Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold928
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: 28993
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Found at i:2100 original size:46 final size:45
Alignment explanation
Indices: 1913--2081 Score: 136
Period size: 45 Copynumber: 3.8 Consensus size: 45
1903 AACCCGCCCC
* ** *
1913 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGT-TCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATCT-GCAACCA
**
1958 TAAGTGAACTC-GACTCAACTCAACGAGTT--G-ATGCCTAGTTA-CA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAAT--CT-GCAACCA
* * * *
2001 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATCTGCAACCA
2048 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2082 TGCTCAACCA
Statistics
Matches: 98, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 2 0.02
44 25 0.26
45 33 0.34
46 30 0.31
47 4 0.04
49 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATCTGCAACCA
Found at i:9059 original size:47 final size:47
Alignment explanation
Indices: 8990--9112 Score: 237
Period size: 47 Copynumber: 2.6 Consensus size: 47
8980 GCCCCTAAGT
*
8990 GAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
9037 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
9084 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
9113 CATTTGCATC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:10251 original size:30 final size:30
Alignment explanation
Indices: 10217--10273 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
10207 GGAAACACGG
10217 CCGTGTAACCTAACCGTGTGTCACACATGA
1 CCGTGTAACCTAACCGTGTGTCACACATGA
10247 CCGTGTAACCTAACCGTGTGTCACACA
1 CCGTGTAACCTAACCGTGTGTCACACA
10274 CGGTTGAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (30 bp):
CCGTGTAACCTAACCGTGTGTCACACATGA
Found at i:12026 original size:21 final size:20
Alignment explanation
Indices: 12002--12044 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
11992 AAACTTGTAT
* *
12002 ATCTATCAACAAGCATTCATA
1 ATCTACCAACAA-AATTCATA
*
12023 ATCTACCAAGAAAATTCATA
1 ATCTACCAACAAAATTCATA
12043 AT
1 AT
12045 ACATATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.28
Consensus pattern (20 bp):
ATCTACCAACAAAATTCATA
Found at i:13674 original size:13 final size:13
Alignment explanation
Indices: 13616--13677 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
13606 TTTACATCTC
*
13616 AAAAAAT-TATAA
1 AAAAAATATATAT
13628 AAAAGAATTATATAT
1 AAAA-AA-TATATAT
*
13643 AAAAATTATAAATTAT
1 AAAAA--ATATA-TAT
13659 AAAAAATATATAT
1 AAAAAATATATAT
13672 AAAAAA
1 AAAAAA
13678 CAAGCCCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.10
13 11 0.27
14 6 0.15
15 11 0.27
16 9 0.22
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAAAATATATAT
Found at i:18553 original size:29 final size:29
Alignment explanation
Indices: 18521--18586 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
18511 GGTTATTCTC
* *
18521 ATAAATTTTTAAAAAATTGGTCTATTTTT-
1 ATAAATTTTAAAAAAATTGATCT-TTTTTG
18550 ATAATATTTTAAAAAAATTGATCTTTTTTG
1 ATAA-ATTTTAAAAAAATTGATCTTTTTTG
18580 A-AAATTT
1 ATAAATTT
18587 AGTCTTAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 4 0.12
29 11 0.33
30 18 0.55
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (29 bp):
ATAAATTTTAAAAAAATTGATCTTTTTTG
Found at i:20285 original size:38 final size:38
Alignment explanation
Indices: 20229--20317 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
20219 ACAGTACAAC
* * * * *
20229 ATAGGAACAATAGACATGCTTATCATGCAATTAGTT-T
1 ATAGTAACAGTAGACATGCTGAACATGCAATCAGTTAT
*
20266 AATAGTAACAGTAGGCATGCTGAACATGCAATCAGTTAT
1 -ATAGTAACAGTAGACATGCTGAACATGCAATCAGTTAT
*
20305 ATAGTAGCAGTAG
1 ATAGTAACAGTAG
20318 CAATAGTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 42 0.98
39 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (38 bp):
ATAGTAACAGTAGACATGCTGAACATGCAATCAGTTAT
Found at i:22443 original size:40 final size:39
Alignment explanation
Indices: 22398--22586 Score: 184
Period size: 40 Copynumber: 4.8 Consensus size: 39
22388 ATAACCACAA
* * *
22398 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-TAGCAACTC
*
22438 GCACAAATGCCTTCGGGTCTTAGCCCGGATTATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATTAGCAACTC
** *
22477 GCACAAATGCCTTCGGGTCTTAGCCCGGA-TAAAATCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATTAGCA--ACTC
* * ** *
22517 GCATAAATGCCTTCGGGACTTAGCCCGGA-TAAAATCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATTAGCA--ACTC
* * *
22557 GCATAAATGCCTTCGGGACTTAGCCTGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
22587 ATCATTCAAA
Statistics
Matches: 136, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
38 3 0.02
39 37 0.27
40 96 0.71
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATTAGCAACTC
Found at i:22481 original size:79 final size:79
Alignment explanation
Indices: 22398--22587 Score: 213
Period size: 79 Copynumber: 2.4 Consensus size: 79
22388 ATAACCACAA
* * * * *
22398 GCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAAGC-ACTAGCACAAATGCCTTCGGGACTTAGC
22462 CCGGATTATCAACTC
65 CCGGATTATCAACTC
* * *
22477 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAAAAGCACTAGCACAAATGCCTTCGGGACTTAGCC
* *
22542 CGGATAAAATC-ACTA
66 CGGAT--TATCAACTC
* * * *
22557 GCATAAATGCCTTCGGGACTTAGCCTGGATA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATA
22588 TCATTCAAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 58 0.61
80 34 0.36
81 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAAAAGCACTAGCACAAATGCCTTCGGGACTTAGCC
CGGATTATCAACTC
Found at i:22587 original size:40 final size:40
Alignment explanation
Indices: 22442--22587 Score: 215
Period size: 40 Copynumber: 3.7 Consensus size: 40
22432 CAACTCGCAC
* * * *
22442 AAATGCCTTCGGGTCTTAGCCCGGAT--TATCAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTAGCAT
*
22481 AAATGCCTTCGGGTCTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
22521 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
*
22561 AAATGCCTTCGGGACTTAGCCTGGATA
1 AAATGCCTTCGGGACTTAGCCCGGATA
22588 TCATTCAAAT
Statistics
Matches: 100, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
39 26 0.26
40 71 0.71
41 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATAAAATCACTAGCAT
Done.