Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1941
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: 30713
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:1528 original size:46 final size:44
Alignment explanation
Indices: 1431--1546 Score: 198
Period size: 46 Copynumber: 2.6 Consensus size: 44
1421 CTTTCTACAC
*
1431 ATATAAACTATAACAATGAAAAATTA-CACGCACACACACACAT
1 ATATAAACTATAACAATGAAAAATTATCACACACACACACACAT
1474 ATATAAACTATAACAATGAAAAATTATCACACACACACACACATAT
1 ATATAAACTATAACAATGAAAAATTATCACACACACACACAC--AT
1520 ATATAAACTATAACAATGAAAAATTAT
1 ATATAAACTATAACAATGAAAAATTAT
1547 TAGAGCCTCC
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
43 26 0.38
44 14 0.20
46 29 0.42
ACGTcount: A:0.55, C:0.19, G:0.03, T:0.22
Consensus pattern (44 bp):
ATATAAACTATAACAATGAAAAATTATCACACACACACACACAT
Found at i:12617 original size:26 final size:25
Alignment explanation
Indices: 12561--12625 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
12551 TTAATAAAAA
**
12561 TAAATTTAATTTTTATATTTACTTT
1 TAAATTTAATTTTTATATTTAAATT
*
12586 TGAATTTAATTATTTATATTTAAATT
1 TAAATTTAATT-TTTATATTTAAATT
*
12612 TAAATTAAATTTTT
1 TAAATTTAATTTTT
12626 TAAATAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 13 0.38
26 21 0.62
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (25 bp):
TAAATTTAATTTTTATATTTAAATT
Found at i:12698 original size:21 final size:21
Alignment explanation
Indices: 12647--12713 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
12637 TAAAAATAAA
**
12647 AAATATTAAATT-TTTTTATT
1 AAATATTAAATTATTTAAATT
*
12667 AAATTTATAAATTATTTAAATT
1 AAATAT-TAAATTATTTAAATT
* *
12689 AAATATTAAAATATTAAAATT
1 AAATATTAAATTATTTAAATT
12710 AAAT
1 AAAT
12714 TTACTCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
20 5 0.13
21 23 0.59
22 11 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATATTAAATTATTTAAATT
Found at i:12753 original size:44 final size:43
Alignment explanation
Indices: 12664--12757 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 43
12654 AAATTTTTTT
12664 ATTAAATTTATAAATTATTTAAATTAAATATTAAAATATTAAA
1 ATTAAATTTATAAATTATTTAAATTAAATATTAAAATATTAAA
* *
12707 ATTAAATTTACT-CATTAATTTAAATTTAAT-TTAATAATAATTAAA
1 ATTAAATTTA-TAAATT-ATTTAAATTAAATATTAA-AAT-ATTAAA
*
12752 TTTAAA
1 ATTAAA
12758 ATTTTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
43 17 0.39
44 16 0.36
45 11 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (43 bp):
ATTAAATTTATAAATTATTTAAATTAAATATTAAAATATTAAA
Found at i:13986 original size:2 final size:2
Alignment explanation
Indices: 13981--14024 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
13971 TTAATGTTTA
13981 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
14023 CT
1 CT
14025 TTACAACCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:15580 original size:16 final size:16
Alignment explanation
Indices: 15511--15605 Score: 70
Period size: 16 Copynumber: 6.0 Consensus size: 16
15501 TTAAAAAGTC
*
15511 AAAAACCCAAACTCGA
1 AAAAACCCGAACTCGA
* *
15527 AATAACTCGAACT-GA
1 AAAAACCCGAACTCGA
* * * *
15542 AATAGCTCAAACTC-A
1 AAAAACCCGAACTCGA
15557 AAAGAACCCGAACTCGA
1 AAA-AACCCGAACTCGA
15574 AAAAACCCGAA-TCCGA
1 AAAAACCCGAACT-CGA
**
15590 AAAAACTTGAACTCGA
1 AAAAACCCGAACTCGA
15606 GAGAACCTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
15 17 0.27
16 41 0.65
17 5 0.08
ACGTcount: A:0.49, C:0.26, G:0.12, T:0.13
Consensus pattern (16 bp):
AAAAACCCGAACTCGA
Found at i:20119 original size:16 final size:16
Alignment explanation
Indices: 20098--20131 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
20088 ACCAGAAAAA
20098 AGCCCGAACCCGAACG
1 AGCCCGAACCCGAACG
*
20114 AGCCCGAACTCGAACG
1 AGCCCGAACCCGAACG
20130 AG
1 AG
20132 TACGAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.38, G:0.26, T:0.03
Consensus pattern (16 bp):
AGCCCGAACCCGAACG
Found at i:21676 original size:11 final size:11
Alignment explanation
Indices: 21662--21687 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21652 TATGTATACC
21662 ATATAATATAT
1 ATATAATATAT
21673 ATATAATATAT
1 ATATAATATAT
21684 ATAT
1 ATAT
21688 GCAAACGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATAATATAT
Found at i:25097 original size:21 final size:19
Alignment explanation
Indices: 25073--25126 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
25063 TTCAACAAAT
25073 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* *
25094 TGTATCGATACATAAGTAT
1 TGTATCGATACAAAAGTAA
25113 TGTATCGATACAAA
1 TGTATCGATACAAA
25127 GTTGCCCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:25118 original size:19 final size:19
Alignment explanation
Indices: 25070--25128 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 19
25060 AATTTCAACA
25070 AATTGTATCGATACAAACAGT
1 AATTGTATCGATAC-AA-AGT
*
25091 AAATGTATCGATACATAAGT
1 AATTGTATCGATACA-AAGT
25111 -ATTGTATCGATACAAAGT
1 AATTGTATCGATACAAAGT
25129 TGCCCTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 4 0.11
19 13 0.37
20 4 0.11
21 14 0.40
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (19 bp):
AATTGTATCGATACAAAGT
Found at i:27492 original size:87 final size:85
Alignment explanation
Indices: 27396--27558 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 85
27386 TCCAAGAGAT
27396 GATACTCCAACCCCACTTTT-AACTT-TC-AGATTTTTTTTTACATAAATTATCATTGTCGGGGA
1 GATACTCCAACCCCACTTTTAAACTTGTCAAGA---TTTTTTACATAAATTATC-TTGTCGGGGA
27458 C-CATTCCAAACCCCATATCTCGAGG
62 CAC-TT-CAAACCCCATATCTCGAGG
* *
27483 GATACTCCAACCCCATTTTTAAACTTGTCAAGATTTTTTACATAGATTATCTTGTCGGGGACACT
1 GATACTCCAACCCCACTTTTAAACTTGTCAAGATTTTTTACATAAATTATCTTGTCGGGGACACT
27548 TCAAACCCCAT
66 TCAAACCCCAT
27559 TCCTTCGAGA
Statistics
Matches: 70, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
85 10 0.14
86 13 0.19
87 37 0.53
88 5 0.07
89 2 0.03
90 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (85 bp):
GATACTCCAACCCCACTTTTAAACTTGTCAAGATTTTTTACATAAATTATCTTGTCGGGGACACT
TCAAACCCCATATCTCGAGG
Found at i:29162 original size:20 final size:20
Alignment explanation
Indices: 29133--29170 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29123 CATTTATTTT
*
29133 AATCTCATCATTTCAATAAC
1 AATCTCATCATTCCAATAAC
*
29153 AATCTTATCATTCCAATA
1 AATCTCATCATTCCAATA
29171 TTAATTCACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AATCTCATCATTCCAATAAC
Found at i:29794 original size:16 final size:18
Alignment explanation
Indices: 29773--29811 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
29763 TTAATTTAAT
29773 TAAATTTAA-TAT-AAAA
1 TAAATTTAATTATAAAAA
29789 TAAATTTAATTATAAAAA
1 TAAATTTAATTATAAAAA
29807 TAAAT
1 TAAAT
29812 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATTTAATTATAAAAA
Found at i:29812 original size:22 final size:23
Alignment explanation
Indices: 29786--29838 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29776 ATTTAATATA
29786 AAATAAATTTAAT-TATAAAAAT
1 AAATAAATTTAATATATAAAAAT
** *
29808 AAATATTTTTAATATATAATAAT
1 AAATAAATTTAATATATAAAAAT
*
29831 AATTAAAT
1 AAATAAAT
29839 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATAAATTTAATATATAAAAAT
Done.