Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold695
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: 19613
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:820 original size:23 final size:25
Alignment explanation
Indices: 785--868 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 25
775 ATAAAAAAAT
785 AATATAATATAAATTATTAAAATATTAA
1 AATATAA-ATAAA-TA-TAAAATATTAA
* *
813 AATTTAAATAAATATAAAATATTTAT
1 AATATAAATAAATATAAAATA-TTAA
* *
839 AATAATACATAAATATATAA-ATTAA
1 AAT-ATAAATAAATATAAAATATTAA
*
864 TATAT
1 AATAT
869 GGACAAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 2 0.04
25 12 0.26
26 9 0.19
27 18 0.38
28 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATAAATAAATATAAAATATTAA
Found at i:1088 original size:16 final size:17
Alignment explanation
Indices: 1069--1102 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1059 ATATTATTTT
1069 TAAATTATAAT-TAATA
1 TAAATTATAATATAATA
*
1085 TAAATTTTAATATAATA
1 TAAATTATAATATAATA
1102 T
1 T
1103 GATATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTATAATATAATA
Found at i:3873 original size:28 final size:33
Alignment explanation
Indices: 3795--3879 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 33
3785 ATAATTTAAA
*
3795 ATATATTAAAATATTAA-TAATTATTTATTTAT
1 ATATATTTAAATATTAATTAATTATTTATTTAT
*
3827 ATATATTTATAA-ATAAATTAA-TA-TT-TTT-T
1 ATATATTTA-AATATTAATTAATTATTTATTTAT
3856 AT-TATTTAAATATTAATTTAATTA
1 ATATATTTAAATATTAA-TTAATTA
3880 ACCTAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 2 0.04
28 10 0.22
29 7 0.16
30 5 0.11
31 2 0.04
32 14 0.31
33 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
ATATATTTAAATATTAATTAATTATTTATTTAT
Found at i:4068 original size:7 final size:7
Alignment explanation
Indices: 4030--4090 Score: 50
Period size: 7 Copynumber: 7.9 Consensus size: 7
4020 AAAAAATCAT
4030 AATTTAAA
1 AATTT-AA
*
4038 AATCTAAA
1 AAT-TTAA
*
4046 AAATTATA
1 AATTTA-A
4054 AATATTAA
1 AAT-TTAA
4062 AATTTAA
1 AATTTAA
4069 AATTTAA
1 AATTTAA
4076 AATTATTAA
1 AA-T-TTAA
4085 AATTTA
1 AATTTA
4091 CTTTTTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
7 18 0.41
8 16 0.36
9 10 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (7 bp):
AATTTAA
Found at i:4070 original size:23 final size:23
Alignment explanation
Indices: 4044--4090 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
4034 TAAAAATCTA
4044 AAAAATTATAAA-TATTAAAATTT
1 AAAAATTA-AAATTATTAAAATTT
*
4067 AAAATTTAAAATTATTAAAATTT
1 AAAAATTAAAATTATTAAAATTT
4090 A
1 A
4091 CTTTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATTAAAATTATTAAAATTT
Found at i:4086 original size:16 final size:16
Alignment explanation
Indices: 4045--4090 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
4035 AAAAATCTAA
4045 AAAATTA-T-AAATATT
1 AAAATTATTAAAAT-TT
4060 AAAA-T-TTAAAATTT
1 AAAATTATTAAAATTT
4074 AAAATTATTAAAATTT
1 AAAATTATTAAAATTT
4090 A
1 A
4091 CTTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.30
15 9 0.33
16 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATTATTAAAATTT
Found at i:4839 original size:23 final size:22
Alignment explanation
Indices: 4798--4859 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 22
4788 ATATAATTAA
4798 ATATGATATAAATATAATAAAATAT
1 ATAT-ATATAAATA-AATAAAAT-T
4823 ATATATATAAATAAATAAAATT
1 ATATATATAAATAAATAAAATT
4845 ATA-ATATAAA-AAATA
1 ATATATATAAATAAATA
4860 TATGATTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.14
21 7 0.19
22 4 0.11
23 8 0.22
24 9 0.24
25 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATATATAAATAAATAAAATT
Found at i:4853 original size:21 final size:22
Alignment explanation
Indices: 4785--4854 Score: 90
Period size: 21 Copynumber: 3.2 Consensus size: 22
4775 GTGATAATTG
* *
4785 TAAATATAATTAAA-TATGATA
1 TAAATATAATAAAATTATAATA
4806 TAAATATAATAAAATATATATATA
1 TAAATATAATAAAAT-TATA-ATA
4830 TAAATA-AATAAAATTATAATA
1 TAAATATAATAAAATTATAATA
4851 TAAA
1 TAAA
4855 AAATATATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
21 20 0.45
22 4 0.09
23 11 0.25
24 9 0.20
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (22 bp):
TAAATATAATAAAATTATAATA
Found at i:4867 original size:22 final size:21
Alignment explanation
Indices: 4798--4865 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 21
4788 ATATAATTAA
4798 ATATGATATAAATATAATAAAAT
1 ATATGATAT-AATATAA-AAAAT
*
4821 ATAT-ATAT-ATA-AATAAAT
1 ATATGATATAATATAAAAAAT
*
4839 A-A-AATTATAATATAAAAAAT
1 ATATGA-TATAATATAAAAAAT
4859 ATATGAT
1 ATATGAT
4866 TACACATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
17 2 0.06
18 8 0.22
19 5 0.14
20 10 0.28
21 2 0.06
22 5 0.14
23 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
ATATGATATAATATAAAAAAT
Found at i:5060 original size:6 final size:6
Alignment explanation
Indices: 5051--5091 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
5041 ATATATTATA
*
5051 AAAATT AAAATT AAAAAAT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT -AAAATT AAAATT AAAATT AAAATT AAAA
5092 CTTGTTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:6176 original size:2 final size:2
Alignment explanation
Indices: 6169--6219 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6159 ATTTGTAACT
6169 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6211 TA TA TA TA T
1 TA TA TA TA T
6220 TTCTTCTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11554 original size:19 final size:21
Alignment explanation
Indices: 11505--11557 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
11495 TATTTTTATT
11505 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
11526 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
11546 -AAATTTTAATAT
1 TAAATTTTAATAT
11558 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 11 0.38
22 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:11955 original size:13 final size:13
Alignment explanation
Indices: 11939--11969 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11929 AAATTATATT
11939 TATTTTAAAAATA
1 TATTTTAAAAATA
*
11952 TATTTTAAAATTA
1 TATTTTAAAAATA
11965 TATTT
1 TATTT
11970 CAGTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTAAAAATA
Found at i:12747 original size:19 final size:21
Alignment explanation
Indices: 12696--12741 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12686 TAAGAATTTT
* * *
12696 TTAATATTTTAATTTAAGAGA
1 TTAACATTTTATTTTAAGAAA
12717 TTAACATTTTATTTTAAGAAA
1 TTAACATTTTATTTTAAGAAA
12738 TTAA
1 TTAA
12742 TTTTATCACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (21 bp):
TTAACATTTTATTTTAAGAAA
Found at i:12876 original size:20 final size:19
Alignment explanation
Indices: 12843--12913 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 19
12833 TTAAATTATT
12843 TTATTTAATT-TAAATTTA
1 TTATTTAATTATAAATTTA
12861 TTATTTAATTACTAAATAATATA
1 TTATTTAATTA-TAAAT--T-TA
* *
12884 TTTAATTTAATTATAAAATAA
1 -TT-ATTTAATTATAAATTTA
12905 TTATTTAAT
1 TTATTTAAT
12914 ACTTATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
18 10 0.23
19 7 0.16
20 7 0.16
21 1 0.02
22 2 0.05
23 2 0.05
24 6 0.14
25 9 0.20
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (19 bp):
TTATTTAATTATAAATTTA
Found at i:12892 original size:25 final size:24
Alignment explanation
Indices: 12836--12913 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 24
12826 TTATGATTTA
*
12836 AATTATTTTATTTAATT-T-AAAT
1 AATTATTTAATTTAATTATAAAAT
12858 --TTA-TT-ATTTAATTACT-AAAT
1 AATTATTTAATTTAATTA-TAAAAT
12878 AATATATTTAATTTAATTATAAAAT
1 AAT-TATTTAATTTAATTATAAAAT
12903 AATTATTTAAT
1 AATTATTTAAT
12914 ACTTATAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
18 8 0.17
19 2 0.04
20 8 0.17
22 1 0.02
23 2 0.04
24 11 0.23
25 16 0.33
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATTTAATTTAATTATAAAAT
Found at i:14748 original size:16 final size:16
Alignment explanation
Indices: 14702--14751 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
14692 TTTAGCATTT
14702 AATTTATAATT-AAATA
1 AATTT-TAATTAAAATA
*
14718 AATTTTAA-AATAAATA
1 AATTTTAATTA-AAATA
14734 AATTTTAATTAAAATA
1 AATTTTAATTAAAATA
14750 AA
1 AA
14752 AATTTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 3 0.10
16 25 0.86
17 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTAATTAAAATA
Found at i:15510 original size:18 final size:17
Alignment explanation
Indices: 15478--15517 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
15468 ATTTAAACTC
*
15478 AAAATAATTAAAATTAA
1 AAAATAATAAAAATTAA
*
15495 AAAATATATAAAAATTTA
1 AAAATA-ATAAAAATTAA
15513 AAAAT
1 AAAAT
15518 TCAAATTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATAATAAAAATTAA
Found at i:15749 original size:2 final size:2
Alignment explanation
Indices: 15742--15781 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
15732 AAAATCTATC
*
15742 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15782 AACAAAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.