Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3115
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: 30970
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3996 original size:26 final size:26
Alignment explanation
Indices: 3966--4016 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
3956 ACCAATGAAC
*
3966 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
3992 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
4017 CTTTCACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:4050 original size:103 final size:104
Alignment explanation
Indices: 3829--4093 Score: 428
Period size: 103 Copynumber: 2.6 Consensus size: 104
3819 TAACCGTTAT
* * *
3829 TGGTGGATCTCGCACTTAGCACCACCACTGAATCGGGGAATCATCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
3894 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
3933 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTC-GGG
1 TGGTGGATCA-CGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
3996 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* * **
4036 TGGTGGATCACGCACATAGCACCACC-ATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
4094 TTTATATACA
Statistics
Matches: 150, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
102 28 0.19
103 66 0.44
104 56 0.37
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATCACGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:4455 original size:29 final size:29
Alignment explanation
Indices: 4422--4485 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
4412 TAATCCACCA
4422 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
4451 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
4481 CCCAA
1 CCCAA
4486 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:4459 original size:30 final size:30
Alignment explanation
Indices: 4429--4485 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4419 CCACCCAACT
4429 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
4458 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
4486 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:11546 original size:104 final size:104
Alignment explanation
Indices: 11424--11647 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
11414 AATGGATATC
11424 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
11489 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
11528 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
11593 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
11632 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
11648 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:12009 original size:29 final size:29
Alignment explanation
Indices: 11976--12039 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
11966 TAATCCACCA
11976 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
12005 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
12035 CCCAA
1 CCCAA
12040 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:12013 original size:30 final size:30
Alignment explanation
Indices: 11983--12039 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11973 CCACCCAACT
11983 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
12012 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
12040 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:20104 original size:15 final size:15
Alignment explanation
Indices: 20061--20104 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
20051 CCATTTAAGT
20061 TTAAAGATAATTTAA
1 TTAAAGATAATTTAA
*
20076 AT-AAGATTAA-TTAA
1 TTAAAGA-TAATTTAA
20090 TTAAAGATAATTTAA
1 TTAAAGATAATTTAA
20105 AAATACACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (15 bp):
TTAAAGATAATTTAA
Found at i:21057 original size:23 final size:23
Alignment explanation
Indices: 20972--21059 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
20962 TTGGTATCCG
*
20972 AATTTGATATTT-TATTTTAATTG
1 AATTTGATATTTATA-TTTAATTA
*
20995 AATTTGATATTTATATTTAA-AA
1 AATTTGATATTTATATTTAATTA
*
21017 AGATTTTAT-TTTAT-TTTAATTA
1 A-ATTTGATATTTATATTTAATTA
21039 AATTTGATATTTATATTTAAT
1 AATTTGATATTTATATTTAAT
21060 AAAAGTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.20
22 13 0.24
23 29 0.53
24 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
AATTTGATATTTATATTTAATTA
Found at i:21069 original size:44 final size:44
Alignment explanation
Indices: 20979--21069 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
20969 CCGAATTTGA
* *
20979 TATTTTATTTTAATTGAATTTGATATTTATATTTAAAAAGATTT
1 TATTTTATTTTAATTAAATTTGATATTTATATTTAAAAAGAGTT
21023 TATTTTATTTTAATTAAATTTGATATTTATATTTAATAAA-AGTT
1 TATTTTATTTTAATTAAATTTGATATTTATATTTAA-AAAGAGTT
21067 TAT
1 TAT
21070 ATACTCTGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 41 0.93
45 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.57
Consensus pattern (44 bp):
TATTTTATTTTAATTAAATTTGATATTTATATTTAAAAAGAGTT
Found at i:21071 original size:23 final size:22
Alignment explanation
Indices: 20972--21071 Score: 82
Period size: 23 Copynumber: 4.4 Consensus size: 22
20962 TTGGTATCCG
**
20972 AATTTGATATTT-TATTTTAATTG
1 AATTT-ATATTTATA-TTTAATAA
20995 AATTTGATATTTATATTTAA-AA
1 AATTT-ATATTTATATTTAATAA
*
21017 AGATTT-TATTT-TATTTTAATTA
1 A-ATTTATATTTATA-TTTAATAA
21039 AATTTGATATTTATATTTAATAA
1 AATTT-ATATTTATATTTAATAA
21062 AAGTTTATAT
1 AA-TTTATAT
21072 ACTCTGATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
20 2 0.03
21 14 0.22
22 3 0.05
23 39 0.60
24 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
AATTTATATTTATATTTAATAA
Found at i:22216 original size:17 final size:18
Alignment explanation
Indices: 22191--22228 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
22181 AATTATTTTA
22191 AAATATTAAAAAAATT-T
1 AAATATTAAAAAAATTGT
*
22208 AAATTTTAAAAAAATTGT
1 AAATATTAAAAAAATTGT
22226 AAA
1 AAA
22229 AACATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AAATATTAAAAAAATTGT
Found at i:22522 original size:28 final size:29
Alignment explanation
Indices: 22471--22527 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
22461 AGAAAAATTG
* *
22471 TAAATTTTATTATAATTTTTACAATTTTT
1 TAAATTTTATTATAATATTCACAATTTTT
*
22500 TAAA-TTTATTATGATATTCACAATTTTT
1 TAAATTTTATTATAATATTCACAATTTTT
22528 AAACAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (29 bp):
TAAATTTTATTATAATATTCACAATTTTT
Found at i:22555 original size:31 final size:29
Alignment explanation
Indices: 22520--22578 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
22510 ATGATATTCA
*
22520 CAATTTTTAAACAATTTTAAAAGAATATTTG
1 CAATTTTT-AA-AATTTTAAAAAAATATTTG
*
22551 CAATTTTTAATATTTTAAAAAAATATTT
1 CAATTTTTAAAATTTTAAAAAAATATTT
22579 TAATGATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.62
30 2 0.08
31 8 0.31
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (29 bp):
CAATTTTTAAAATTTTAAAAAAATATTTG
Found at i:23837 original size:17 final size:19
Alignment explanation
Indices: 23811--23845 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23801 TCTCTCTCTT
23811 TTTTTCAG-TTTTACTTTG
1 TTTTTCAGTTTTTACTTTG
23829 TTTTT-AGTTTTTACTTT
1 TTTTTCAGTTTTTACTTT
23846 TAAAAGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (19 bp):
TTTTTCAGTTTTTACTTTG
Done.