Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3087
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: 50795
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:13576 original size:43 final size:44
Alignment explanation
Indices: 13420--13577 Score: 134
Period size: 43 Copynumber: 3.7 Consensus size: 44
13410 ATGTGTTATT
* *
13420 GTGTAAGACCACATTTGGGAC-GTTGGCATC-A-ACTTATGATTTAC
1 GTGTAAGACCACGTCTGGGACAGTTGGCATCGATA-TT-TGA-TTAC
* * * * *
13464 GTGTAAGACCATGTCTTGGACA-TCGACATCG-TATTTGATTTC
1 GTGTAAGACCACGTCTGGGACAGTTGGCATCGATATTTGATTAC
* *
13506 GTGTAAGACC-CTGTTTAGGACAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACAGTTGGCATCGATATTTGATTAC
*
13549 ATGTAAGACCACGTCTGGGA-AGTTGGCAT
1 GTGTAAGACCACGTCTGGGACAGTTGGCAT
13578 TGTATGAGCT
Statistics
Matches: 90, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
42 29 0.32
43 34 0.38
44 26 0.29
45 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (44 bp):
GTGTAAGACCACGTCTGGGACAGTTGGCATCGATATTTGATTAC
Found at i:14173 original size:10 final size:10
Alignment explanation
Indices: 14158--14182 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
14148 ATATGAAATG
14158 TGATGCAATA
1 TGATGCAATA
14168 TGATGCAATA
1 TGATGCAATA
14178 TGATG
1 TGATG
14183 TGTTTATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (10 bp):
TGATGCAATA
Found at i:14652 original size:13 final size:13
Alignment explanation
Indices: 14634--14667 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
14624 TCAGTTTCGA
14634 ACACGGGCTAGAC
1 ACACGGGCTAGAC
14647 ACACGGGCTAGAC
1 ACACGGGCTAGAC
14660 ACACGGGC
1 ACACGGGC
14668 ATTTGATTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.32, T:0.06
Consensus pattern (13 bp):
ACACGGGCTAGAC
Found at i:25719 original size:21 final size:21
Alignment explanation
Indices: 25656--25723 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
25646 GGGGTCTACC
**
25656 CGCCCATGTG-AAGGCCACACA
1 CGCCCATGTGAAAGG-GGCACA
*
25677 CGCCCGTGTGAAAGGGGCACA
1 CGCCCATGTGAAAGGGGCACA
*
25698 CGCCCATGTG-AAGAGGGTACA
1 CGCCCATGTGAAAG-GGGCACA
25719 CGCCC
1 CGCCC
25724 GTGTAAGTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.08
21 33 0.82
22 4 0.10
ACGTcount: A:0.25, C:0.34, G:0.31, T:0.10
Consensus pattern (21 bp):
CGCCCATGTGAAAGGGGCACA
Found at i:27045 original size:25 final size:25
Alignment explanation
Indices: 27017--27066 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27007 TTTGGCTTGG
* *
27017 CATTTACTAAGCAATGTCAGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
27042 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
27067 TAAATTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:28087 original size:21 final size:21
Alignment explanation
Indices: 28039--28080 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28029 TGCTTGAAAC
* * *
28039 GACATACGAGGTGCCTGATAT
1 GACACACGAGGTGCCTAAAAT
28060 GACACACGAGGTGCCTAAAAT
1 GACACACGAGGTGCCTAAAAT
28081 ACGACACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
GACACACGAGGTGCCTAAAAT
Found at i:28096 original size:23 final size:23
Alignment explanation
Indices: 28070--28123 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
28060 GACACACGAG
28070 GTGCCTAAAATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
* * *
28093 GTGCTTGATATACGACACATAAA
1 GTGCCTAAAATACGACACATAAA
28116 GTGCCTAA
1 GTGCCTAA
28124 TCAGCAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (23 bp):
GTGCCTAAAATACGACACATAAA
Found at i:34624 original size:61 final size:61
Alignment explanation
Indices: 34557--34695 Score: 187
Period size: 60 Copynumber: 2.3 Consensus size: 61
34547 ATTAGAGTTA
* *
34557 ATTGGGCCTTAGCCTATATCAATATTAATCTGGGCCATAGCCC-ATTAC-AGTATCAGAGTAT
1 ATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGT-TCAGA-TAT
* * *
34618 ATTGGGCC-TAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGTTGAGATAT
1 ATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTTCAGATAT
34678 ATTGGGCCTT-GCCCATAT
1 ATTGGGCCTTAGCCCATAT
34696 TAACATAGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
60 49 0.70
61 18 0.26
62 3 0.04
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (61 bp):
ATTGGGCCTTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATTACAAGTTCAGATAT
Found at i:34659 original size:28 final size:27
Alignment explanation
Indices: 34559--34659 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
34549 TAGAGTTAAT
* * *
34559 TGGGCCTTAGCCTATATCAATATTAATC
1 TGGGCC-TAGCCCATATCAGTATCAATC
*
34587 TGGGCCATAGCCCAT-TACAGTATCAGAGTATAT
1 TGGGCC-TAGCCCATAT-CAGTATC--A--AT-C
34620 TGGGCCTAGCCCATATCAGTATCAATC
1 TGGGCCTAGCCCATATCAGTATCAATC
34647 TGGGCCGTAGCCC
1 TGGGCC-TAGCCC
34660 TATTACAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
27 7 0.12
28 26 0.44
30 2 0.03
32 17 0.29
33 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (27 bp):
TGGGCCTAGCCCATATCAGTATCAATC
Found at i:42518 original size:39 final size:40
Alignment explanation
Indices: 42417--42679 Score: 308
Period size: 39 Copynumber: 6.7 Consensus size: 40
42407 TTGAATGATG
* *
42417 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
42456 ATCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
42497 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
42536 TCTGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
42575 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
42614 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
42653 AACCGGGCTATGTCCCGAAGGCGTTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
42680 AACGAGTAGC
Statistics
Matches: 198, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
39 111 0.56
40 75 0.38
41 11 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:42701 original size:79 final size:79
Alignment explanation
Indices: 42470--42712 Score: 260
Period size: 78 Copynumber: 3.1 Consensus size: 79
42460 GGACTAAGAT
* * * ** *
42470 CCGAAGGCATTTGTGTGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
* * *
42535 TTCTGGGCTAAG-C
66 ATCCGGGTTAAGTC
* * **
42548 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
42613 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
42627 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCGTTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* * *
42690 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAGTC
42706 CCGAAGG
1 CCGAAGG
42713 TACGTGATTT
Statistics
Matches: 146, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
78 74 0.51
79 48 0.33
80 24 0.16
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Done.