Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold929
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: 22864
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Found at i:3593 original size:189 final size:187
Alignment explanation
Indices: 3351--3729 Score: 534
Period size: 190 Copynumber: 2.0 Consensus size: 187
3341 ATCCAATATA
* *
3351 TAAATTTTGAACAAATCCTTGAAAGCTGAGCCTATCCATGTGTCAGTTATTA-TTATTTT-TTTT
1 TAAATTTTGAACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTATTTATTTTATTTT
**
3414 TCCTTTGGTTGC-CATGTAGCCATTTCTATTGTTTTTTCTCAATTCTTTGTACTCAACCTATTTG
66 TCCTTTGG--GCACATGTAGCCATTTCTATTACTTTTTCTC----CTTTGTACTCAACCTATTTG
* *
3478 TCTAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTTTACAGAGATATTAAAAGATTTTATGTT
125 TCGAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGTT
* *
3541 TAAATTTT-AGACAAATCCCTGAAAG-TGAGTCTATCCATGTGTCAGCTATTATTTTTGTTTTCA
1 TAAATTTTGA-ACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTA--TTTATTTT-A
* *
3604 TTTTTCCTTTGGGCATCGTGTAGTCATTTCTATTACTTTTTCTCCTTTGTACTCAACCTATTTGT
62 TTTTTCCTTTGGGCA-CATGTAGCCATTTCTATTACTTTTTCTCCTTTGTACTCAACCTATTTGT
3669 CGAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGT
126 CGAAGTTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGT
3730 ATTATTTAAT
Statistics
Matches: 171, Mismatches: 10, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
189 25 0.15
190 102 0.60
192 8 0.05
194 36 0.21
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (187 bp):
TAAATTTTGAACAAATCCCTGAAAGCTGAGCCTATCCATGTGTCAGCTATTATTTATTTTATTTT
TCCTTTGGGCACATGTAGCCATTTCTATTACTTTTTCTCCTTTGTACTCAACCTATTTGTCGAAG
TTAAAAAGCTGATGAGTTTAGAAAAGATTCTACAGAGATATTAAAAGATTTTATGTT
Found at i:9106 original size:50 final size:51
Alignment explanation
Indices: 9015--9159 Score: 231
Period size: 50 Copynumber: 2.9 Consensus size: 51
9005 TTTTAACTAG
*
9015 ATGTATCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
9066 ATGTATCGATACATTG-AAAATGTATCGATACATCTAGGT-AAAAGACTGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
* *
9115 ATATATCAATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
9160 TGTGACTTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 23 0.27
50 43 0.50
51 20 0.23
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:11336 original size:13 final size:13
Alignment explanation
Indices: 11315--11348 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
11305 TAAATTTTTT
11315 ATAAAAAAATAAA
1 ATAAAAAAATAAA
11328 ATTAAAAAAATAAA
1 A-TAAAAAAATAAA
11342 ATAAAAA
1 ATAAAAA
11349 TTATTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:13150 original size:13 final size:13
Alignment explanation
Indices: 13134--13158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13124 CGGAAGCGAG
13134 TTTTTTTTTCGGT
1 TTTTTTTTTCGGT
13147 TTTTTTTTTCGG
1 TTTTTTTTTCGG
13159 GATTTAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.16, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCGGT
Found at i:13591 original size:30 final size:27
Alignment explanation
Indices: 13548--13620 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
13538 ATTTATATTC
*
13548 ATTATTTATTATTAAAATATAATATTTTA
1 ATTA-TTAATATTAAAATATAATA-TTTA
* *
13577 TATTATATAATATTAATATATACTATTTA
1 -ATTAT-TAATATTAAAATATAATATTTA
13606 ATTATT-ATATTAAAA
1 ATTATTAATATTAAAA
13621 ATTTAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 8 0.21
27 1 0.03
28 5 0.13
29 5 0.13
30 19 0.50
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATTAATATTAAAATATAATATTTA
Found at i:13670 original size:23 final size:23
Alignment explanation
Indices: 13605--13697 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 23
13595 TATACTATTT
*
13605 AATTATTATATT-AAAAATTTAA
1 AATTTTTATATTAAAAAATTTAA
* * *
13627 AAATTTTA-AAT-AAAAA--CAA
1 AATTTTTATATTAAAAAATTTAA
*
13646 AATTTTTATT-TAAAAAATATTAA
1 AATTTTTATATTAAAAAAT-TTAA
* *
13669 AATCTTATATATTAAATAATTT-A
1 AAT-TTTTATATTAAAAAATTTAA
13692 AATTTT
1 AATTTT
13698 AAATTTTAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
19 10 0.19
20 5 0.09
21 7 0.13
22 8 0.15
23 9 0.17
24 7 0.13
25 7 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTTTATATTAAAAAATTTAA
Found at i:14177 original size:20 final size:20
Alignment explanation
Indices: 14161--14199 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
14151 TAATATTGAC
14161 ATAAATATTAAAATATTATA
1 ATAAATATTAAAATATTATA
*
14181 ATAATTATTAAAATATTAT
1 ATAAATATTAAAATATTAT
14200 TTTTAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATATTAAAATATTATA
Found at i:14616 original size:17 final size:18
Alignment explanation
Indices: 14591--14628 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
14581 TGTTACAATT
14591 TATTATTAAAAT-AATAA
1 TATTATTAAAATAAATAA
* *
14608 TATTTTTAAATTAAATAA
1 TATTATTAAAATAAATAA
14626 TAT
1 TAT
14629 GTTATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATTAAAATAAATAA
Found at i:15018 original size:14 final size:14
Alignment explanation
Indices: 14999--15025 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14989 AAAATAAAAA
14999 AAAATATTTTTCAC
1 AAAATATTTTTCAC
15013 AAAATATTTTTCA
1 AAAATATTTTTCA
15026 TTAAACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATATTTTTCAC
Found at i:16765 original size:22 final size:22
Alignment explanation
Indices: 16740--16787 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16730 TTGACTCTAT
*
16740 TTTTGTCATTGATTTATATAT-A
1 TTTTGTCA-TGATTTAAATATAA
*
16762 TTTTTTCATGATTTAAATATAA
1 TTTTGTCATGATTTAAATATAA
16784 TTTT
1 TTTT
16788 TGGAAAGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (22 bp):
TTTTGTCATGATTTAAATATAA
Found at i:16788 original size:22 final size:23
Alignment explanation
Indices: 16737--16789 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
16727 TGATTGACTC
*
16737 TATTTTTGTCATTGATTTATATA
1 TATTTTTGTCATTGATTTAAATA
16760 TATTTTT-TCA-TGATTTAAATA
1 TATTTTTGTCATTGATTTAAATA
16781 TAATTTTTG
1 T-ATTTTTG
16790 GAAAGTCGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (23 bp):
TATTTTTGTCATTGATTTAAATA
Found at i:18068 original size:2 final size:2
Alignment explanation
Indices: 18056--18086 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18046 AACTGTACAA
18056 AT AT A- 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 AT AT
18087 TATGTTAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.