Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2125
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: 15169
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:83 original size:28 final size:28
Alignment explanation
Indices: 26--89 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
16 AATAACATTA
*
26 TTAAAGTT-TATTATAATGTTAATAGGTT
1 TTAAA-TTATATTATAATATTAATAGGTT
* * **
54 TTTAATTATATTATAATATTGATATTTT
1 TTAAATTATATTATAATATTAATAGGTT
82 TTAAATTA
1 TTAAATTA
90 ACAAAAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (28 bp):
TTAAATTATATTATAATATTAATAGGTT
Found at i:113 original size:18 final size:19
Alignment explanation
Indices: 86--125 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
76 TATTTTTTAA
*
86 ATTAACAAAA-ATTATATT
1 ATTAACAAAAGATAATATT
*
104 ATTAATAAAAGATAATATT
1 ATTAACAAAAGATAATATT
123 ATT
1 ATT
126 TTAGTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAACAAAAGATAATATT
Found at i:4985 original size:16 final size:17
Alignment explanation
Indices: 4948--4984 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
4938 TAATTGTGTA
4948 TAAAATAAAATTATATT
1 TAAAATAAAATTATATT
4965 TAAAAT-AAA-TATATT
1 TAAAATAAAATTATATT
4980 TAAAA
1 TAAAA
4985 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAAAATTATATT
Found at i:6754 original size:33 final size:32
Alignment explanation
Indices: 6691--6755 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
6681 TTTTTATTTT
6691 TTAAATATATTTTTTTAATTTAATTTTTAATAA
1 TTAAATATATTTTTTTAATTT-ATTTTTAATAA
*
6724 TTAAATATATTTTTATTACTTT-TTTGTTAATA
1 TTAAATATATTTTT-TTAATTTATTT-TTAATA
6756 TTCTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.10
33 20 0.69
34 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (32 bp):
TTAAATATATTTTTTTAATTTATTTTTAATAA
Found at i:6851 original size:17 final size:16
Alignment explanation
Indices: 6816--6858 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
6806 TTAATAACTA
6816 ATAAAATAAAATTATT
1 ATAAAATAAAATTATT
6832 ATAAAATATAAA-T-TT
1 ATAAAATA-AAATTATT
*
6847 ATATAATAAAAT
1 ATAAAATAAAAT
6859 ACTTTATTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 3 0.12
15 9 0.38
16 9 0.38
17 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAAATAAAATTATT
Found at i:6962 original size:18 final size:18
Alignment explanation
Indices: 6919--6962 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
6909 AAGGCTCTAA
6919 CTTATTTTTTAAATAAAT
1 CTTATTTTTTAAATAAAT
* * *
6937 TTTATTTTTT-ACTCAAT
1 CTTATTTTTTAAATAAAT
6954 CTTATTTTT
1 CTTATTTTT
6963 AAGATTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTATTTTTTAAATAAAT
Found at i:7008 original size:19 final size:19
Alignment explanation
Indices: 6984--7040 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 19
6974 ATTTTGTTTC
6984 AAATTTTTTAAATATT-AAT
1 AAATTTTTTAAAT-TTAAAT
7003 AAA-TTTTTAAATTTAAAT
1 AAATTTTTTAAATTTAAAT
*
7021 AAATAATTTTTAATTTTAAA
1 AAAT--TTTTTAAATTTAAA
7041 GTACAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.06
18 15 0.45
19 3 0.09
21 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTTTTAAATTTAAAT
Found at i:7030 original size:21 final size:23
Alignment explanation
Indices: 6990--7040 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
6980 TTTCAAATTT
6990 TTTAAATATTAATAAATTTTTAAA
1 TTTAAATA-TAATAAATTTTTAAA
*
7014 TTTAAATA-AAT-AATTTTTAAT
1 TTTAAATATAATAAATTTTTAAA
7035 TTTAAA
1 TTTAAA
7041 GTACAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 15 0.58
22 3 0.12
24 8 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAAATATAATAAATTTTTAAA
Done.