Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1981
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: 4592
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Found at i:777 original size:15 final size:15
Alignment explanation
Indices: 757--824 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 15
747 ATTGAGCGTG
757 ATATAAAGAAATAT-A
1 ATATAAA-AAATATAA
772 ATATAATAAAATATAA
1 ATATAA-AAAATATAA
788 ATATAAATATAA-ATAA
1 ATATAAA-A-AATATAA
804 ATATAATAAAAATATAA
1 ATAT-A-AAAAATATAA
821 ATAT
1 ATAT
825 TTTAAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.28
16 19 0.41
17 12 0.26
18 2 0.04
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (15 bp):
ATATAAAAAATATAA
Found at i:779 original size:10 final size:10
Alignment explanation
Indices: 766--845 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
756 GATATAAAGA
766 AATATAATAT
1 AATATAATAT
*
776 AATAAAATAT
1 AATATAATAT
786 AAATATAAATAT
1 -AATAT-AATAT
798 AA-ATAAATAT
1 AATAT-AATAT
*
808 AATAAAAATAT
1 AAT-ATAATAT
* *
819 AA-ATATTTT
1 AATATAATAT
*
828 AAAATTAATAT
1 AATA-TAATAT
839 AATATAA
1 AATATAA
846 ATTATTAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
9 6 0.11
10 23 0.42
11 20 0.36
12 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AATATAATAT
Found at i:790 original size:21 final size:22
Alignment explanation
Indices: 765--820 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
755 TGATATAAAG
765 AAATAT-AATATAATAAAATAT
1 AAATATAAATATAATAAAATAT
786 AAATATAAATATAA-ATAAATAT
1 AAATATAAATATAATA-AAATAT
*
808 -AATAAAAATATAA
1 AAATATAAATATAA
821 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATATAAATATAATAAAATAT
Found at i:791 original size:6 final size:6
Alignment explanation
Indices: 765--824 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
755 TGATATAAAG
765 AAATAT -AATAT -AATA- AAATAT AAATAT AAATAT -AA-AT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
*
808 -AATAA AAATAT AAATAT
1 AAATAT AAATAT AAATAT
825 TTTAAAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
4 2 0.04
5 21 0.45
6 24 0.51
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:832 original size:27 final size:27
Alignment explanation
Indices: 765--824 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
755 TGATATAAAG
* *
765 AAATAT-AATATAATAAAATATAAATAT
1 AAATATAAATA-AATATAATAAAAATAT
792 AAATATAAATAAATATAATAAAAATAT
1 AAATATAAATAAATATAATAAAAATAT
819 AAATAT
1 AAATAT
825 TTTAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATATAAATAAATATAATAAAAATAT
Found at i:860 original size:32 final size:31
Alignment explanation
Indices: 765--862 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
755 TGATATAAAG
**
765 AAATATAATATAAT-AAAATATAAATATAAATA
1 AAATA-AATATAATAAAAATATAAATAT-TTTA
797 TAAATAAATATAATAAAAATATAAATATTTTA
1 -AAATAAATATAATAAAAATATAAATATTTTA
* * *
829 AAATTAATATAATATAAATTATTAATATTTTA
1 AAATAAATATAATA-AAAATATAAATATTTTA
861 AA
1 AA
863 TTTTATAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
31 13 0.22
32 27 0.47
33 18 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATAAATATAATAAAAATATAAATATTTTA
Found at i:888 original size:32 final size:33
Alignment explanation
Indices: 798--888 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 33
788 ATATAAATAT
* *
798 AAATAAATATAATAAAAATA--TAAATATTTTA
1 AAATTAATATAAAAAAAATATTTAAATATTTTA
* *
829 AAATTAATATAATATAAAT-TATT-AATATTTTA
1 AAATTAATATAAAAAAAATAT-TTAAATATTTTA
* *
861 AATTTTATA-AAAAAAAATATTTAAATAT
1 AAATTAATATAAAAAAAATATTTAAATAT
889 AATTATAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.53
32 22 0.45
33 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATTAATATAAAAAAAATATTTAAATATTTTA
Found at i:4108 original size:16 final size:16
Alignment explanation
Indices: 4087--4119 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4077 CAATAAACAA
4087 GGAAATTGACACATTT
1 GGAAATTGACACATTT
4103 GGAAATTGACACATTT
1 GGAAATTGACACATTT
4119 G
1 G
4120 ACTCAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (16 bp):
GGAAATTGACACATTT
Done.