Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold737
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: 14321
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Found at i:711 original size:48 final size:44
Alignment explanation
Indices: 655--747 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 44
645 AAAATAAATT
* * *
655 TAAATATAAAATTTTAATAT-TTATTATTTAAATTTATTTTATTTTTA
1 TAAATAT-AAATTTAAATATGATATTATTT--ATTT-TTTTATTATTA
702 TAAATTATAAATTTAAATATGATATTATTTATTTTTTTATTATTA
1 TAAA-TATAAATTTAAATATGATATTATTTATTTTTTTATTATTA
747 T
1 T
748 TTAATTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
45 11 0.27
46 4 0.10
47 15 0.37
48 11 0.27
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (44 bp):
TAAATATAAATTTAAATATGATATTATTTATTTTTTTATTATTA
Found at i:747 original size:18 final size:18
Alignment explanation
Indices: 724--760 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
714 TTAAATATGA
* *
724 TATTATTTATTTTTTTAT
1 TATTATTTAATTTTATAT
742 TATTATTTAATTTTATAT
1 TATTATTTAATTTTATAT
760 T
1 T
761 TAAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TATTATTTAATTTTATAT
Found at i:911 original size:13 final size:13
Alignment explanation
Indices: 893--917 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
883 GCAACTATCG
893 TCTTTTTTTTTTT
1 TCTTTTTTTTTTT
906 TCTTTTTTTTTT
1 TCTTTTTTTTTT
918 CCCTACAAAC
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:0.00, T:0.92
Consensus pattern (13 bp):
TCTTTTTTTTTTT
Found at i:1087 original size:21 final size:21
Alignment explanation
Indices: 1061--1101 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1051 CAATAACAAT
*
1061 AATAATAATTAATATATTAAA
1 AATAATAAATAATATATTAAA
*
1082 AATAATAAATAATATTTTAA
1 AATAATAAATAATATATTAA
1102 CTTTCTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATAAATAATATATTAAA
Found at i:1596 original size:20 final size:21
Alignment explanation
Indices: 1573--1612 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1563 AAATTTTAAA
*
1573 AATA-TTATTAAAATATATAT
1 AATACTTATCAAAATATATAT
1593 AATACCTTATCAAAATATAT
1 AATA-CTTATCAAAATATAT
1613 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
22 13 0.76
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
AATACTTATCAAAATATATAT
Found at i:1715 original size:18 final size:18
Alignment explanation
Indices: 1692--1742 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
1682 AGTCTCAATT
1692 TTATAATATTTAATTTTA
1 TTATAATATTTAATTTTA
* *
1710 TTATAATTTTTTATTTTA
1 TTATAATATTTAATTTTA
1728 TTA-AA-A-TTAATTTTA
1 TTATAATATTTAATTTTA
1743 CCGCTCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 8 0.28
17 2 0.07
18 19 0.66
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATAATATTTAATTTTA
Found at i:4774 original size:20 final size:20
Alignment explanation
Indices: 4722--4803 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
4712 AAAAAAAAAA
4722 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
4741 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
4762 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
4782 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
4803 A
1 A
4804 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:4783 original size:41 final size:40
Alignment explanation
Indices: 4722--4803 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
4712 AAAAAAAAAA
* *
4722 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
4762 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
4803 A
1 A
4804 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:4863 original size:19 final size:19
Alignment explanation
Indices: 4839--4906 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
4829 AATTCAACGA
4839 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4858 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4873 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4890 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4907 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4877 original size:32 final size:32
Alignment explanation
Indices: 4841--4903 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4831 TTCAACGATT
*
4841 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
4873 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
4904 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:4878 original size:13 final size:13
Alignment explanation
Indices: 4860--4884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4850 ACATAAGTTT
4860 TGTATCGATACAA
1 TGTATCGATACAA
4873 TGTATCGATACA
1 TGTATCGATACA
4885 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4983 original size:33 final size:33
Alignment explanation
Indices: 4926--4988 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
4916 GCCAAGGAAA
***
4926 TGTATCGATACATTTTTCTGTGTATCGATATAT
1 TGTATCGATACATGGATCTGTGTATCGATATAT
*
4959 TGTATCGATACATGGATCTTTGTATCGATA
1 TGTATCGATACATGGATCTGTGTATCGATA
4989 CATTTGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATATAT
Found at i:7412 original size:28 final size:27
Alignment explanation
Indices: 7348--7413 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
7338 CACAATCGGA
**
7348 GATACTCCAACCCCGTTAATCATCGGG
1 GATACTCCAACCCCGTTAATCAGAGGG
* *
7375 GATACTCCAACCCCGTTATTTCCGAGGG
1 GATACTCCAACCCCGTTA-ATCAGAGGG
7403 GATACTCCAAC
1 GATACTCCAAC
7414 TCCGGTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 18 0.53
28 16 0.47
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (27 bp):
GATACTCCAACCCCGTTAATCAGAGGG
Found at i:7462 original size:52 final size:51
Alignment explanation
Indices: 7400--7569 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 51
7390 TTATTTCCGA
*
7400 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * **
7452 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
7504 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
7556 GAGGATACTCCAAC
1 GGGGATACTCCAAC
7570 CTTGTTATTT
Statistics
Matches: 96, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
51 10 0.10
52 69 0.72
53 12 0.12
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:7589 original size:28 final size:28
Alignment explanation
Indices: 7553--7629 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
7543 ATTTTTCACA
* ** *
7553 ATCGAGGATACTCCAACCTTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
7581 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
7609 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
7630 GCTTTATTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:7732 original size:79 final size:79
Alignment explanation
Indices: 7583--7785 Score: 239
Period size: 79 Copynumber: 2.6 Consensus size: 79
7573 GTTATTTCAT
* * * *
7583 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCTCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCTCAAAATAT
* * *
7648 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * *
7662 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCTCAAAAT-A
7726 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
7741 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
7786 TGTTATTATC
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
78 8 0.08
79 97 0.92
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCTCAAAATAT
CGATTTCTCACAAC
Found at i:9844 original size:95 final size:96
Alignment explanation
Indices: 9609--9896 Score: 450
Period size: 95 Copynumber: 3.1 Consensus size: 96
9599 AAATTTATAA
9609 AATATTCCATTAATGAAATTTGAATTACATATAAAGTTTGTTTAATGTGAAAATTATATC-AATT
1 AATATT-CATTAATGAAATTTGAATTACATATAAAGTTTGTTTAATGTGAAAATTATATCAAATT
*
9673 AATAT-AAATTTATTACTTTTAATATGAATGT
65 AATATAAAATTTATTACTTTTAATATTAATGT
9704 -A-A-T-ATTAATGAAATTTTGAATTACATATAAAG-TTGTTTAATGTGAAAATTATATCAAATT
1 AATATTCATTAATGAAA-TTTGAATTACATATAAAGTTTGTTTAATGTGAAAATTATATCAAATT
*
9764 AATATAAAATTTATTACTCTT-ATATTAATGT
65 AATATAAAATTTATTACTTTTAATATTAATGT
* *
9795 AATATTCATTAATGAAATATGAATTACATATAAAGTTTGTTTAATGTGAAAATTTTATCAAATTA
1 AATATTCATTAATGAAATTTGAATTACATATAAAGTTTGTTTAATGTGAAAATTATATCAAATTA
9860 ATATAAAATTTATT-CTTTTTAATATTAATGT
66 ATATAAAATTTATTAC-TTTTAATATTAATGT
9891 AATATT
1 AATATT
9897 AAAAGCATAA
Statistics
Matches: 178, Mismatches: 5, Indels: 19
0.88 0.02 0.09
Matches are distributed among these distances:
90 33 0.19
91 36 0.20
92 16 0.09
93 2 0.01
94 20 0.11
95 55 0.31
96 16 0.09
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (96 bp):
AATATTCATTAATGAAATTTGAATTACATATAAAGTTTGTTTAATGTGAAAATTATATCAAATTA
ATATAAAATTTATTACTTTTAATATTAATGT
Found at i:12337 original size:15 final size:16
Alignment explanation
Indices: 12317--12346 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12307 TTAAAAAGAG
12317 TTTTATTG-TAACTAA
1 TTTTATTGATAACTAA
12332 TTTTATTGATAACTA
1 TTTTATTGATAACTA
12347 TAACATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTATTGATAACTAA
Done.