Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1295
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: 36008
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:409 original size:17 final size:17
Alignment explanation
Indices: 368--412 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
358 ATTTTAAATA
*
368 AATTATT-TATAATTTG
1 AATTATTATTTAATTTG
*
384 AA-T-TGATTTAATTTG
1 AATTATTATTTAATTTG
399 AATTATTATTTAAT
1 AATTATTATTTAAT
413 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.48
16 3 0.13
17 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (17 bp):
AATTATTATTTAATTTG
Found at i:660 original size:70 final size:70
Alignment explanation
Indices: 547--689 Score: 232
Period size: 70 Copynumber: 2.0 Consensus size: 70
537 ACTTTAACTC
*
547 ATAAACAAATATACTCGAGTGAAGCTTAATATATTAAAAGAAAATGACAAAATAAACACAGAATG
1 ATAAACAAATATACTCGAGTGAAGCTTAATATATTAAAAGAAAACGACAAAATAAACACAGAATG
612 ATAAA
66 ATAAA
* * * * *
617 ATAAACAAATATACTTGAGTGCAGCTTAATATGTTAAAAGAAAACGACAAAATAAATACAGGATG
1 ATAAACAAATATACTCGAGTGAAGCTTAATATATTAAAAGAAAACGACAAAATAAACACAGAATG
682 ATAAA
66 ATAAA
687 ATA
1 ATA
690 GTTCAACAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (70 bp):
ATAAACAAATATACTCGAGTGAAGCTTAATATATTAAAAGAAAACGACAAAATAAACACAGAATG
ATAAA
Found at i:886 original size:2 final size:2
Alignment explanation
Indices: 879--922 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
869 AGATTTGGTT
879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
920 TA T
1 TA T
923 TAACAACCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2823 original size:25 final size:26
Alignment explanation
Indices: 2791--2844 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
2781 TATGTATTAA
2791 AATTGGTAA-TT-CGACATCGGAATTT
1 AATTGGTAAGTTAC-ACATCGGAATTT
2816 AATTGGTAAGTTTACACATCGGAATTT
1 AATTGGTAAG-TTACACATCGGAATTT
2843 AA
1 AA
2845 GTTAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 9 0.35
27 16 0.62
28 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (26 bp):
AATTGGTAAGTTACACATCGGAATTT
Found at i:3693 original size:24 final size:24
Alignment explanation
Indices: 3648--3694 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3638 GAGTGCAAGA
*
3648 ACGATAAATAATTCGTACATACTC
1 ACGATAAATAATTCGAACATACTC
*
3672 ACGATAAA-AATATCGAAGATACT
1 ACGATAAATAAT-TCGAACATACT
3695 ATATAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
ACGATAAATAATTCGAACATACTC
Found at i:4515 original size:2 final size:2
Alignment explanation
Indices: 4508--4532 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4498 CTCGAAACGC
4508 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
4533 CAGAAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:6325 original size:6 final size:6
Alignment explanation
Indices: 6308--6375 Score: 57
Period size: 6 Copynumber: 11.0 Consensus size: 6
6298 TATTTAAAAC
* * **
6308 TTTTATA TTTTAA TTTTAA TTTTAA TTTAAA ATTTAA AATTAA TATTTAA
1 TTTTA-A TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T-TTTAA
*
6358 -TTAAA TTTTAAA TTTTAA
1 TTTTAA TTTT-AA TTTTAA
6376 ATTTCGAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
5 4 0.08
6 31 0.62
7 15 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTTAA
Found at i:6343 original size:18 final size:18
Alignment explanation
Indices: 6299--6375 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
6289 ATCTTTTAAT
6299 ATTTAAAACTTTTATATTTTA
1 ATTTAAAA--TTTA-ATTTTA
* * *
6320 ATTTTAATTTTAATTTAAA
1 ATTTAAAATTTAATTT-TA
6339 ATTTAAAA-TTAATATTTA
1 ATTTAAAATTTAAT-TTTA
*
6357 A-TTAAATTTTAAATTTTA
1 ATTTAAAATTT-AATTTTA
6375 A
1 A
6376 ATTTCGAGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
17 5 0.11
18 18 0.40
19 16 0.36
21 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTAAAATTTAATTTTA
Found at i:6365 original size:30 final size:30
Alignment explanation
Indices: 6317--6378 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
6307 CTTTTATATT
*
6317 TTAATTTTAATTTTAATTTAAAATTTAAAA
1 TTAATTTTAATTTAAATTTAAAATTTAAAA
* *
6347 TTAATATTTAA-TTAAATTTTAAATTTTAAA
1 TTAAT-TTTAATTTAAATTTAAAATTTAAAA
6377 TT
1 TT
6379 TCGAGTTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTAATTTTAATTTAAATTTAAAATTTAAAA
Found at i:6368 original size:7 final size:7
Alignment explanation
Indices: 6292--6379 Score: 51
Period size: 7 Copynumber: 12.4 Consensus size: 7
6282 TAAATTTATC
6292 TTTTAATA
1 TTTTAA-A
*
6300 TTTAAAA
1 TTTTAAA
*
6307 CTTTTATA
1 -TTTTAAA
6315 TTTT-AA
1 TTTTAAA
6321 TTTT-AA
1 TTTTAAA
6327 TTTT-AA
1 TTTTAAA
6333 -TTTAAA
1 TTTTAAA
*
6339 ATTTAAA
1 TTTTAAA
*
6346 -ATTAATA
1 TTTTAA-A
6353 TTTAATTAAA
1 -TT--TTAAA
6363 TTTTAAA
1 TTTTAAA
6370 TTTTAAA
1 TTTTAAA
6377 TTT
1 TTT
6380 CGAGTTGAGC
Statistics
Matches: 66, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
5 3 0.05
6 19 0.29
7 27 0.41
8 10 0.15
9 2 0.03
10 1 0.02
11 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTTAAA
Found at i:6379 original size:24 final size:25
Alignment explanation
Indices: 6309--6379 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
6299 ATTTAAAACT
* *
6309 TTTATATTTT-AATTTTAATTTTAA
1 TTTAAATTTTAAATTTTAAATTTAA
* *
6333 TTTAAAATTTAAA-ATTAATATTTAA
1 TTTAAATTTTAAATTTTAA-ATTTAA
6358 -TTAAATTTTAAATTTTAAATTT
1 TTTAAATTTTAAATTTTAAATTT
6380 CGAGTTGAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
24 27 0.71
25 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAAATTTTAAATTTTAAATTTAA
Found at i:9853 original size:20 final size:17
Alignment explanation
Indices: 9830--9871 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 17
9820 AATTTATTAA
9830 TAATTTTTATAATAAATAAT
1 TAATTTTT-TAA-AAA-AAT
9850 TAATTTTTTAAAAAAAT
1 TAATTTTTTAAAAAAAT
9867 TAATT
1 TAATT
9872 ATGTGATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 3 0.14
20 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATTTTTTAAAAAAAT
Found at i:9857 original size:21 final size:21
Alignment explanation
Indices: 9825--9872 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9815 TTAATAATTT
*
9825 ATTAA-TAA-TTTTTATAATAA
1 ATTAATTAATTTTTTA-AAAAA
9845 A-TAATTAATTTTTTAAAAAA
1 ATTAATTAATTTTTTAAAAAA
9865 ATTAATTA
1 ATTAATTA
9873 TGTGATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.12
20 9 0.38
21 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATTAATTTTTTAAAAAA
Found at i:10431 original size:17 final size:18
Alignment explanation
Indices: 10409--10455 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
10399 ATCATGTTCG
10409 TATTATTTTTTAAATTA-
1 TATTATTTTTTAAATTAT
* *
10426 TGTTA-TATTTAAATTAT
1 TATTATTTTTTAAATTAT
10443 TATTATTTTTTAA
1 TATTATTTTTTAA
10456 TATCAGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTATTTTTTAAATTAT
Found at i:10839 original size:10 final size:10
Alignment explanation
Indices: 10824--10874 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
10814 CAAAATGGTC
10824 TATATATGCA
1 TATATATGCA
10834 TATATATTGCA
1 TATATA-TGCA
*
10845 TATATATGTA
1 TATATATGCA
* *
10855 TATACATACA
1 TATATATGCA
10865 TATATATGCA
1 TATATATGCA
10875 AACCTATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
10 24 0.71
11 10 0.29
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (10 bp):
TATATATGCA
Found at i:10882 original size:14 final size:14
Alignment explanation
Indices: 10865--10892 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10855 TATACATACA
10865 TATATATGCAAACC
1 TATATATGCAAACC
10879 TATATATGCAAACC
1 TATATATGCAAACC
10893 GAATTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
TATATATGCAAACC
Found at i:11995 original size:3 final size:3
Alignment explanation
Indices: 11987--12018 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11977 ATACTGAAAC
11987 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12019 AGAGTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23020 original size:2 final size:2
Alignment explanation
Indices: 23015--23051 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
23005 TTCAAAAGAT
23015 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 T
23052 TTCTTCTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23379 original size:20 final size:20
Alignment explanation
Indices: 23349--23411 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
23339 TTTTTAATAT
*
23349 TTTTATTAATTTAAATTTAAA
1 TTTTATTAATTT-AAGTTAAA
23370 TTTT-TTAATTTAAGTTAAA
1 TTTTATTAATTTAAGTTAAA
*
23389 TTTTGATTCGATTT-AGTTAAA
1 TTTT-ATT-AATTTAAGTTAAA
23410 TT
1 TT
23412 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 11 0.30
20 7 0.19
21 15 0.41
22 4 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (20 bp):
TTTTATTAATTTAAGTTAAA
Found at i:23439 original size:29 final size:28
Alignment explanation
Indices: 23406--23491 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
23396 TCGATTTAGT
23406 TAAATTATTTTTTAAATATTATATAAAA
1 TAAATTATTTTTTAAATATTATATAAAA
* ** * * *
23434 TAAAATATTTTTATATTTTTTATTTGAAA
1 TAAATTATTTTT-TAAATATTATATAAAA
*
23463 TAAGTTAATTTTTTAAATATTTATATAAA
1 TAAATT-ATTTTTTAAATA-TTATATAAA
23492 TTATAAATAT
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
28 11 0.26
29 18 0.43
30 13 0.31
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
TAAATTATTTTTTAAATATTATATAAAA
Found at i:23548 original size:22 final size:22
Alignment explanation
Indices: 23510--23551 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23500 ATTTAATTTT
*
23510 ATTAAATTTTTATTATTAACAA
1 ATTAAATTTTCATTATTAACAA
23532 ATTAAATTATTCA-TATTAAC
1 ATTAAATT-TTCATTATTAAC
23552 TCGATAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTAAATTTTCATTATTAACAA
Found at i:23684 original size:20 final size:21
Alignment explanation
Indices: 23641--23704 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
23631 AAAAAATAAG
* *
23641 TTATATAAAAATATCAAATTAAT
1 TTAT-TAATAATAT-AATTTAAT
* *
23664 TTTTTTATAAT-TAATTTAAT
1 TTATTAATAATATAATTTAAT
23684 TTATTAATAATATAATTTAAT
1 TTATTAATAATATAATTTAAT
23705 AAAATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 16 0.47
21 10 0.29
22 5 0.15
23 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTAATAATATAATTTAAT
Done.