Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold780
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: 21948
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:6122 original size:10 final size:10
Alignment explanation
Indices: 6109--6147 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
6099 AGCTCACTTG
6109 AGCTCGTTTT
1 AGCTCGTTTT
*
6119 AGCTCGTTTG
1 AGCTCGTTTT
**
6129 AGCTCGAATT
1 AGCTCGTTTT
6139 AGCTCGTTT
1 AGCTCGTTT
6148 CACAGCCTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:6129 original size:20 final size:20
Alignment explanation
Indices: 6106--6147 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
6096 ATCAGCTCAC
**
6106 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGAATTAGCTCGT
6126 TTGAGCTCGAATTAGCTCGT
1 TTGAGCTCGAATTAGCTCGT
6146 TT
1 TT
6148 CACAGCCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGAATTAGCTCGT
Found at i:9328 original size:17 final size:18
Alignment explanation
Indices: 9303--9340 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9293 TTTCTTCAAC
* *
9303 TTCTTTTTCA-ATTTCTT
1 TTCTGTTTCACATTCCTT
9320 TTCTGTTTCACATTCCTT
1 TTCTGTTTCACATTCCTT
9338 TTC
1 TTC
9341 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.11, C:0.24, G:0.03, T:0.63
Consensus pattern (18 bp):
TTCTGTTTCACATTCCTT
Found at i:12867 original size:23 final size:24
Alignment explanation
Indices: 12817--12868 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
12807 GCAAACAAAC
*
12817 TTTTCTTTTTACTTTCTTTTCTTCT
1 TTTTCTTTTTAC-TTCTTTTCTTAT
12842 TTTTCTTTTTA-TTCTTTTAC-TAT
1 TTTTCTTTTTACTTCTTTT-CTTAT
12865 TTTT
1 TTTT
12869 GCATGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 13 0.52
24 1 0.04
25 11 0.44
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTTTTTACTTCTTTTCTTAT
Found at i:19324 original size:24 final size:25
Alignment explanation
Indices: 19271--19324 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
19261 AACAAATTCT
* *
19271 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
19296 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
19319 TTTTTT
1 TTTTTT
19325 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:21584 original size:12 final size:11
Alignment explanation
Indices: 21569--21614 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 11
21559 AGACCGTATG
21569 CAATTTTTTTT
1 CAATTTTTTTT
21580 GCAATTTTTTTT
1 -CAATTTTTTTT
21592 CAGA-TTTTTTT
1 CA-ATTTTTTTT
21603 CAACTTTTTTTT
1 CAA-TTTTTTTT
21615 AACAAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 11 0.35
12 19 0.61
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:21647 original size:27 final size:25
Alignment explanation
Indices: 21584--21647 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
21574 TTTTTTGCAA
*
21584 TTTTTTTTCAGATTTTTTTCAACTT
1 TTTTTTTTCAAATTTTTTTCAACTT
** *
21609 TTTTTTAACAAACTTTTTTTTTAACTT
1 TTTTTTTTCAAA--TTTTTTTCAACTT
21636 TTTTTTTTCAAA
1 TTTTTTTTCAAA
21648 GCTACGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 9 0.29
27 22 0.71
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTTTTTCAAATTTTTTTCAACTT
Done.