Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold829
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: 38829
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:634 original size:8 final size:8
Alignment explanation
Indices: 621--663 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
611 TATTTTTGAC
621 TTTGATTT
1 TTTGATTT
629 TTTGA--T
1 TTTGATTT
635 TTTGATTTTT
1 TTTGA--TTT
645 TTTGATTT
1 TTTGATTT
653 TTTGATTT
1 TTTGATTT
661 TTT
1 TTT
664 TAGCTTGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.19
8 19 0.61
10 6 0.19
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (8 bp):
TTTGATTT
Found at i:655 original size:18 final size:16
Alignment explanation
Indices: 613--664 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
603 TCTTCTCCTA
*
613 TTTTTGACTTTGA--T
1 TTTTTGATTTTGATTT
627 TTTTTGATTTTGATTT
1 TTTTTGATTTTGATTT
643 TTTTTGATTTTTTGATTT
1 TTTTTGA--TTTTGATTT
661 TTTT
1 TTTT
665 AGCTTGAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
14 12 0.36
16 8 0.24
18 13 0.39
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.75
Consensus pattern (16 bp):
TTTTTGATTTTGATTT
Found at i:661 original size:14 final size:14
Alignment explanation
Indices: 613--661 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
603 TCTTCTCCTA
*
613 TTTTTGACTTTGAT
1 TTTTTGATTTTGAT
627 TTTTTGATTTTGA-
1 TTTTTGATTTTGAT
640 -TTTT--TTTTGAT
1 TTTTTGATTTTGAT
651 TTTTTGATTTT
1 TTTTTGATTTT
662 TTTAGCTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 6 0.20
12 8 0.27
14 16 0.53
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.73
Consensus pattern (14 bp):
TTTTTGATTTTGAT
Found at i:3301 original size:19 final size:20
Alignment explanation
Indices: 3272--3321 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
3262 CACTTTGTCA
* *
3272 AAATCTAATGCATATG-ATG
1 AAATGTAATGCACATGCATG
*
3291 CAATGTAATGCACATGCATG
1 AAATGTAATGCACATGCATG
3311 AAATG-AATGCA
1 AAATGTAATGCA
3322 AAAAGAGACG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (20 bp):
AAATGTAATGCACATGCATG
Found at i:5435 original size:29 final size:29
Alignment explanation
Indices: 5396--5462 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
5386 CAAAAGATAT
5396 AAACAAATACATAATGATAACATATAATA
1 AAACAAATACATAATGATAACATATAATA
5425 AAACAAATACATAATGATAACATATAATA
1 AAACAAATACATAATGATAACATATAATA
5454 AAACAAATA
1 AAACAAATA
5463 TAAATATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.22
Consensus pattern (29 bp):
AAACAAATACATAATGATAACATATAATA
Found at i:5454 original size:16 final size:16
Alignment explanation
Indices: 5406--5454 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 16
5396 AAACAAATAC
5406 ATAATGATAACATATA
1 ATAATGATAACATATA
*
5422 AT-A--A-AACAAATA
1 ATAATGATAACATATA
5434 CATAATGATAACATATA
1 -ATAATGATAACATATA
5451 ATAA
1 ATAA
5455 AACAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 1 0.04
15 1 0.04
16 7 0.27
17 7 0.27
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAATGATAACATATA
Found at i:5517 original size:13 final size:13
Alignment explanation
Indices: 5499--5524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5489 AACACAAAGC
5499 TAATAATATAATA
1 TAATAATATAATA
5512 TAATAATATAATA
1 TAATAATATAATA
5525 AGGAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:7996 original size:6 final size:6
Alignment explanation
Indices: 7985--8014 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
7975 ACTTGAGGCA
7985 GAAGCG GAAGCG GAAGCG GAAGCG GAAGCG
1 GAAGCG GAAGCG GAAGCG GAAGCG GAAGCG
8015 AGGTGATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGCG
Found at i:12361 original size:17 final size:19
Alignment explanation
Indices: 12339--12381 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
12329 TAAATACATA
12339 ATAAATAAAG-TTTAAG-T
1 ATAAATAAAGATTTAAGAT
12356 ATAAAT-AAGATTTAAGAAT
1 ATAAATAAAGATTTAAG-AT
12375 ATAAATA
1 ATAAATA
12382 GCAGAATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
19 7 0.32
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
ATAAATAAAGATTTAAGAT
Found at i:12609 original size:68 final size:68
Alignment explanation
Indices: 12530--12666 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
12520 AATTAAACTC
12530 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAA
1 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAA
12595 TTT
66 TTT
12598 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAA
1 TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAA
12663 TTT
66 TTT
12666 T
1 T
12667 ATTTATTCTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.38, C:0.13, G:0.01, T:0.47
Consensus pattern (68 bp):
TCTTAATTTTTTTTTAAAATTCTCATTAATCTCAAAAAAATTTAAAATTTTAATTAGTCACCCAA
TTT
Found at i:20050 original size:19 final size:18
Alignment explanation
Indices: 20021--20062 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
20011 TTACAACACC
20021 AAAAAAGTATATAATTGATT
1 AAAAAAGTATAT--TTGATT
20041 AAAAAA-TATATTTGATT
1 AAAAAAGTATATTTGATT
20058 AAAAA
1 AAAAA
20063 TAAAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AAAAAAGTATATTTGATT
Found at i:22217 original size:14 final size:14
Alignment explanation
Indices: 22198--22228 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22188 TTTAAAACAG
*
22198 GTGCGTTGATAATT
1 GTGCGTTGACAATT
22212 GTGCGTTGACAATT
1 GTGCGTTGACAATT
22226 GTG
1 GTG
22229 TGCTCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.32, T:0.39
Consensus pattern (14 bp):
GTGCGTTGACAATT
Found at i:23835 original size:24 final size:24
Alignment explanation
Indices: 23808--23856 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23798 CTTTCATTCC
23808 ATTGTTTCAGTTAATGACTTCCCA
1 ATTGTTTCAGTTAATGACTTCCCA
23832 ATTGTTTCAGTTAATGACTTCCCA
1 ATTGTTTCAGTTAATGACTTCCCA
23856 A
1 A
23857 AAATGTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (24 bp):
ATTGTTTCAGTTAATGACTTCCCA
Found at i:26884 original size:21 final size:22
Alignment explanation
Indices: 26846--26890 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
26836 TAAAACTTAT
*
26846 TTTTTAAAAATTAAATAAAAATA
1 TTTTAAAAAATT-AATAAAAATA
*
26869 TTTTAAAAAATT-ATAAATATA
1 TTTTAAAAAATTAATAAAAATA
26890 T
1 T
26891 AAAAGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAAAATTAATAAAAATA
Found at i:26888 original size:19 final size:18
Alignment explanation
Indices: 26864--26937 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 18
26854 AATTAAATAA
26864 AAATATTTTAAAAAATTAT
1 AAATA-TTTAAAAAATTAT
* *
26883 AAATATATAAAAGTATTAT
1 AAATATTTAAAA-AATTAT
*
26902 CAAA-ATTTATAAAAATAAT
1 -AAATATTTA-AAAAATTAT
26921 AAATAAATTTAAAAAAT
1 AAAT--ATTTAAAAAAT
26938 ATTCAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
18 9 0.20
19 18 0.41
20 12 0.27
21 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (18 bp):
AAATATTTAAAAAATTAT
Found at i:26906 original size:29 final size:30
Alignment explanation
Indices: 26850--26966 Score: 91
Period size: 29 Copynumber: 3.9 Consensus size: 30
26840 ACTTATTTTT
*
26850 TAAAAATTAAATAAAAATATTTTAAAAAATTA
1 TAAAAA-T-AATAAAAATATTATAAAAAATTA
* * * *
26882 TAAATAT-ATAAAAGTATTATCAAAATTTA
1 TAAAAATAATAAAAATATTATAAAAAATTA
26911 TAAAAATAATAAATAA-ATT-TAAAAAA-TA
1 TAAAAATAATAAA-AATATTATAAAAAATTA
*
26939 TTCAAAATTAATAAAAATCATT-TAAAAA
1 -T-AAAAATAATAAAAAT-ATTATAAAAA
26967 TTGAAGCCCA
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.03
29 32 0.46
30 19 0.28
31 11 0.16
32 5 0.07
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (30 bp):
TAAAAATAATAAAAATATTATAAAAAATTA
Found at i:38186 original size:21 final size:22
Alignment explanation
Indices: 38156--38196 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38146 CCAAAACAGG
**
38156 TTTTTAGCGGCGTTTTTTAGGC
1 TTTTTAGCGGCACTTTTTAGGC
38178 TTTTT-GCGGCACTTTTTAG
1 TTTTTAGCGGCACTTTTTAG
38197 TGCCACTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (22 bp):
TTTTTAGCGGCACTTTTTAGGC
Found at i:38744 original size:13 final size:13
Alignment explanation
Indices: 38726--38791 Score: 78
Period size: 13 Copynumber: 5.1 Consensus size: 13
38716 AGTTTGGCAA
38726 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
38739 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
** * *
38752 TAATGTGGAAAAG
1 TGCTTTTGAAAAG
*
38765 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
38778 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
38791 T
1 T
38792 TTAGTTTAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Done.