Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2401
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: 18478
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:2952 original size:18 final size:20
Alignment explanation
Indices: 2929--2967 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2919 AATATGAGAA
2929 TATAAG-TT-AAAAAATTAT
1 TATAAGATTAAAAAAATTAT
2947 TATAAGACTTAAAAAAATTAT
1 TATAAGA-TTAAAAAAATTAT
2968 AAAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TATAAGATTAAAAAAATTAT
Found at i:3441 original size:2 final size:2
Alignment explanation
Indices: 3434--3463 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3424 TAAGCTCTAG
3434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3464 CTATTCCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3730 original size:15 final size:14
Alignment explanation
Indices: 3711--3747 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3701 ATAATTATAA
3711 ATATAATAAATATT
1 ATATAATAAATATT
3725 ATTATAA-AAATATT
1 A-TATAATAAATATT
3739 A-ATAATAAA
1 ATATAATAAA
3748 AAAATATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.19
13 3 0.14
14 9 0.43
15 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAATAAATATT
Found at i:3737 original size:14 final size:15
Alignment explanation
Indices: 3712--3749 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3702 TAATTATAAA
3712 TATAATAAATATT-AT
1 TATAA-AAATATTAAT
3727 TATAAAAATATTAAT
1 TATAAAAATATTAAT
*
3742 AATAAAAA
1 TATAAAAA
3750 AATATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAAAAATATTAAT
Found at i:4486 original size:17 final size:19
Alignment explanation
Indices: 4464--4527 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 19
4454 GATTATAATA
4464 TAAAAA-TAATATATTATT
1 TAAAAATTAATATATTATT
*
4482 TAAAAATTAAAATTAATTATT
1 TAAAAATTAATA-T-ATTATT
4503 ATAATAAATTAATATATTATT
1 -TAA-AAATTAATATATTATT
4524 TAAA
1 TAAA
4528 GTTAAAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.15
19 5 0.13
20 4 0.10
21 12 0.31
22 4 0.10
23 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATTAATATATTATT
Found at i:4493 original size:24 final size:23
Alignment explanation
Indices: 4466--4552 Score: 73
Period size: 21 Copynumber: 4.1 Consensus size: 23
4456 TTATAATATA
4466 AAAATAATATATTATTTAAAAATT
1 AAAATAATATATTATTT-AAAATT
*
4490 AAAAT--TA-ATTA-TTATAA-T
1 AAAATAATATATTATTTAAAATT
* *
4508 AAATTAATATATTATTTAAAGTT
1 AAAATAATATATTATTTAAAATT
*
4531 AAAAT--TATATTA-TTATAATT
1 AAAATAATATATTATTTAAAATT
4551 AA
1 AA
4553 TTATGTAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.10
19 3 0.06
20 12 0.24
21 15 0.29
22 6 0.12
23 5 0.10
24 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
AAAATAATATATTATTTAAAATT
Found at i:4501 original size:42 final size:42
Alignment explanation
Indices: 4462--4555 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
4452 ATGATTATAA
4462 TATAA-AAA-TAATATATTATTTAAAAATTAAAATTA-ATTAT
1 TATAATAAATTAATATATTATTT-AAAATTAAAATTATATTAT
*
4502 TATAATAAATTAATATATTATTTAAAGTTAAAATTATATTAT
1 TATAATAAATTAATATATTATTTAAAATTAAAATTATATTAT
*
4544 TATAATTAATTA
1 TATAATAAATTA
4556 TGTAAATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
40 5 0.10
41 15 0.31
42 29 0.59
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (42 bp):
TATAATAAATTAATATATTATTTAAAATTAAAATTATATTAT
Found at i:4532 original size:18 final size:17
Alignment explanation
Indices: 4491--4556 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
4481 TTAAAAATTA
*
4491 AAATTAATTATTATAAT
1 AAATTAATTATTATATT
4508 AAATTAATATATTAT-TT
1 AAATTAAT-TATTATATT
4525 AAAGTTAAAATTA-TATTATT
1 AAA-TT--AATTATTA-TATT
4545 ATAATTAATTAT
1 A-AATTAATTAT
4557 GTAAATATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 12 0.30
18 15 0.38
19 3 0.08
20 8 0.20
21 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTAATTATTATATT
Found at i:5935 original size:21 final size:21
Alignment explanation
Indices: 5910--5949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5900 ATCATTTATA
*
5910 ATTATGAATATATTA-AATATT
1 ATTAT-AATAAATTACAATATT
5931 ATTATAATAAATTACAATA
1 ATTATAATAAATTACAATA
5950 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTATAATAAATTACAATATT
Found at i:5954 original size:25 final size:25
Alignment explanation
Indices: 5923--5989 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
5913 ATGAATATAT
5923 TAAATATT-ATTATAATAAATTACAA
1 TAAATATTCATTATAATAAA-TACAA
* *
5948 TAAATATTCATAACAA-AAATACAA
1 TAAATATTCATTATAATAAATACAA
*
5972 AAAATATTTCATTATAAT
1 TAAATA-TTCATTATAAT
5990 CACTATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
24 10 0.29
25 19 0.56
26 5 0.15
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAATATTCATTATAATAAATACAA
Found at i:6330 original size:20 final size:18
Alignment explanation
Indices: 6296--6335 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
6286 AAATTTATAA
6296 ATTTTAATTTTTTTTATT
1 ATTTTAATTTTTTTTATT
6314 ATTTATAATTATTTTTTATT
1 ATTT-TAATT-TTTTTTATT
6334 AT
1 AT
6336 AATTAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTTAATTTTTTTTATT
Found at i:6342 original size:20 final size:18
Alignment explanation
Indices: 6299--6342 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
6289 TTTATAAATT
*
6299 TTAATTTTTTTTATTATT
1 TTAATTTTTTTTATTATA
6317 TATAATTATTTTTTATTATAA
1 T-TAATT-TTTTTTATTAT-A
6338 TTAAT
1 TTAAT
6343 CATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.05
19 5 0.23
20 15 0.68
21 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATTTTTTTTATTATA
Found at i:6350 original size:16 final size:15
Alignment explanation
Indices: 6331--6382 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 15
6321 ATTATTTTTT
6331 ATTATAATTAATCATA
1 ATTATAATTAAT-ATA
6347 ATTAT-ATT--TATA
1 ATTATAATTAATATA
*
6359 ATTATAA-AAATATA
1 ATTATAATTAATATA
6373 A-TATAATTAA
1 ATTATAATTAA
6383 AAAAAATGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 8 0.27
13 7 0.23
14 7 0.23
15 3 0.10
16 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATAATTAATATA
Found at i:6373 original size:26 final size:25
Alignment explanation
Indices: 6317--6374 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
6307 TTTTATTATT
* *
6317 TATAATTATTTTTTATTATAATTAA
1 TATAATTATTTTTAATTATAATAAA
6342 TCATAATTATATTTATAATTATAA-AAA
1 T-ATAATTAT-TTT-TAATTATAATAAA
6369 TATAAT
1 TATAAT
6375 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 1 0.04
26 13 0.46
27 6 0.21
28 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATAATTATTTTTAATTATAATAAA
Found at i:6740 original size:11 final size:11
Alignment explanation
Indices: 6724--6755 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
6714 TAAATATTTA
6724 TTTTAATAATT
1 TTTTAATAATT
6735 TTTTAATAATT
1 TTTTAATAATT
6746 TTTATAATAA
1 TTT-TAATAA
6756 ATTATTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:7809 original size:2 final size:2
Alignment explanation
Indices: 7802--7827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7792 CAATTGTTGA
7802 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
7828 GATTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8515 original size:209 final size:209
Alignment explanation
Indices: 8155--8575 Score: 779
Period size: 209 Copynumber: 2.0 Consensus size: 209
8145 TTTGATTTTG
*
8155 CTACGTGGTGAATGATACGTATTGGGTGATGGTTCAATTTGGTGCCTGTTAATATGCCTCCAACT
1 CTACGTGGTGAATGATACGTATTGGGTGATGGTTCAATTTGGTGCCGGTTAATATGCCTCCAACT
8220 GCATTTTTTTCCCATGTGCCTGATTTTGTTAACATTGGTTGAGTATATGGCTATCTTACATTCAT
66 GCATTTTTTTCCCATGTGCCTGATTTTGTTAACATTGGTTGAGTATATGGCTATCTTACATTCAT
*
8285 AGGGCATACAGCGTAATGATCATTAATTAGTATGGTCCCAATTAAAGAAGCTGAGCAAATGCAAA
131 AGGGCATACAGCGTAATGATCATTAATTAGTATGGTCCCAATTAAAAAAGCTGAGCAAATGCAAA
8350 GAATTTGATTGATT
196 GAATTTGATTGATT
* *
8364 CTACGTGGTTAATGATATGTATTGGGTGATGGTTCAATTTGGTGCCGGTTAATATGCCTCCAACT
1 CTACGTGGTGAATGATACGTATTGGGTGATGGTTCAATTTGGTGCCGGTTAATATGCCTCCAACT
* *
8429 GCATTTTTTTCCCATGTGCCTGATTTTGTTAGCATTGGTTGAGTATATGGCTATCTTACATTCGT
66 GCATTTTTTTCCCATGTGCCTGATTTTGTTAACATTGGTTGAGTATATGGCTATCTTACATTCAT
*
8494 AGGGCATACAGTGTAATGATCATTAATTAGTATGGTCCCAATTAAAAAAGCTGAGCAAATGCAAA
131 AGGGCATACAGCGTAATGATCATTAATTAGTATGGTCCCAATTAAAAAAGCTGAGCAAATGCAAA
8559 GAATTTGATTGATT
196 GAATTTGATTGATT
8573 CTA
1 CTA
8576 GGGTTATGTA
Statistics
Matches: 205, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 205 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (209 bp):
CTACGTGGTGAATGATACGTATTGGGTGATGGTTCAATTTGGTGCCGGTTAATATGCCTCCAACT
GCATTTTTTTCCCATGTGCCTGATTTTGTTAACATTGGTTGAGTATATGGCTATCTTACATTCAT
AGGGCATACAGCGTAATGATCATTAATTAGTATGGTCCCAATTAAAAAAGCTGAGCAAATGCAAA
GAATTTGATTGATT
Done.