Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1713
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: 18346
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:5562 original size:21 final size:22
Alignment explanation
Indices: 5544--5594 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
5534 ATTCTAATTA
5544 TATTTTGAAATAAAATAATTAAAT
1 TATTTTGAAA-AAAATAATT-AAT
*
5568 TATTTTGAAAAAAATATTTAAT
1 TATTTTGAAAAAAATAATTAAT
5590 CTATT
1 -TATT
5595 GTTAGTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 3 0.12
23 12 0.48
24 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (22 bp):
TATTTTGAAAAAAATAATTAAT
Found at i:5594 original size:23 final size:24
Alignment explanation
Indices: 5544--5588 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
5534 ATTCTAATTA
5544 TATTTTGAAATAAAATAATTAAAT
1 TATTTTGAAATAAAATAATTAAAT
*
5568 TATTTTGAAA-AAAATATTTAA
1 TATTTTGAAATAAAATAATTAA
5589 TCTATTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TATTTTGAAATAAAATAATTAAAT
Found at i:7185 original size:7 final size:7
Alignment explanation
Indices: 7173--7199 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
7163 AGTTAGATAG
7173 AAAATTC
1 AAAATTC
7180 AAAATTC
1 AAAATTC
7187 AAAATTC
1 AAAATTC
7194 AAAATT
1 AAAATT
7200 TGAAATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (7 bp):
AAAATTC
Found at i:8590 original size:24 final size:25
Alignment explanation
Indices: 8560--8652 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 25
8550 TAGCTACAAA
* *
8560 TTTTGACAAACAACATG-CCACCAT
1 TTTTGACAAACAAAAAGACCACCAT
*
8584 TTTTGACAAATAAAAAGAAACCACCAT
1 TTTTGACAAACAAAAAG--ACCACCAT
* * *
8611 TTTTGACAAATACAAAGTAACCACAAT
1 TTTTGACAAACAAAAAG--ACCACCAT
*
8638 TTTTTACAAACAAAA
1 TTTTGACAAACAAAA
8653 GGTGGTTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.25
27 43 0.75
ACGTcount: A:0.47, C:0.20, G:0.06, T:0.26
Consensus pattern (25 bp):
TTTTGACAAACAAAAAGACCACCAT
Found at i:8615 original size:27 final size:27
Alignment explanation
Indices: 8577--8652 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
8567 AAACAACATG
8577 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAATAAAAAGAAA
* *
8604 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAATAAAAAGAAA
* * *
8631 CCACAATTTTTTACAAACAAAA
1 CCACCATTTTTGACAAATAAAA
8653 GGTGGTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (27 bp):
CCACCATTTTTGACAAATAAAAAGAAA
Found at i:10568 original size:21 final size:22
Alignment explanation
Indices: 10530--10575 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
10520 ATCTATTGAA
* **
10530 ACTCCACCTATTTTGGAGTA-T
1 ACTCCACCTACTGCGGAGTACT
10551 ACTCCACCTACTGCGGAGTACT
1 ACTCCACCTACTGCGGAGTACT
10573 ACT
1 ACT
10576 TGTCTGAACA
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:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (22 bp):
ACTCCACCTACTGCGGAGTACT
Found at i:13197 original size:27 final size:27
Alignment explanation
Indices: 13127--13200 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
13117 AACAATATGT
*
13127 CATCATTTTTGACAAATAAAAAGAAAC
1 CATCATTTTTGACAAACAAAAAGAAAC
* * * * *
13154 CATTATTTTTTATAAACATAAAGTAAC
1 CATCATTTTTGACAAACAAAAAGAAAC
13181 CATCATTTTTGACAAACAAA
1 CATCATTTTTGACAAACAAA
13201 TGGTGGTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.32
Consensus pattern (27 bp):
CATCATTTTTGACAAACAAAAAGAAAC
Found at i:15133 original size:18 final size:18
Alignment explanation
Indices: 15110--15144 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15100 ATAGTCTTTG
15110 TTATTTT-ATTTCTCCATT
1 TTATTTTAATTT-TCCATT
15128 TTATTTTAATTTTCCAT
1 TTATTTTAATTTTCCAT
15145 GAATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (18 bp):
TTATTTTAATTTTCCATT
Found at i:15262 original size:18 final size:18
Alignment explanation
Indices: 15239--15274 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
15229 TAACACAAAA
*
15239 ATTATATAAAATTAATTT
1 ATTATATAAAATCAATTT
15257 ATTATATAAAATCAATTT
1 ATTATATAAAATCAATTT
15275 GTTAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATATAAAATCAATTT
Found at i:15283 original size:18 final size:18
Alignment explanation
Indices: 15239--15283 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
15229 TAACACAAAA
* *
15239 ATTATATAAAATTAATTT
1 ATTAAATAAAATCAATTT
*
15257 ATTATATAAAATCAATTT
1 ATTAAATAAAATCAATTT
*
15275 GTTAAATAA
1 ATTAAATAA
15284 TTGAATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTAAATAAAATCAATTT
Done.