Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1275
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: 25621
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:2437 original size:20 final size:20
Alignment explanation
Indices: 2412--2466 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2402 TGTGGTTCAA
*
2412 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
2432 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
2452 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
2467 TTTTAACTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:5598 original size:39 final size:39
Alignment explanation
Indices: 5514--5624 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
5504 AGATACTAAT
** *
5514 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
5554 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
5594 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
5625 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:13453 original size:39 final size:39
Alignment explanation
Indices: 13369--13479 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 39
13359 AGATACTAAT
** *
13369 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA
* **
13409 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA
* *
13449 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
13480 GAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
39 25 0.42
40 35 0.58
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Found at i:15806 original size:56 final size:56
Alignment explanation
Indices: 15701--15807 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
15691 ATTAATGCCA
* * * *
15701 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAATATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
15757 TCCATACATGG-GAATATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAATATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
15808 CAGCAAGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 22 0.48
56 24 0.52
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAATATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:16456 original size:20 final size:20
Alignment explanation
Indices: 16431--16485 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
16421 ACGAGTTAAA
* *
16431 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
16451 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
16471 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
16486 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:17718 original size:4 final size:4
Alignment explanation
Indices: 17711--17735 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17701 AAAGTTTTTT
17711 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
17736 ATTCAGTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:20101 original size:13 final size:12
Alignment explanation
Indices: 20071--20124 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
20061 AATGTGAAAC
*
20071 AAAAAGAAATTG
1 AAAAAGAAGTTG
20083 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
20095 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
20107 AAAATG-AGTT-
1 AAAAAGAAGTTG
20117 AAAAAGAA
1 AAAAAGAA
20125 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 7 0.21
11 4 0.12
12 16 0.47
13 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:24825 original size:56 final size:55
Alignment explanation
Indices: 24709--24826 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
24699 TGCATGCTTT
* * * *
24709 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
24763 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
24819 CATTAAAT
1 CATTAAAT
24827 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:25474 original size:20 final size:20
Alignment explanation
Indices: 25449--25503 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
25439 ACGAGTTAAA
* *
25449 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
25469 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
25489 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
25504 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Done.