Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3415
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: 26874
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2195 original size:12 final size:11
Alignment explanation
Indices: 2178--2233 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 11
2168 AGTTCGTACG
2178 TTTAAATAGTGT
1 TTTAAATA-TGT
2190 TTTAAATTATACG-
1 TTTAAA-TAT--GT
2203 TTTAAATAGTGT
1 TTTAAATA-TGT
2215 TTTAAATTATGT
1 TTTAAA-TATGT
2227 TTTAAAT
1 TTTAAAT
2234 GTTATTATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
11 2 0.05
12 24 0.63
13 11 0.29
14 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.52
Consensus pattern (11 bp):
TTTAAATATGT
Found at i:2202 original size:25 final size:25
Alignment explanation
Indices: 2174--2224 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2164 GGTAAGTTCG
2174 TACGTTTAAATAGTGTTTTAAATTA
1 TACGTTTAAATAGTGTTTTAAATTA
2199 TACGTTTAAATAGTGTTTTAAATTA
1 TACGTTTAAATAGTGTTTTAAATTA
2224 T
1 T
2225 GTTTTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (25 bp):
TACGTTTAAATAGTGTTTTAAATTA
Found at i:2352 original size:30 final size:30
Alignment explanation
Indices: 2307--2371 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
2297 TCGACTAATG
* *
2307 GAAAA-GGATATCTTCGGCTGTCAAATTAT
1 GAAAAGGGATAGCTTCGGCTATCAAATTAT
2336 GAAAAGGGATAGCTTCGGCTATCAAATTAT
1 GAAAAGGGATAGCTTCGGCTATCAAATTAT
*
2366 GGAAAG
1 GAAAAG
2372 AGATGGTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (30 bp):
GAAAAGGGATAGCTTCGGCTATCAAATTAT
Found at i:2405 original size:29 final size:30
Alignment explanation
Indices: 2368--2434 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
2358 CAAATTATGG
* *
2368 AAAGAGATGGTGACAATCA-TCAACAATGA
1 AAAGGGATGGTGACAACCATTCAACAATGA
* * *
2397 AAAGGGATGGTGACGACCATTGAACTATGA
1 AAAGGGATGGTGACAACCATTCAACAATGA
2427 AAAGGGAT
1 AAAGGGAT
2435 AGCTTCAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.43, C:0.12, G:0.27, T:0.18
Consensus pattern (30 bp):
AAAGGGATGGTGACAACCATTCAACAATGA
Found at i:2479 original size:30 final size:30
Alignment explanation
Indices: 2356--2488 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
2346 AGCTTCGGCT
* * *
2356 ATCAAATTATGGAAAGAGATGGTGACA-ATC
1 ATCAAATTATGAAAAGGGATGGTGA-AGACC
*
2386 ATCAACA--ATGAAAAGGGATGGTGACGACC
1 ATCAA-ATTATGAAAAGGGATGGTGAAGACC
** * * ** **
2415 ATTGAACTATGAAAAGGGATAGCTTCAG-TT
1 ATCAAATTATGAAAAGGGAT-GGTGAAGACC
2445 ATCAAATTATGAAAAGGGATGGTGAAGACC
1 ATCAAATTATGAAAAGGGATGGTGAAGACC
2475 ATC-AATTATGAAAA
1 ATCAAATTATGAAAA
2489 TATGAATAGG
Statistics
Matches: 77, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
28 1 0.01
29 35 0.45
30 37 0.48
31 4 0.05
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTGAAGACC
Found at i:4928 original size:10 final size:11
Alignment explanation
Indices: 4913--4950 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
4903 TTGCTATAAT
4913 TATTA-ATTAA
1 TATTATATTAA
4923 TATTAATATTAA
1 TATT-ATATTAA
4935 TATTATATT-A
1 TATTATATTAA
4945 TATTAT
1 TATTAT
4951 GAAATAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.42
11 6 0.23
12 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTATATTAA
Found at i:4929 original size:6 final size:6
Alignment explanation
Indices: 4918--4949 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4908 ATAATTATTA
4918 ATTAAT ATTAAT ATTAAT ATT-AT ATT-AT ATTA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTA
4950 TGAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTAAT
Found at i:5109 original size:31 final size:32
Alignment explanation
Indices: 5068--5130 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
5058 TTATTTATAA
*
5068 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
5099 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
5131 GACAAGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:7032 original size:53 final size:47
Alignment explanation
Indices: 6911--7027 Score: 164
Period size: 47 Copynumber: 2.5 Consensus size: 47
6901 GATATTGTTA
* * *
6911 CTGT-TACCGTTACTGTTACTATTTCGGATTTGTTCCGATGAGGTACT
1 CTGTGTACCG-TACTGTTACTGTTCCGGATTTGTACCGATGAGGTACT
*
6958 CTGTGTACCGTACTGTCACTGTTCCGGATTTGTACCGATGAGGTACT
1 CTGTGTACCGTACTGTTACTGTTCCGGATTTGTACCGATGAGGTACT
* *
7005 CTGTGTACCGTATTGCTACTGTT
1 CTGTGTACCGTACTGTTACTGTT
7028 ACTGTTACTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
47 57 0.92
48 5 0.08
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (47 bp):
CTGTGTACCGTACTGTTACTGTTCCGGATTTGTACCGATGAGGTACT
Found at i:7203 original size:18 final size:18
Alignment explanation
Indices: 7152--7240 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
7142 TGGAAAGATC
*
7152 GATTGTTACTGAATAATTT
1 GATTGTTACTGAATAA-CT
*
7171 AATTGTTACTGAATAACT
1 GATTGTTACTGAATAACT
* * *
7189 GATTATTATTGAATAATT
1 GATTGTTACTGAATAACT
*
7207 GATTGTTACCGAATAACT
1 GATTGTTACTGAATAACT
*
7225 GACTGTTACTGAATAA
1 GATTGTTACTGAATAA
7241 ATAATCGTTC
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
18 43 0.74
19 15 0.26
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (18 bp):
GATTGTTACTGAATAACT
Found at i:7221 original size:36 final size:37
Alignment explanation
Indices: 7152--7240 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 37
7142 TGGAAAGATC
*
7152 GATTGTTACTGAATAATTTAATTGTTACTGAATAACT
1 GATTGTTACTGAATAATTTAATTGTTACCGAATAACT
* * *
7189 GATTATTATTGAATAA-TTGATTGTTACCGAATAACT
1 GATTGTTACTGAATAATTTAATTGTTACCGAATAACT
*
7225 GACTGTTACTGAATAA
1 GATTGTTACTGAATAA
7241 ATAATCGTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 31 0.69
37 14 0.31
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
GATTGTTACTGAATAATTTAATTGTTACCGAATAACT
Found at i:16618 original size:39 final size:40
Alignment explanation
Indices: 16509--16687 Score: 123
Period size: 40 Copynumber: 4.5 Consensus size: 40
16499 AAATCACGTA
* * *** *
16509 CCTTCGGAATTTAA-CCGGATTATAGCTCCTCGTTCAAGTG
1 CCTTCGGGACTTAACCCGGATTATAGAAACTCATTCAA-TG
* * *
16549 CCTTCGGGACATAGCCCGG-TTATAGTAACTCATTCAATG
1 CCTTCGGGACTTAACCCGGATTATAGAAACTCATTCAATG
* ***
16588 CCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTATAGAAACTCATTC-AATG
* * * *** *
16628 CCTTCGGGACTTAACCCGGAAT-TAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTATAGAAACTCATTC-AATG
16668 CCTTCGGGACTTAACCCGGA
1 CCTTCGGGACTTAACCCGGA
16688 ATTAATAACT
Statistics
Matches: 115, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 27 0.23
40 84 0.73
41 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGATTATAGAAACTCATTCAATG
Found at i:16682 original size:80 final size:80
Alignment explanation
Indices: 16587--16767 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
16577 CTCATTCAAT
* * *
16587 GCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-A
1 GCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA
*
16649 TTAGT-A-TCTCGCACAAA
64 -TAGTCACT-TAGCACAAA
**
16666 GGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATAT
1 -GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATAT
16731 AGTCACTTAGCACAAA
65 AGTCACTTAGCACAAA
*
16747 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
16768 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGAATTAATAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:16688 original size:40 final size:40
Alignment explanation
Indices: 16584--16767 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
16574 TAACTCATTC
* * *
16584 AATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAGTAACTCGCACA
*
16624 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
* *
16664 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
* ** * *
16704 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAGTAAC-TCGCACA
*
16745 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16768 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACA
Found at i:18488 original size:28 final size:28
Alignment explanation
Indices: 18425--18578 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
18415 ATATTAAGTC
*
18425 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18452 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18480 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
18508 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
18536 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
18565 CGCACACTTAGTGC
1 CGCACACTTAGTGC
18579 CAATCTCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.18
28 76 0.66
29 19 0.16
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:26571 original size:27 final size:26
Alignment explanation
Indices: 26541--26703 Score: 125
Period size: 27 Copynumber: 6.0 Consensus size: 26
26531 GATTCAAAAG
* *
26541 TATATATTAAGTCCGCACACTCAGTGC
1 TATATATCAA-TCCGCACACTTAGTGC
26568 TATATAATCAA-CTCGCACACTTAGTGC
1 TATAT-ATCAATC-CGCACACTTAGTGC
* *
26595 TACTA-ATCAAACTGCACACTTAGTGC
1 TA-TATATCAATCCGCACACTTAGTGC
*
26621 TATATAATCAAACTCGCACACTTAGTGC
1 TATAT-ATCAATC-CGCACACTTAGTGC
*
26649 TA-ATAATCAAACTCGCACACTTAGTGC
1 TATAT-ATCAATC-CGCACACTTAGTGC
* * * *
26676 TGTACAATTTAACCCGCACACTTAGTGC
1 TATA-TA-TCAATCCGCACACTTAGTGC
26704 CAATCTCATG
Statistics
Matches: 118, Mismatches: 8, Indels: 19
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.02
26 21 0.18
27 54 0.46
28 37 0.31
29 4 0.03
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.28
Consensus pattern (26 bp):
TATATATCAATCCGCACACTTAGTGC
Found at i:26694 original size:55 final size:55
Alignment explanation
Indices: 26554--26703 Score: 214
Period size: 55 Copynumber: 2.8 Consensus size: 55
26544 ATATTAAGTC
* * *
26554 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACTAATCAAACT
1 CGCACACTTAGTGCTATATAATTAAACTCGCACACTTAGTGCTAATAATCAAACT
*
26608 -GCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTGCTAATAATCAAACT
1 CGCACACTTAGTGCTATATAATTAAACTCGCACACTTAGTGCTAATAATCAAACT
* * * *
26662 CGCACACTTAGTGCTGTACAATTTAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATATAATTAAACTCGCACACTTAGTGC
26704 CAATCTCATG
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
53 19 0.22
54 30 0.35
55 36 0.42
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTATATAATTAAACTCGCACACTTAGTGCTAATAATCAAACT
Done.