Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2372
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: 9555
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Found at i:1049 original size:26 final size:27
Alignment explanation
Indices: 1020--1076 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
1010 GTTAATAATT
*
1020 TATTTT-ATTAATTTTAATA-TATATTA
1 TATTTTAATT-ATTTTAATATTATATAA
*
1046 TATTTTAATTATTTTTATATTATATAA
1 TATTTTAATTATTTTAATATTATATAA
1073 TATT
1 TATT
1077 ACATTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTTAATTATTTTAATATTATATAA
Found at i:1067 original size:11 final size:12
Alignment explanation
Indices: 1039--1070 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1029 AATTTTAATA
1039 TATATTATATTT
1 TATATTATATTT
1051 TA-ATTAT-TTT
1 TATATTATATTT
1061 TATATTATAT
1 TATATTATAT
1071 AATATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.28
11 10 0.56
12 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTATATTT
Found at i:3838 original size:25 final size:25
Alignment explanation
Indices: 3804--3872 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
3794 TAAGATAATT
3804 AAATATTTTTATATTATATATATTTA
1 AAATA-TTTTATATTATATATATTTA
* *
3830 AAATATTTTATATTAATAAATTTTTA
1 AAATATTTTATATT-ATATATATTTA
*
3856 AAA-AATTTATATTATAT
1 AAATATTTTATATTATAT
3873 TTTAATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.08
25 18 0.47
26 17 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATATTTTATATTATATATATTTA
Found at i:3868 original size:32 final size:31
Alignment explanation
Indices: 3832--3919 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
3822 TATATTTAAA
3832 ATATTTTATATTAATAAATTTTTAAAA-AATTT
1 ATATTTTATATTAAT-AATTTTTAAAATAA-TT
* * *
3864 ATATTATATTTTAATTATTTTTAAAATAATT
1 ATATTTTATATTAATAATTTTTAAAATAATT
*
3895 ATATTTAATATATT-ATTATTTTTAA
1 ATATTT--TATATTAATAATTTTTAA
3920 TTTATATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
31 17 0.35
32 26 0.54
33 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATATTTTATATTAATAATTTTTAAAATAATT
Found at i:3887 original size:31 final size:32
Alignment explanation
Indices: 3849--3919 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
3839 ATATTAATAA
*
3849 ATTTTTAAAA-AATT-TATATT-ATATTTTAATT
1 ATTTTTAAAATAATTATAT-TTAATATATT-ATT
3880 ATTTTTAAAATAATTATATTTAATATATTATT
1 ATTTTTAAAATAATTATATTTAATATATTATT
3912 ATTTTTAA
1 ATTTTTAA
3920 TTTATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 10 0.28
32 17 0.47
33 9 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
ATTTTTAAAATAATTATATTTAATATATTATT
Found at i:3895 original size:15 final size:17
Alignment explanation
Indices: 3875--3954 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
3865 TATTATATTT
3875 TAATTATTTTTAA-A-A
1 TAATTATTTTTAATATA
*
3890 TAATTATATTTAATATA
1 TAATTATTTTTAATATA
* *
3907 TTATTATTTTTAATTTA
1 TAATTATTTTTAATATA
*
3924 TATATATATTTCTTAGTACT-
1 TA-AT-TATTT-TTAATA-TA
3944 TAATTATTTTT
1 TAATTATTTTT
3955 TAAAAGGAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
15 12 0.23
16 1 0.02
17 18 0.35
18 7 0.13
19 7 0.13
20 6 0.12
21 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (17 bp):
TAATTATTTTTAATATA
Found at i:8603 original size:15 final size:14
Alignment explanation
Indices: 8583--8625 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
8573 TCAAAAATTT
*
8583 AAATTATTATTCAAA
1 AAATTAATATT-AAA
8598 AAATTAAATATTAAA
1 AAATT-AATATTAAA
*
8613 AAATTAATTTTAA
1 AAATTAATATTAA
8626 TTAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.28
15 13 0.52
16 5 0.20
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATTAATATTAAA
Found at i:8609 original size:19 final size:20
Alignment explanation
Indices: 8573--8610 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8563 GTGGACTAAC
*
8573 TCAAAAATTTAAATTATTAT
1 TCAAAAAATTAAATTATTAT
8593 TCAAAAAATTAAA-TATTA
1 TCAAAAAATTAAATTATTA
8611 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAAAATTAAATTATTAT
Found at i:8625 original size:14 final size:15
Alignment explanation
Indices: 8590--8619 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
8580 TTTAAATTAT
8590 TATTCAAAAAATTAAA
1 TATT-AAAAAATTAAA
8606 TATTAAAAAATTAA
1 TATTAAAAAATTAA
8620 TTTTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TATTAAAAAATTAAA
Done.