Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1567
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: 18418
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1961 original size:20 final size:20
Alignment explanation
Indices: 1938--1984 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1928 GGGTTAAGAT
*
1938 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
1958 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
1978 TGAGCTG
1 TGAGCTG
1985 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:3708 original size:48 final size:48
Alignment explanation
Indices: 3653--3758 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
3643 TTGTCTTTTC
*
3653 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
3701 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
3749 TTTCTTTTTC
1 TTTCTTTTTC
3759 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:6390 original size:20 final size:20
Alignment explanation
Indices: 6367--6413 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
6357 GGGTTAAGAT
*
6367 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
6387 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
6407 TGAGCTG
1 TGAGCTG
6414 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:6801 original size:9 final size:9
Alignment explanation
Indices: 6787--6820 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
6777 GAATTTCGTA
*
6787 TTTTTTGAT
1 TTTTTTGAC
6796 TTTTTTGAC
1 TTTTTTGAC
6805 TTTTTTGAC
1 TTTTTTGAC
6814 TATTTTT
1 T-TTTTT
6821 TTGCGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:9224 original size:20 final size:19
Alignment explanation
Indices: 9201--9265 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
9191 AAGCTCAAAC
9201 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
9221 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
9241 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
9261 GAGCT
1 GAGCT
9266 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:11079 original size:33 final size:33
Alignment explanation
Indices: 11041--11103 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
11031 GATTACTCAC
11041 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
11074 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
11104 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:11130 original size:21 final size:21
Alignment explanation
Indices: 11101--11156 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
11091 CAAGCTCTCT
*
11101 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
11122 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
11143 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
11157 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:11149 original size:14 final size:14
Alignment explanation
Indices: 11100--11156 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
11090 TCAAGCTCTC
11100 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
11113 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
11127 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
11141 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
11155 TT
1 TT
11157 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:11237 original size:6 final size:6
Alignment explanation
Indices: 11118--11215 Score: 70
Period size: 6 Copynumber: 15.8 Consensus size: 6
11108 TCTTTTTTCG
* * * **
11118 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
11169 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTT
11216 GTTTTCTTTC
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
6 55 0.82
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:12311 original size:29 final size:28
Alignment explanation
Indices: 12257--12312 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
12247 TTAAACTTGA
*
12257 TTTTTTTGCTCACCTTTTTTTTCTTTTCT
1 TTTTTTTGCTCA-CTTTTTTTACTTTTCT
12286 TTTTTTTGCTCGA-TTTTTTTCACTTTT
1 TTTTTTTGCTC-ACTTTTTTT-ACTTTT
12313 TTTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.29
29 16 0.67
30 1 0.04
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (28 bp):
TTTTTTTGCTCACTTTTTTTACTTTTCT
Done.