Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1551
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: 11469
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Found at i:2819 original size:21 final size:21
Alignment explanation
Indices: 2782--2848 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
2772 ATTCAATGAG
2782 ATGC-TGAAA-AT-ATAAAAA
1 ATGCATGAAACATAATAAAAA
2800 ATGCATGAAACATAATAAAAA
1 ATGCATGAAACATAATAAAAA
2821 ATGCATGAAACATAATAAAAA
1 ATGCATGAAACATAATAAAAA
2842 ATGCATG
1 ATGCATG
2849 GTCAAAGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.09
19 5 0.11
20 2 0.04
21 35 0.76
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (21 bp):
ATGCATGAAACATAATAAAAA
Found at i:3737 original size:40 final size:39
Alignment explanation
Indices: 3689--3766 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
3679 GGTAAAAAGA
* *
3689 CATAATGTATTGATACATTGAAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
*
3728 CATACATGTATCGATACATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3767 CTGGGTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3781 original size:24 final size:20
Alignment explanation
Indices: 3692--3766 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
3682 AAAAAGACAT
* *
3692 AATGTATTGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
3712 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
3732 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
3752 AATGTATCGATACAT
1 AATGTATCGATACAT
3767 CTGGGTAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:5466 original size:23 final size:23
Alignment explanation
Indices: 5440--5484 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5430 GTATTAAAAT
* *
5440 TTAAATATCAAAATTATTATATA
1 TTAAATATAAAAATAATTATATA
* *
5463 TTAATTTTAAAAATAATTATAT
1 TTAAATATAAAAATAATTATAT
5485 TAATTAATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAATATAAAAATAATTATATA
Found at i:5724 original size:22 final size:22
Alignment explanation
Indices: 5698--5743 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
5688 AATTTTATTT
*
5698 ATAAAAAAGTTATTAAT-TTAAA
1 ATAAAAAA-TTATAAATATTAAA
5720 ATAAAAAATTATAAATATTAAA
1 ATAAAAAATTATAAATATTAAA
5742 AT
1 AT
5744 TTAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAAAAAATTATAAATATTAAA
Found at i:5731 original size:21 final size:21
Alignment explanation
Indices: 5698--5769 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
5688 AATTTTATTT
5698 ATAAAAAAGTTATTAATTTAAA
1 ATAAAAAA-TTATTAATTTAAA
*
5720 ATAAAAAATTATAAATATTAAA
1 ATAAAAAATTATTAAT-TTAAA
* * *
5742 ATTTAAATATTATT-TTTTAAAA
1 A-TAAAAAATTATTAATTT-AAA
5764 ATAAAA
1 ATAAAA
5770 GTATGAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.32
22 19 0.46
23 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAAAAAATTATTAATTTAAA
Found at i:5752 original size:14 final size:15
Alignment explanation
Indices: 5724--5753 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5714 TTTAAAATAA
5724 AAAATTATAAATATT
1 AAAATTATAAATATT
5739 AAAATT-TAAATATT
1 AAAATTATAAATATT
5753 A
1 A
5754 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:7132 original size:28 final size:27
Alignment explanation
Indices: 7077--7147 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
7067 GTCATTTATT
7077 TGTTTGTCAAAAATGGTGATTATTTTG
1 TGTTTGTCAAAAATGGTGATTATTTTG
7104 TGTTTGTCAAAAATGGTGATT-TCCTTTG
1 TGTTTGTCAAAAATGGTGATTAT--TTTG
* *
7132 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
7148 AAGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGATTATTTTG
Found at i:9752 original size:21 final size:22
Alignment explanation
Indices: 9723--9768 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
9713 TGTTCAGACA
** *
9723 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
9745 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
9766 AGT
1 AGT
9769 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Done.