Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold767
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: 7381
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Found at i:430 original size:22 final size:22
Alignment explanation
Indices: 402--450 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
392 AAATTAAAAA
402 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
424 ATATA-TTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
*
445 AAATAT
1 ATATAT
451 AAAATAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:434 original size:21 final size:21
Alignment explanation
Indices: 402--450 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
392 AAATTAAAAA
402 ATATATTTT-TATATTAATATTT
1 ATATATTTTATA-ATTAA-ATTT
424 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
*
445 AAATAT
1 ATATAT
451 AAAATAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 14 0.56
23 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:560 original size:16 final size:17
Alignment explanation
Indices: 539--570 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
529 AATAACTTGA
539 TTATAAA-AAATTTAAT
1 TTATAAATAAATTTAAT
555 TTATAAATAAATTTAA
1 TTATAAATAAATTTAA
571 ATAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATAAATAAATTTAAT
Found at i:952 original size:17 final size:17
Alignment explanation
Indices: 930--974 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
920 AAATTTTAAA
930 ATATTTATATTATTTTT
1 ATATTTATATTATTTTT
947 ATATTT-TAATTATTTTT
1 ATATTTAT-ATTATTTTT
*
964 TTATTATATAT
1 ATATT-TATAT
975 AATATCGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 3 0.12
19 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTATATTATTTTT
Found at i:1218 original size:19 final size:19
Alignment explanation
Indices: 1176--1219 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
1166 TTTTGATTTA
1176 ATTTAAAATAATATTTTTT
1 ATTTAAAATAATATTTTTT
1195 A-TTAAAATAATATTTTTT
1 ATTTAAAATAATATTTTTT
1213 ATTTAAA
1 ATTTAAA
1220 TTAAATTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAAAATAATATTTTTT
Found at i:3002 original size:25 final size:24
Alignment explanation
Indices: 2952--3021 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 24
2942 ATAAGCGATT
* *
2952 AATAAAAATAAAATTATTAATATAA
1 AATAAAAATCAAATTATCAATAT-A
*
2977 AATAAAAATCAGATTATCAAGT-TA
1 AATAAAAATCAAATTATCAA-TATA
* *
3001 AATGAAAATCAATCTTATCAA
1 AATAAAAATCAA-ATTATCAA
3022 ACTTCCAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 11 0.30
25 25 0.68
26 1 0.03
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (24 bp):
AATAAAAATCAAATTATCAATATA
Found at i:4968 original size:18 final size:18
Alignment explanation
Indices: 4933--4976 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
4923 CAAATCTTCA
* **
4933 CTTTTTTTTTTCTTTTTT
1 CTTTTTTTTTACCCTTTT
4951 CTTTTTTTTTACCCTTTT
1 CTTTTTTTTTACCCTTTT
4969 -TTTTTTTT
1 CTTTTTTTT
4977 ACAATTGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
CTTTTTTTTTACCCTTTT
Done.