTACAAATTAG
Found at i:37289 original size:34 final size:35
Alignment explanation
Indices: 37251--37325 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
37241 CCTTTTCCAG
37251 TAACAGTAG-CAGTCTGGGCCTTAGCCCATTTCAA
1 TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
*
37285 TAACAGT-GACAGTCTGGGCCTTAGCCCATTTCAG
1 TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
37319 T-ACAGTA
1 TAACAGTA
37326 TGCAAGCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
33 6 0.16
34 32 0.84
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (35 bp):
TAACAGTAGACAGTCTGGGCCTTAGCCCATTTCAA
Found at i:40129 original size:20 final size:20
Alignment explanation
Indices: 40106--40169 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
40096 AATAAGACAT
40106 TTATACTTTAAATATCTCAA
1 TTATACTTTAAATATCTCAA
* ***
40126 TTATAAAC-AT-AATAAGAC-A
1 TTAT--ACTTTAAATATCTCAA
40145 TTATACTTTAAATATCTCAA
1 TTATACTTTAAATATCTCAA
40165 TTATA
1 TTATA
40170 AACATTCTTT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 2 0.06
18 1 0.03
19 10 0.32
20 15 0.48
21 1 0.03
22 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATACTTTAAATATCTCAA
Found at i:40155 original size:39 final size:40
Alignment explanation
Indices: 40096--40174 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
40086 ACAATATAAC
40096 AATAAGACATTTATACTTTAAATATCTCAATTATAAACAT
1 AATAAGACATTTATACTTTAAATATCTCAATTATAAACAT
40136 AATAAGACA-TTATACTTTAAATATCTCAATTATAAACAT
1 AATAAGACATTTATACTTTAAATATCTCAATTATAAACAT
40175 TCTTTTCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 30 0.77
40 9 0.23
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.37
Consensus pattern (40 bp):
AATAAGACATTTATACTTTAAATATCTCAATTATAAACAT
Found at i:49746 original size:3 final size:3
Alignment explanation
Indices: 49738--49792 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
49728 ACGGTTTAAA
* * * *
49738 AAT AAT AAT ATT AAT AAT AAT AAT GAT AAT ATT AAT AAT GAT AAT ACA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
49786 AAT AAT A
1 AAT AAT A
49793 GAATACCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:50718 original size:22 final size:21
Alignment explanation
Indices: 50687--50732 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
50677 TTTCTTTCCT
*
50687 TTTTTGATTCGATTC-TCTGTG
1 TTTTTGATTC-AATCGTCTGTG
50708 TTTTTGTATTCAATCGTCTGTG
1 TTTTTG-ATTCAATCGTCTGTG
50730 TTT
1 TTT
50733 ACATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (21 bp):
TTTTTGATTCAATCGTCTGTG
Found at i:51377 original size:22 final size:22
Alignment explanation
Indices: 51352--51403 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
51342 TTATGAAATA
51352 ATAATAACAACAATAATAGATG
1 ATAATAACAACAATAATAGATG
51374 ATAATAACAACAATAATAGATG
1 ATAATAACAACAATAATAGATG
51396 ATAATAAC
1 ATAATAAC
51404 CTATATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.23
Consensus pattern (22 bp):
ATAATAACAACAATAATAGATG
Done.