Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3230
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: 42956
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2481 original size:48 final size:48
Alignment explanation
Indices: 2426--2531 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
2416 ATTGTCTTTC
*
2426 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
2474 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
2522 TTTCTTTTTC
1 TTTCTTTTTC
2532 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:3548 original size:9 final size:9
Alignment explanation
Indices: 3536--3568 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3526 TTTTCACTTT
3536 TTTTTTTTC
1 TTTTTTTTC
*
3545 TTTTTTTAC
1 TTTTTTTTC
3554 -TTTTTTTC
1 TTTTTTTTC
3562 TTTTTTT
1 TTTTTTT
3569 GCTCACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3555 original size:21 final size:20
Alignment explanation
Indices: 3526--3587 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
3516 CTCGCAAGAC
3526 TTTTCACTTTTTTTTTTTCTT
1 TTTTCACTTTTTTTTTTT-TT
*
3547 TTTTTACTTTTTTTCTTTTTT
1 TTTTCACTTTTTTT-TTTTTT
**
3568 TGCTCACTTTTTTTTTTTTT
1 TTTTCACTTTTTTTTTTTTT
3588 GAATTTCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 6 0.17
21 26 0.72
22 4 0.11
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTCACTTTTTTTTTTTTT
Found at i:3587 original size:8 final size:8
Alignment explanation
Indices: 3533--3568 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
3523 GACTTTTCAC
3533 TTTT-TTT
1 TTTTCTTT
3540 TTTTCTTT
1 TTTTCTTT
3548 TTTTACTTT
1 TTTT-CTTT
3557 TTTTCTTT
1 TTTTCTTT
3565 TTTT
1 TTTT
3569 GCTCACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 15 0.56
9 8 0.30
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:5122 original size:20 final size:20
Alignment explanation
Indices: 5099--5145 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5089 GGGTTAAGAT
*
5099 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
5119 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
5139 TGAGCTG
1 TGAGCTG
5146 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:9346 original size:20 final size:20
Alignment explanation
Indices: 9323--9369 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
9313 GGGTTACGAT
*
9323 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
9343 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
9363 TGAGCTG
1 TGAGCTG
9370 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:13612 original size:56 final size:55
Alignment explanation
Indices: 13496--13613 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
13486 TGCATGCTTT
* * * *
13496 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
13550 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
13606 CATTAAAT
1 CATTAAAT
13614 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:17200 original size:23 final size:22
Alignment explanation
Indices: 17148--17200 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
17138 TCCACGTCTT
*
17148 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
17170 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
17193 TTTCTTTT
1 TTTCTTTT
17201 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:21009 original size:15 final size:16
Alignment explanation
Indices: 20970--21010 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
20960 AACAACACTC
20970 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
20986 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
21000 CTTTCTTTTTC
1 CTTTCTTTTTC
21011 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:22229 original size:10 final size:11
Alignment explanation
Indices: 22213--22242 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
22203 GAATACAAAT
22213 TTTTTTTTGAA
1 TTTTTTTTGAA
22224 TTTTTTTTGAA
1 TTTTTTTTGAA
22235 TTTTTTTT
1 TTTTTTTT
22243 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:24273 original size:20 final size:20
Alignment explanation
Indices: 24250--24296 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
24240 AATTGAGGTT
*
24250 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
24270 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
24290 GAATGAG
1 GAATGAG
24297 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:27635 original size:24 final size:23
Alignment explanation
Indices: 27581--27658 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
27571 GGATAATTAA
**
27581 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
27604 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
27628 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
27649 GAAATAGTAT
1 GAAATGGTAT
27659 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:27643 original size:21 final size:21
Alignment explanation
Indices: 27617--27683 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
27607 TTGGTATTTG
27617 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
27638 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
27659 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
27682 GG
1 GG
27684 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:29030 original size:30 final size:30
Alignment explanation
Indices: 28996--29092 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
28986 TAAACTAAAA
28996 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
29026 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
29056 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
29085 ATGAGCTA
1 -TGAGCTA
29093 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:33199 original size:12 final size:12
Alignment explanation
Indices: 33184--33225 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
33174 AAGAAAATCG
*
33184 AAAAAAATTCAA
1 AAAAAAATTGAA
*
33196 AAAAAAAGTGAA
1 AAAAAAATTGAA
33208 AAAAAAATTGAA
1 AAAAAAATTGAA
33220 AAAAAA
1 AAAAAA
33226 GAGAAGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:33315 original size:16 final size:16
Alignment explanation
Indices: 33280--33321 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
33270 AATTGTATTT
*
33280 GAAGTTAAAAAAAATC
1 GAAGTTAAAAAAAATA
33296 GAAGTATAAAAAAAA-A
1 GAAGT-TAAAAAAAATA
*
33312 GAAGTGAAAA
1 GAAGTTAAAA
33322 GTCTTGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.67, C:0.02, G:0.17, T:0.14
Consensus pattern (16 bp):
GAAGTTAAAAAAAATA
Found at i:35754 original size:55 final size:56
Alignment explanation
Indices: 35647--35760 Score: 203
Period size: 55 Copynumber: 2.0 Consensus size: 56
35637 TTCAATAAAG
35647 TGGTGAGGAGTTTATTGCTTGATCGATGAACGGATTAAGTTGAATGTGTCCACATGTC
1 TGGTGAGGAGTTTATTGCTTGATC-A-GAACGGATTAAGTTGAATGTGTCCACATGTC
35705 TGGTGAGGAGTTTATTGCTTGATC-GAACGGATTAAGTTGAATGTGTCCACATGTC
1 TGGTGAGGAGTTTATTGCTTGATCAGAACGGATTAAGTTGAATGTGTCCACATGTC
35760 T
1 T
35761 CTTGAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
55 32 0.57
58 24 0.43
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (56 bp):
TGGTGAGGAGTTTATTGCTTGATCAGAACGGATTAAGTTGAATGTGTCCACATGTC
Found at i:36933 original size:12 final size:13
Alignment explanation
Indices: 36911--36939 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36901 AAGTTTTATT
36911 TTTATTTTATTTA
1 TTTATTTTATTTA
36924 TTTA-TTTATTTA
1 TTTATTTTATTTA
36936 TTTA
1 TTTA
36940 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:40717 original size:12 final size:13
Alignment explanation
Indices: 40695--40723 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40685 GTTGTAAAGT
40695 TTTATTTTATTTA
1 TTTATTTTATTTA
40708 TTTA-TTTATTTA
1 TTTATTTTATTTA
40720 TTTA
1 TTTA
40724 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Done.