Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1404
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: 20573
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Found at i:3537 original size:2 final size:2
Alignment explanation
Indices: 3532--3563 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3522 CACGTGTGTG
3532 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3564 AATTTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3681 original size:20 final size:23
Alignment explanation
Indices: 3638--3683 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3628 TATAAAAATT
*
3638 AAAAATAATACATATTAGTTTTA
1 AAAAATAATACATATTAGTCTTA
3661 AAAAATAATA-A-ATTA-TCTTA
1 AAAAATAATACATATTAGTCTTA
3681 AAA
1 AAA
3684 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 1 0.05
23 10 0.45
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAATAATACATATTAGTCTTA
Found at i:9003 original size:20 final size:20
Alignment explanation
Indices: 8980--9036 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
8970 AAATATTACA
*
8980 AATAAAATTAAAAATTAATG
1 AATAATATTAAAAATTAATG
* * * *
9000 AATACTGTTAATAATAAATG
1 AATAATATTAAAAATTAATG
*
9020 AATAATTTTAAAAATTA
1 AATAATATTAAAAATTA
9037 TGATTTAAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
AATAATATTAAAAATTAATG
Found at i:11476 original size:2 final size:2
Alignment explanation
Indices: 11469--11507 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11459 ACATGAAAAC
11469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11508 TTAGCAGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13451 original size:63 final size:62
Alignment explanation
Indices: 13354--13486 Score: 146
Period size: 63 Copynumber: 2.1 Consensus size: 62
13344 ATTTGATTTG
* **
13354 ATTTAAATTATTATTTAATAATTAAAATTTATTTTT-ATTTAAATTTAATTATAAAAATATAAA
1 ATTTAAATTAATATTTAATAATTAAAATTTATTTTTAATTTAAATAAAATT-TAAAAATA-AAA
* * *
13417 ATTTTAATTAATATTTAAATAA-T-AATTTTGATTTTTAAATTTAGATAAAATTTAAAAATAAAA
1 ATTTAAATTAATATTT-AATAATTAAAATTT-ATTTTT-AATTTAAATAAAATTTAAAAATAAAA
13480 ATTTAAA
1 ATTTAAA
13487 ATTTTAATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
62 5 0.08
63 30 0.51
64 13 0.22
65 11 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (62 bp):
ATTTAAATTAATATTTAATAATTAAAATTTATTTTTAATTTAAATAAAATTTAAAAATAAAA
Found at i:15506 original size:17 final size:18
Alignment explanation
Indices: 15481--15524 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
15471 TTAAAAAATC
15481 ATATATTTATATCA-TTTT
1 ATAT-TTTATATCATTTTT
*
15499 ATATTTTA-ATTATTTTT
1 ATATTTTATATCATTTTT
15516 ATATTTTAT
1 ATATTTTAT
15525 TTATATAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATTTTATATCATTTTT
Found at i:15528 original size:17 final size:17
Alignment explanation
Indices: 15495--15528 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15485 ATTTATATCA
15495 TTTTATATTTTAATTAT
1 TTTTATATTTTAATTAT
*
15512 TTTTATATTTTATTTAT
1 TTTTATATTTTAATTAT
15529 ATAATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATATTTTAATTAT
Found at i:15976 original size:18 final size:18
Alignment explanation
Indices: 15943--15997 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
15933 ATTTTATATC
*
15943 AAATAAAATC-TAATTTA
1 AAATAAAAGCTTAATTTA
15960 AAATAAAAGCTTAATTTA
1 AAATAAAAGCTTAATTTA
* * *
15978 TATTAACAGCTT-ATTTA
1 AAATAAAAGCTTAATTTA
15995 AAA
1 AAA
15998 ATTTTATTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (18 bp):
AAATAAAAGCTTAATTTA
Found at i:16366 original size:3 final size:3
Alignment explanation
Indices: 16358--16386 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16348 TTCACTAACT
16358 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16387 GATTTGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16493 original size:28 final size:30
Alignment explanation
Indices: 16433--16494 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
16423 ATTTAATTAG
16433 TTTTTAAGTAGAAGTGAATAATTTTTAACAA
1 TTTTTAAGTAGAAG-GAATAATTTTTAACAA
*
16464 TTTTTAAGTA-AA-GAATATTTTATTAA-AA
1 TTTTTAAGTAGAAGGAATAATTT-TTAACAA
16492 TTT
1 TTT
16495 GGAAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 13 0.45
29 4 0.14
30 2 0.07
31 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
TTTTTAAGTAGAAGGAATAATTTTTAACAA
Found at i:17616 original size:15 final size:15
Alignment explanation
Indices: 17590--17636 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
17580 GTGACATAAT
17590 ATTTAAAATTTTTTTA
1 ATTT-AAATTTTTTTA
* **
17606 TTTTATTTTTTTTTA
1 ATTTAAATTTTTTTA
17621 ATTTAAATTTTTTTA
1 ATTTAAATTTTTTTA
17636 A
1 A
17637 AAATGCTGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 22 0.88
16 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTAAATTTTTTTA
Found at i:17798 original size:12 final size:12
Alignment explanation
Indices: 17777--17809 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17767 AATTTTAAAA
17777 TAAATA-TAATT
1 TAAATATTAATT
17788 TAAATATTAATT
1 TAAATATTAATT
*
17800 TATATATTAA
1 TAAATATTAA
17810 AAAAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAAATATTAATT
Found at i:18569 original size:3 final size:3
Alignment explanation
Indices: 18561--18586 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18551 ATTTATTTAT
18561 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
18587 TTCAATGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18946 original size:20 final size:20
Alignment explanation
Indices: 18921--18978 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
18911 TAGGTTGAAA
18921 ATAAAAAAAATTAAATAAAT
1 ATAAAAAAAATTAAATAAAT
**
18941 AT-AAAAATTTTAAAATAAAT
1 ATAAAAAAAATT-AAATAAAT
* * *
18961 TTAAATAAAATAAAATAA
1 ATAAAAAAAATTAAATAA
18979 TTTAAAAGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 7 0.24
20 17 0.59
21 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAAAAAAAATTAAATAAAT
Found at i:18995 original size:30 final size:29
Alignment explanation
Indices: 18922--18996 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
18912 AGGTTGAAAA
* *
18922 TAAAAAAAATTAAATAAATATAAAAATTT
1 TAAAATAAATTAAATAAATATAAAAAATT
18951 TAAAATAAATTTAAATAAA-ATAAAATAATT
1 TAAAATAAA-TTAAATAAATATAAAA-AATT
*
18981 TAAAAGTTAATTAAAT
1 TAAAA-TAAATTAAAT
18997 TGTAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 14 0.35
30 23 0.57
31 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
TAAAATAAATTAAATAAATATAAAAAATT
Found at i:19075 original size:19 final size:20
Alignment explanation
Indices: 19051--19115 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
19041 TTGGTATATA
19051 TATTTTT-AGAGAGATTAAT
1 TATTTTTAAGAGAGATTAAT
* *
19070 TATTTTTAAGAAAGATCAACAT
1 TATTTTTAAGAGAGAT-TA-AT
*
19092 T-TTTTTAAAAGAGATTAAT
1 TATTTTTAAGAGAGATTAAT
19111 TATTT
1 TATTT
19116 CTTGTAGAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 10 0.27
20 11 0.30
21 13 0.35
22 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (20 bp):
TATTTTTAAGAGAGATTAAT
Found at i:19085 original size:20 final size:20
Alignment explanation
Indices: 19051--19115 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
19041 TTGGTATATA
*
19051 TATTTTT-AGAGAGATTAAT
1 TATTTTTAAGAAAGATTAAT
*
19070 TATTTTTAAGAAAGATCAACAT
1 TATTTTTAAGAAAGAT-TA-AT
19092 T-TTTTTAA-AAGAGATTAAT
1 TATTTTTAAGAA-AGATTAAT
19111 TATTT
1 TATTT
19116 CTTGTAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.26
20 13 0.34
21 12 0.32
22 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (20 bp):
TATTTTTAAGAAAGATTAAT
Found at i:20043 original size:21 final size:22
Alignment explanation
Indices: 20019--20061 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
20009 TCAATTCACA
20019 AAAAAAAATAAATAAA-AATTT
1 AAAAAAAATAAATAAATAATTT
** *
20040 AAAATTAATAATTAAATAATTT
1 AAAAAAAATAAATAAATAATTT
20062 TTAATAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAAAATAAATAAATAATTT
Found at i:20500 original size:19 final size:18
Alignment explanation
Indices: 20476--20522 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
20466 AAATAAATAA
20476 AATAATTTTAATTATATTT
1 AATAATTTTAATTAT-TTT
*
20495 AATAATTTATATTTATTTT
1 AATAATTT-TAATTATTTT
*
20514 AATTATTTT
1 AATAATTTT
20523 TTTATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.72
20 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATAATTTTAATTATTTT
Found at i:20539 original size:29 final size:29
Alignment explanation
Indices: 20480--20535 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
20470 AAATAAAATA
20480 ATTTTAATTATATTTAATAATTTATATTT
1 ATTTTAATTATATTTAATAATTTATATTT
* *
20509 ATTTTAATTAT-TTT-TTTATTTATATTT
1 ATTTTAATTATATTTAATAATTTATATTT
20536 TTATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 3 0.12
29 11 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (29 bp):
ATTTTAATTATATTTAATAATTTATATTT
Done.