Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold417
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: 511691
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 6 of 6
Found at i:503826 original size:16 final size:17
Alignment explanation
Indices: 503784--503826 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
503774 TTTAATATTT
*
503784 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
503801 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
503816 ATAAAATTTAT
1 ATAAAATTTAT
503827 TTAAAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:504734 original size:18 final size:19
Alignment explanation
Indices: 504711--504747 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
504701 ATACAACTTT
504711 AAATAT-ACA-AAACAATAA
1 AAATATGACATAAA-AATAA
504729 AAATATGACATAAAAATAA
1 AAATATGACATAAAAATAA
504748 TTAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.19
Consensus pattern (19 bp):
AAATATGACATAAAAATAA
Found at i:504767 original size:22 final size:22
Alignment explanation
Indices: 504712--504772 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
504702 TACAACTTTA
*
504712 AATATACAAAACAATAAAAATAT
1 AATATA-AAAATAATAAAAATAT
* * *
504735 GACATAAAAATAATTAAAATAT
1 AATATAAAAATAATAAAAATAT
504757 AATATAAAAATGAATA
1 AATATAAAAAT-AATA
504773 TGACACGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (22 bp):
AATATAAAAATAATAAAAATAT
Found at i:505386 original size:13 final size:13
Alignment explanation
Indices: 505368--505419 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
505358 CGTAAATTTT
505368 TCTTTCTTCTTTC
1 TCTTTCTTCTTTC
505381 TCTTTCTTCTTT-
1 TCTTTCTTCTTTC
505393 TC-TT-TT-TTTC
1 TCTTTCTTCTTTC
*
505403 TCCTTCTTTCTTTC
1 TCTTTC-TTCTTTC
505417 TCT
1 TCT
505420 CTTTTCCCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
9 3 0.09
10 4 0.12
11 4 0.12
12 2 0.06
13 14 0.42
14 6 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTCTTCTTTC
Found at i:505416 original size:22 final size:22
Alignment explanation
Indices: 505366--505423 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
505356 GCCGTAAATT
*
505366 TTTCTTTC-TTCTTTCTCTTTC
1 TTTCTTTCTTTCTTTCTCCTTC
*
505387 -TTCTTTTCTTTTTTTCTCCTTC
1 TTTC-TTTCTTTCTTTCTCCTTC
*
505409 TTTCTTTCTCTCTTT
1 TTTCTTTCTTTCTTT
505424 TCCCTTTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.10
21 4 0.13
22 20 0.67
23 3 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTCTTTCTTTCTTTCTCCTTC
Found at i:505429 original size:22 final size:21
Alignment explanation
Indices: 505364--505430 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 21
505354 AGGCCGTAAA
*
505364 TTTTTCTTTCT-TC-TTTCTC
1 TTTTTCTTTCTCTCTTTTCCC
*
505383 TTTCTTCTTT-TCTTTTTTTCTCC
1 TTT-TTCTTTCTC-TCTTTTC-CC
505406 TTCTTTCTTTCTCTCTTTTCCC
1 TT-TTTCTTTCTCTCTTTTCCC
505428 TTT
1 TTT
505431 CGAAAGGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
19 4 0.11
20 6 0.16
21 2 0.05
22 8 0.21
23 15 0.39
24 3 0.08
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTCTTTCTCTCTTTTCCC
Found at i:505883 original size:17 final size:17
Alignment explanation
Indices: 505861--505921 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
505851 GGTGGGGCGT
505861 GCGGGGGGTGGCGCAGG
1 GCGGGGGGTGGCGCAGG
* *
505878 GCGGGGCGTGGCGGGAGG
1 GCGGGGGGTGGC-GCAGG
* *
505896 G-GGGGGGCGG-GCGGG
1 GCGGGGGGTGGCGCAGG
505911 GCGGGCGGGTG
1 GCGGG-GGGTG
505922 CAGCACATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 22 0.65
18 5 0.15
ACGTcount: A:0.03, C:0.16, G:0.75, T:0.05
Consensus pattern (17 bp):
GCGGGGGGTGGCGCAGG
Found at i:506701 original size:12 final size:12
Alignment explanation
Indices: 506684--506748 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
506674 GGGAAAAGAT
506684 GGAGAGGAGGGG
1 GGAGAGGAGGGG
*
506696 GGAGAGCA--GG
1 GGAGAGGAGGGG
* *
506706 GAAGAAGAGGGG
1 GGAGAGGAGGGG
**
506718 GGAGAGGAAAGG
1 GGAGAGGAGGGG
* *
506730 GGAGAGGCGGGC
1 GGAGAGGAGGGG
506742 GGAGAGG
1 GGAGAGG
506749 GCGAGGAGGG
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
10 7 0.18
12 32 0.82
ACGTcount: A:0.31, C:0.05, G:0.65, T:0.00
Consensus pattern (12 bp):
GGAGAGGAGGGG
Found at i:507857 original size:15 final size:13
Alignment explanation
Indices: 507809--507870 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 13
507799 ATAATTTTAT
*
507809 ATATTGTTA-AAA
1 ATATTGTTATATA
507821 ATA-TGTTATAT-
1 ATATTGTTATATA
* *
507832 -TATTTTTATATC
1 ATATTGTTATATA
507844 ATGATCTGTTATATA
1 AT-AT-TGTTATATA
507859 ATATTGTTATAT
1 ATATTGTTATAT
507871 TAATTTATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 2 0.05
11 12 0.30
12 4 0.10
13 9 0.22
14 4 0.10
15 9 0.22
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (13 bp):
ATATTGTTATATA
Found at i:508276 original size:19 final size:20
Alignment explanation
Indices: 508231--508295 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 20
508221 TAATATATTT
*
508231 TTTTTAAATTTTATAAAAATA
1 TTTTTAAA-TGTATAAAAATA
*
508252 -TGTTAAATGTA-AAAAATA
1 TTTTTAAATGTATAAAAATA
*
508270 TTTTTAAATGATATATAAAAAA
1 TTTTTAAATG-TATA-AAAATA
508292 TTTT
1 TTTT
508296 AAAAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 7 0.19
19 11 0.31
20 8 0.22
21 1 0.03
22 9 0.25
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTTTTAAATGTATAAAAATA
Found at i:510241 original size:24 final size:23
Alignment explanation
Indices: 510208--510252 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
510198 TCTTCTTCTC
510208 CTTTTTTTTCTATTTT-CTTTCCT
1 CTTTTTTTTCT-TTTTGCTTTCCT
510231 CTTTTTATTTCTTTTTGCTTTC
1 CTTTTT-TTTCTTTTTGCTTTC
510253 TTTCTCCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (23 bp):
CTTTTTTTTCTTTTTGCTTTCCT
Found at i:510271 original size:4 final size:4
Alignment explanation
Indices: 510264--510290 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
510254 TTCTCCACTC
510264 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
510291 GCTTGAGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:510658 original size:37 final size:36
Alignment explanation
Indices: 510586--510672 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 36
510576 TTCACTGCTT
* *
510586 AAAATAAT-T-TTGAATATAATAAAAAAATAATATA
1 AAAATAATATATTTAATATAATAAAAAAATAAAATA
510620 AAAATAATATATTTAATA-AATAAAAAAATAAAAAATA
1 AAAATAATATATTTAATATAATAAAAAAAT--AAAATA
*
510657 AATATAATATAATTTA
1 AAAATAATAT-ATTTA
510673 TTTTAATACA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.18
35 12 0.27
36 6 0.13
37 14 0.31
38 5 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (36 bp):
AAAATAATATATTTAATATAATAAAAAAATAAAATA
Found at i:510668 original size:11 final size:11
Alignment explanation
Indices: 510601--510663 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
510591 AATTTTGAAT
*
510601 ATAATAAAAAA
1 ATAATATAAAA
510612 ATAATATAAAA
1 ATAATATAAAA
**
510623 ATAATATATTTA
1 ATAATATA-AAA
510635 ATAA-ATAAAA
1 ATAATATAAAA
510645 A-AATA-AAAA
1 ATAATATAAAA
510654 ATAAATATAA
1 AT-AATATAA
510664 TATAATTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 7 0.17
10 3 0.07
11 25 0.60
12 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATATAAAA
Done.