Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2093
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: 11776
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:737 original size:13 final size:13
Alignment explanation
Indices: 719--744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
709 CAATTTTTTG
719 TGTATCGATACAT
1 TGTATCGATACAT
732 TGTATCGATACAT
1 TGTATCGATACAT
745 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:808 original size:20 final size:20
Alignment explanation
Indices: 783--857 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
773 CTGCCAAGAA
783 ATGTATCGATACATCTTTTT
1 ATGTATCGATACATCTTTTT
****
803 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCT-TTTT
823 ATGTATCGATACATCTTTTT
1 ATGTATCGATACATCTTTTT
843 CATGTATCGATACAT
1 -ATGTATCGATACAT
858 TGCAACATGT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.02
20 28 0.64
21 15 0.34
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATCTTTTT
Found at i:860 original size:41 final size:40
Alignment explanation
Indices: 783--875 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 40
773 CTGCCAAGAA
783 ATGTATCGATACATCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTATGTATCGATACATTGCAAC
823 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTT-ATGTATCGATACATTGCAAC
864 ATGTATCGATAC
1 ATGTATCGATAC
876 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 20 0.38
41 32 0.62
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (40 bp):
ATGTATCGATACATCTTTTTATGTATCGATACATTGCAAC
Found at i:868 original size:20 final size:20
Alignment explanation
Indices: 803--875 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
793 ACATCTTTTT
803 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
823 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
844 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
864 ATGTATCGATAC
1 ATGTATCGATAC
876 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:5591 original size:46 final size:48
Alignment explanation
Indices: 5478--5595 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
5468 TAACTTGTTG
* * * * *
5478 CTTTTGCACAAACAAAGATACAAATTCTTCTCACAAAATAACTTGTAA
1 CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATAA
* * *
5526 CTTTTGCACAGATCAAGTTACAAACTCTCCTCAC-AAA-AAGTTATATA
1 CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATA-A
5573 -TTTTGCACAAATAAAGTTACAAA
1 CTTTTGCACAAATAAAGTTACAAA
5596 TCCTTTAACA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 27 0.46
47 4 0.07
48 28 0.47
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (48 bp):
CTTTTGCACAAATAAAGTTACAAACTCTCCTCACAAAATAACTTATAA
Found at i:5623 original size:46 final size:46
Alignment explanation
Indices: 5468--5641 Score: 129
Period size: 46 Copynumber: 3.7 Consensus size: 46
5458 AACACTAATT
* * * * *
5468 TAACTTGTTGCTTTTGCACAAACAAAGATACAAATTCTTCTCACAAAA
1 TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTT-TCAC-AAA
* * * * *
5516 TAACTTGTAACTTTTGCACAGATCAAGTTACAAA-CTCTCCTCACAAA
1 TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATC-CT-TTCACAAA
* ** *
5563 -AAGTTA-TATATTTTGCACAAATAAAGTTACAAATCCTTTAACAAA
1 TAA-CTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTTTCACAAA
* *
5608 TAACTAGTAGCTTTTGTATGAAATAAAGTTACAA
1 TAACTAGTAGCTTTTGCA-CAAATAAAGTTACAA
5642 TTTTTTTAAA
Statistics
Matches: 98, Mismatches: 21, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
45 8 0.08
46 37 0.38
47 19 0.19
48 34 0.35
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (46 bp):
TAACTAGTAGCTTTTGCACAAATAAAGTTACAAATCCTTTCACAAA
Found at i:9441 original size:15 final size:15
Alignment explanation
Indices: 9421--9450 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9411 ATGTAAGAAA
9421 CACTTAATCACTTTT
1 CACTTAATCACTTTT
9436 CACTTAATCACTTTT
1 CACTTAATCACTTTT
9451 AAAATGCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CACTTAATCACTTTT
Found at i:10601 original size:20 final size:19
Alignment explanation
Indices: 10578--10623 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
10568 ATTTGTATGG
*
10578 ATACATGTCATAATGTATCA
1 ATACATG-CACAATGTATCA
*
10598 ATACAATGCACAATGTATCG
1 ATAC-ATGCACAATGTATCA
10618 ATACAT
1 ATACAT
10624 TATGTGAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
ATACATGCACAATGTATCA
Done.