Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1025
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: 25940
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:503 original size:35 final size:34
Alignment explanation
Indices: 450--517 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
440 ATATAATGAC
* *
450 AAATAATTAAAACTATATTTATATTAATAATAAA
1 AAATAATTAAAACTATATTAATATAAATAATAAA
*
484 AAATAAATTAAAAAC-ATATTAATGTAAATAATAA
1 AAAT-AATT-AAAACTATATTAATATAAATAATAA
518 TCTAATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 20 0.69
36 5 0.17
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (34 bp):
AAATAATTAAAACTATATTAATATAAATAATAAA
Found at i:7192 original size:2 final size:2
Alignment explanation
Indices: 7185--7212 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7175 ATTTCTGTAG
7185 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7213 AGAGTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9843 original size:119 final size:119
Alignment explanation
Indices: 9594--9830 Score: 361
Period size: 119 Copynumber: 2.0 Consensus size: 119
9584 AAGAATGAAA
* * * *
9594 TTGCTTCGTTTAATAAT-GAGAAACTAAAATGCATTTGTCATTATAATATAAAGATTGTAGAAGA
1 TTGCTTAGTTTAACAATAAAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGA
* * * ** *
9658 ACTCTTATCTACCAGTATGTTAATTTTTTTATTTTTTTCAAAAATATTTATTTT
66 ACTCCTATCTACAAGTATATTAAGCTTTTTATTTTTTTAAAAAATATTTATTTT
*
9712 TTGCTTAGTTTAACAATAAAGAAATTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGA
1 TTGCTTAGTTTAACAATAAAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGA
9777 ACTCCTATCTACAAGTATATT-AGCTTTTTATTTTTTTAAAAAATATTTATTTT
66 ACTCCTATCTACAAGTATATTAAGCTTTTTATTTTTTTAAAAAATATTTATTTT
9830 T
1 T
9831 AATGTATATT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
118 45 0.42
119 62 0.58
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (119 bp):
TTGCTTAGTTTAACAATAAAGAAACTAAAATGCATTTCTCATTATAATATAAAGATTGTAGAAGA
ACTCCTATCTACAAGTATATTAAGCTTTTTATTTTTTTAAAAAATATTTATTTT
Found at i:11743 original size:16 final size:15
Alignment explanation
Indices: 11717--11752 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
11707 ATATTTAATT
*
11717 TTTTTAAAAATTATA
1 TTTTAAAAAATTATA
11732 TATTTAAAAAATTATA
1 T-TTTAAAAAATTATA
11748 TTTTA
1 TTTTA
11753 TATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTAAAAAATTATA
Found at i:11769 original size:14 final size:14
Alignment explanation
Indices: 11719--11773 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
11709 ATTTAATTTT
11719 TTTAAAAATTATATA
1 TTTAAAAATT-TATA
*
11734 TTTAAAAAATTATA
1 TTTAAAAATTTATA
* *
11748 TTT-TATATTTATA
1 TTTAAAAATTTATA
*
11761 TTTAAATATTTAT
1 TTTAAAAATTTAT
11774 TAAATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 10 0.29
14 15 0.44
15 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAAAAATTTATA
Found at i:11789 original size:13 final size:13
Alignment explanation
Indices: 11771--11797 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11761 TTTAAATATT
11771 TATTAAATATAAA
1 TATTAAATATAAA
11784 TATTAAATATAAA
1 TATTAAATATAAA
11797 T
1 T
11798 TAAAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATTAAATATAAA
Found at i:11812 original size:21 final size:22
Alignment explanation
Indices: 11788--11834 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
11778 TATAAATATT
*
11788 AAATATAAATTAA-AAAATAAA-
1 AAAT-TAAAGTAACAAAATAAAG
*
11809 AAATTAAAGTAACTAAATAAAG
1 AAATTAAAGTAACAAAATAAAG
11831 AAAT
1 AAAT
11835 GCTACTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (22 bp):
AAATTAAAGTAACAAAATAAAG
Found at i:12249 original size:20 final size:20
Alignment explanation
Indices: 12224--12275 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12214 TAAATTTTAA
*
12224 ATTTTTTATATATTTAAATT
1 ATTTTTTAAATATTTAAATT
12244 ATTTTTTAAATATTTAAA-T
1 ATTTTTTAAATATTTAAATT
* *
12263 ATATATTAAATAT
1 ATTTTTTAAATAT
12276 AAATATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAAATATTTAAATT
Found at i:12283 original size:36 final size:34
Alignment explanation
Indices: 12190--12284 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 34
12180 TTAGATAAAA
12190 ATATTAAATATAAATAATATATTTTAAATTTTAAATT
1 ATATTAAATATAAAT-AT-T-TTTTAAATTTTAAATT
* *
12227 -TTTTATATATTTAAATTATTTTTTAAATATTTAAATAT
1 ATATTA-A-ATATAAA-TATTTTTTAAAT-TTTAAAT-T
12265 ATATTAAATATAAATATTTT
1 ATATTAAATATAAATATTTT
12285 AAAATTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
36 18 0.38
37 15 0.31
38 10 0.21
39 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
ATATTAAATATAAATATTTTTTAAATTTTAAATT
Found at i:16523 original size:14 final size:14
Alignment explanation
Indices: 16484--16528 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
16474 TAATTTTTTA
*
16484 TATATTTAAAAATT
1 TATATTTAAATATT
* *
16498 AATATTT-TATATT
1 TATATTTAAATATT
16511 TATATTTAAATATT
1 TATATTTAAATATT
16525 TATA
1 TATA
16529 AATATAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTTAAATATT
Found at i:16575 original size:24 final size:25
Alignment explanation
Indices: 16529--16575 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
16519 AATATTTATA
**
16529 AATATAAATGTAAAATATTGATACT
1 AATATAAATGTAAAATACAGATACT
*
16554 AATA-AAATGTAAAATCCAGATA
1 AATATAAATGTAAAATACAGATA
16576 ATATAGGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (25 bp):
AATATAAATGTAAAATACAGATACT
Found at i:16761 original size:2 final size:2
Alignment explanation
Indices: 16754--16781 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16744 ACATCAACAA
16754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16782 GTACAGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17319 original size:26 final size:26
Alignment explanation
Indices: 17261--17355 Score: 113
Period size: 26 Copynumber: 3.7 Consensus size: 26
17251 TAGCCACCAA
* *
17261 TTTTGACAAACAACAAG--TCACCAT
1 TTTTGACAAACAAAAAGAATCACTAT
*
17285 TTTTGACAAACAAAAAGAATAACTAT
1 TTTTGACAAACAAAAAGAATCACTAT
* *
17311 TTTTGACAAACAAAAAGGAACCATTAT
1 TTTTGACAAACAAAAA-GAATCACTAT
17338 TTTTGACAAACACAAAAG
1 TTTTGACAAACA-AAAAG
17356 GTGGCTTTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
24 16 0.26
26 21 0.34
27 20 0.33
28 4 0.07
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.25
Consensus pattern (26 bp):
TTTTGACAAACAAAAAGAATCACTAT
Found at i:17326 original size:27 final size:27
Alignment explanation
Indices: 17283--17355 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
17273 ACAAGTCACC
*
17283 ATTTTTGACAAAC-AAAAAGAATAACT
1 ATTTTTGACAAACAAAAAAGAACAACT
* * *
17309 ATTTTTGACAAACAAAAAGGAACCATT
1 ATTTTTGACAAACAAAAAAGAACAACT
*
17336 ATTTTTGACAAACACAAAAG
1 ATTTTTGACAAACAAAAAAG
17356 GTGGCTTTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 13 0.32
27 27 0.68
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAAGAACAACT
Found at i:20842 original size:52 final size:52
Alignment explanation
Indices: 20682--20834 Score: 229
Period size: 52 Copynumber: 2.9 Consensus size: 52
20672 TGTGGGGATG
* *
20682 AATTCGCCCAGATGTATCGATACACTGATCT--TTGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACT-AT-TAAATGTATCGATACATGCAGGCA
* **
20734 AATTTGCCCAGATGTATCGATACATTAGAAAATGTATCGATACATGCAGGCA
1 AATTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGCA
20786 AATTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAG
1 AATTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAG
20835 ATAAATTTTC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 1 0.01
52 90 0.99
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (52 bp):
AATTTGCCCAGATGTATCGATACACTATTAAATGTATCGATACATGCAGGCA
Done.