Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3293
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: 17211
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Found at i:824 original size:38 final size:38
Alignment explanation
Indices: 736--853 Score: 179
Period size: 37 Copynumber: 3.2 Consensus size: 38
726 CTCAGACGAA
* * *
736 ATCTCCACACGAAGTTATCGGGTCTTACCCGGACA-AA
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAT
773 ATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAT
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAT
811 ATCTCCACACGTAGTCATC-GGTCTTACCCGGA-ATAT
1 ATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAT
*
847 ATTTCCA
1 ATCTCCA
854 AGTTTCATGT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
36 10 0.13
37 46 0.61
38 20 0.26
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (38 bp):
ATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAT
Found at i:1142 original size:47 final size:47
Alignment explanation
Indices: 1047--1238 Score: 289
Period size: 47 Copynumber: 4.1 Consensus size: 47
1037 CATACATATT
* * *
1047 TCACATTAGCCATTCGGCTTTA-CACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* *
1093 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1140 TCACATTGGCCATTCGGCCTT-TCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
1186 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1233 TCACAT
1 TCACAT
1239 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 11, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
46 64 0.48
47 69 0.52
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:1166 original size:93 final size:93
Alignment explanation
Indices: 1047--1238 Score: 296
Period size: 93 Copynumber: 2.1 Consensus size: 93
1037 CATACATATT
*
1047 TCACATTAGCCATTCGGCTTTACACATATATGCATGTTCATATTCATCACATTGGCCATTCGGCC
1 TCACATTAGCCATTCGGCTTTACACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
* **
1112 TTATCACACATATGCATGCTCACATTCA
66 TTATCACACATATACACACTCACATTCA
*
1140 TCACATTGGCCATTCGGCCTTT-CACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 TCACATTAGCCATTCGG-CTTTACACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
* * *
1204 CTTATCTCATATATACACATTCACATTCA
65 CTTATCACACATATACACACTCACATTCA
1233 TCACAT
1 TCACAT
1239 AAAATCCTAA
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 86 0.96
94 4 0.04
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.34
Consensus pattern (93 bp):
TCACATTAGCCATTCGGCTTTACACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCC
TTATCACACATATACACACTCACATTCA
Found at i:5567 original size:40 final size:40
Alignment explanation
Indices: 5535--5842 Score: 498
Period size: 40 Copynumber: 7.8 Consensus size: 40
5525 CCAGCATGAT
* * * *
5535 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
5575 TGCTCTTCGGG-TTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5614 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5654 TGCTCTTCGGGACTTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5693 TGCTCTTC-GGACTTAG-CCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
5731 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5771 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
*
5811 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCTTCGGGACTTAGCCCGGATACATCACT
5843 CTCAATTCTC
Statistics
Matches: 254, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
38 38 0.15
39 71 0.28
40 145 0.57
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:5638 original size:79 final size:80
Alignment explanation
Indices: 5535--5842 Score: 498
Period size: 79 Copynumber: 3.9 Consensus size: 80
5525 CCAGCATGAT
* * * * * *
5535 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGG-TTTAGCACGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
5599 TATCACTAGCACGAA
66 CATCACTAGCACGAA
*
5614 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAG-CCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
5678 CATCACTAGCACGAA
66 CATCACTAGCACGAA
5693 TGCTCTTC-GGACTTAG-CCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
5756 CATCACTAGCACGAA
66 CATCACTAGCACGAA
*
5771 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
*
5836 TATCACT
66 CATCACT
5843 CTCAATTCTC
Statistics
Matches: 214, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
77 39 0.18
78 37 0.17
79 82 0.38
80 56 0.26
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
CATCACTAGCACGAA
Found at i:5766 original size:157 final size:159
Alignment explanation
Indices: 5535--5842 Score: 496
Period size: 157 Copynumber: 1.9 Consensus size: 159
5525 CCAGCATGAT
* * *
5535 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGTTTAGCACGGATAT
1 TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGCTTAGCACGGATAC
5600 ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGG
66 ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGG
5665 ACTTAG-CCGGATACATCACTAGCACGAA
131 ACTTAGCCCGGATACATCACTAGCACGAA
* * * *
5693 TGCTCTTC-GGACTTAG-CCGGATACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATA
1 TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGG-CTTAGCACGGATA
* *
5756 CATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGG
65 CATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG
*
5821 GACTTAGCCCGGATATATCACT
130 GACTTAGCCCGGATACATCACT
5843 CTCAATTCTC
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
156 30 0.22
157 87 0.63
158 21 0.15
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (159 bp):
TGCTCTTCGGGACCTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGGCTTAGCACGGATAC
ATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGG
ACTTAGCCCGGATACATCACTAGCACGAA
Found at i:7169 original size:37 final size:37
Alignment explanation
Indices: 7110--7218 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
7100 AGCTCAGACG
* *
7110 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
7147 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
7184 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
7219 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:7464 original size:31 final size:31
Alignment explanation
Indices: 7411--7480 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 31
7401 ATACATATCT
7411 CATATATTTCACATTGCCATTCGGC-TTA-CA
1 CATATA-TTCACATTGCCATTCGGCTTTACCA
7441 CATATATTCACATTTAGCCATTCGGCTTTACCA
1 CATATATTCACA-TT-GCCATTCGGCTTTACCA
7474 CATATAT
1 CATATAT
7481 GCATGTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.17
30 8 0.22
31 10 0.28
32 3 0.08
33 9 0.25
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (31 bp):
CATATATTCACATTGCCATTCGGCTTTACCA
Found at i:7506 original size:76 final size:76
Alignment explanation
Indices: 7366--7525 Score: 197
Period size: 76 Copynumber: 2.1 Consensus size: 76
7356 CACATCGCCT
7366 ACATAT-TTCACACTAGCCATTCGGCTTTACCACATATACATATCTCATATATTTCACATTGCCA
1 ACATATATTCACACTAGCCATTCGGCTTTACCACATATACATATCTCA-ATATTTCACATTGCCA
7430 TTCGG-CTTA-C
65 TTCGGCCTTATC
* *
7440 ACATATATTCACATTTAGCCATTCGGCTTTACCACATATATGCATGT-TC-ATA-TTCATCATTG
1 ACATATATTCACA-CTAGCCATTCGGCTTTACCACATATA--CATATCTCAATATTTCA-CATT-
7502 GCCATTCGGCCTTATC
61 GCCATTCGGCCTTATC
*
7518 ACACATAT
1 ACATATAT
7526 GCATGTTCAC
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
74 10 0.13
75 13 0.17
76 34 0.45
77 6 0.08
78 12 0.16
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (76 bp):
ACATATATTCACACTAGCCATTCGGCTTTACCACATATACATATCTCAATATTTCACATTGCCAT
TCGGCCTTATC
Found at i:7549 original size:47 final size:47
Alignment explanation
Indices: 7448--7640 Score: 282
Period size: 47 Copynumber: 4.1 Consensus size: 47
7438 ACACATATAT
* * * *
7448 TCACATTTAGCCATTCGGCTTTACCACATATATGCATGTTCATATTCA
1 TCACA-TTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
*
7496 T--CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
7541 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
* * **
7588 TCACATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
7635 TCACAT
1 TCACAT
7641 AAAATCCTAA
Statistics
Matches: 133, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
45 38 0.29
46 2 0.02
47 92 0.69
48 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
Found at i:7567 original size:22 final size:22
Alignment explanation
Indices: 7540--7611 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
7530 GTTCACATTC
7540 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
7562 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
7586 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
7609 ATC
1 ATC
7612 TCATATATAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:12116 original size:40 final size:40
Alignment explanation
Indices: 12056--12307 Score: 271
Period size: 40 Copynumber: 6.2 Consensus size: 40
12046 GGTTTAGCGA
*
12056 CGGATATATCACTAGCCACGAATTGCTCTTTC-GAACTTAG-C
1 CGGATACATCACTAG-CACGAA-TGCTC-TTCGGAACTTAGTC
* *
12097 CGGATACATCACAAGCACGAATGCTCTTCCGGGACCTTAGTC
1 CGGATACATCACTAGCACGAATGCTCTT-C-GGAACTTAGTC
12139 CGGATACATCACTAGCACGAATGCTCTTCGGGAACTTAGTC
1 CGGATACATCACTAGCACGAATGCTCTTC-GGAACTTAGTC
* *
12180 CGGA-ACATCACTAGCACGAATGCTCTTGGGGACTGTAG-C
1 CGGATACATCACTAGCACGAATGCTCTTCGGAACT-TAGTC
* * *
12219 CCGATATATCACTAGCACGAATGCTCTTC-GATTCTTAGTC
1 CGGATACATCACTAGCACGAATGCTCTTCGGA-ACTTAGTC
* * *
12259 CGGATATATCACTAAGCACGACAATGCTCTTCGGGACTTAGCC
1 CGGATACATCACT-AGCACG--AATGCTCTTCGGAACTTAGTC
12302 CGGATA
1 CGGATA
12308 TATACTCTAA
Statistics
Matches: 183, Mismatches: 16, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.01
39 19 0.10
40 69 0.38
41 42 0.23
42 28 0.15
43 22 0.12
44 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTC
Found at i:12188 original size:82 final size:78
Alignment explanation
Indices: 12030--12310 Score: 318
Period size: 80 Copynumber: 3.4 Consensus size: 78
12020 ATATAACATC
**
12030 AGCACGAATGC-CTT-GGGGTTTAGCGACGGATATATCACTAGCCACGAATTGCTCTTTCGAACT
1 AGCACGAATGCTCTTCGGGACTTAGC--CGGATATATCACTAG-CACGAA-TGCTC-TTCGAACT
12093 TAG-CCGGATACATCACA
61 TAGTCCGGATACATCACA
*
12110 AGCACGAATGCTCTTCCGGGACCTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGGAACT
1 AGCACGAATGCTCTT-CGGGA-CTTAG-CCGGATATATCACTAGCACGAATGCTCTTC--GAACT
*
12175 TAGTCCGGA-ACATCACT
61 TAGTCCGGATACATCACA
* * *
12192 AGCACGAATGCTCTTGGGGACTGTAGCCCGATATATCACTAGCACGAATGCTCTTCGATTCTTAG
1 AGCACGAATGCTCTTCGGGACT-TAGCCGGATATATCACTAGCACGAATGCTCTTCGA-ACTTAG
*
12257 TCCGGATATATCACTA
64 TCCGGATACATCAC-A
12273 AGCACGACAATGCTCTTCGGGACTTAGCCCGGATATAT
1 AGCACG--AATGCTCTTCGGGACTTAG-CCGGATATAT
12311 ACTCTAATCG
Statistics
Matches: 174, Mismatches: 12, Indels: 27
0.82 0.06 0.13
Matches are distributed among these distances:
78 2 0.01
79 11 0.06
80 50 0.29
81 21 0.12
82 39 0.22
83 46 0.26
84 4 0.02
85 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (78 bp):
AGCACGAATGCTCTTCGGGACTTAGCCGGATATATCACTAGCACGAATGCTCTTCGAACTTAGTC
CGGATACATCACA
Found at i:12198 original size:122 final size:122
Alignment explanation
Indices: 12063--12305 Score: 316
Period size: 122 Copynumber: 2.0 Consensus size: 122
12053 CGACGGATAT
* *
12063 ATCACTAGCCACGAATTGCTCTTTCGAACT-TAGCCGGATACATCACAAGCACGAATGCTCTTCC
1 ATCACTAGCCACGAA-TGCTCTTGCGAACTGTAGCCCGATACATCACAAGCACGAATGCTCTT-C
*
12127 GGGA-CCTTAGTCCGGATACATCACT-AGCACG-AATGCTCTTCGGGAACTTAGTCCGGAAC
64 --GATCCTTAGTCCGGATACATCACTAAGCACGAAATGCTCTTCGGG-ACTTAGCCCGGAAC
* * * *
12186 ATCACTAG-CACGAATGCTCTTGGGGACTGTAGCCCGATATATCACTAGCACGAATGCTCTTCGA
1 ATCACTAGCCACGAATGCTCTTGCGAACTGTAGCCCGATACATCACAAGCACGAATGCTCTTCGA
* *
12250 TTCTTAGTCCGGATATATCACTAAGCACGACAATGCTCTTCGGGACTTAGCCCGGA
66 TCCTTAGTCCGGATACATCACTAAGCACGA-AATGCTCTTCGGGACTTAGCCCGGA
12306 TATATACTCT
Statistics
Matches: 106, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
119 2 0.02
120 19 0.18
121 18 0.17
122 46 0.43
123 21 0.20
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (122 bp):
ATCACTAGCCACGAATGCTCTTGCGAACTGTAGCCCGATACATCACAAGCACGAATGCTCTTCGA
TCCTTAGTCCGGATACATCACTAAGCACGAAATGCTCTTCGGGACTTAGCCCGGAAC
Found at i:14071 original size:48 final size:45
Alignment explanation
Indices: 13968--14121 Score: 176
Period size: 46 Copynumber: 3.4 Consensus size: 45
13958 TCTCAACATC
* * *
13968 CATCACATTGGCCCATTCGGCTTTACCCATATA-GTATGTTCATATT
1 CATCACATTGG-CCATTCGGCTTTTCACATATATGCATGTTCA-ATT
14014 CATCAACATTGG-CATTCGGCCTTTTCACATATATCGCATGTTCACGATT
1 CATC-ACATTGGCCATTCGG-CTTTTCACATATAT-GCATGTTCA--ATT
14063 CATCACATTGGCCATTC-GC-TTTCACATA-ATGCATGTTCAATT
1 CATCACATTGGCCATTCGGCTTTTCACATATATGCATGTTCAATT
14105 CATCA-ATTGGCCATTCG
1 CATCACATTGGCCATTCG
14122 TCCTTATCTA
Statistics
Matches: 97, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
41 11 0.11
42 8 0.08
44 9 0.09
45 9 0.09
46 24 0.25
47 8 0.08
48 16 0.16
49 12 0.12
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.35
Consensus pattern (45 bp):
CATCACATTGGCCATTCGGCTTTTCACATATATGCATGTTCAATT
Done.