Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2902
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: 11311
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Found at i:417 original size:27 final size:28
Alignment explanation
Indices: 377--430 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
367 CCCTAAACCT
* *
377 TAAAATAATAAACCCAAAACTCAAAATC
1 TAAAACAATAAACCCAAAACCCAAAATC
*
405 TAAAACAA-AAACCCATAACCCAAAAT
1 TAAAACAATAAACCCAAAACCCAAAAT
431 AATAACATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (28 bp):
TAAAACAATAAACCCAAAACCCAAAATC
Found at i:590 original size:40 final size:40
Alignment explanation
Indices: 540--634 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
530 ATTTTAAGAA
* * *
540 AAAACGCCGCTAATGATTAACATTTTGCAGCGTTTTACA-
1 AAAACGCCGCTAATGATCAACATGTTGCAGCATTTTACAC
** * *
579 ACAAACGCCGCTAATTCTCGATATGTTGCAGCATTTTACAC
1 A-AAACGCCGCTAATGATCAACATGTTGCAGCATTTTACAC
620 AAAACGCCGCTAATG
1 AAAACGCCGCTAATG
635 CCTCTATAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.02
40 44 0.96
41 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
AAAACGCCGCTAATGATCAACATGTTGCAGCATTTTACAC
Found at i:2492 original size:27 final size:27
Alignment explanation
Indices: 2457--2513 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
2447 ACTAGAATAC
*
2457 CCCTATGTATGCAAAATTACCATTATA
1 CCCTATGTATGCAAAATGACCATTATA
* *
2484 CCCTATGTATGTAAAATGACCTTTATA
1 CCCTATGTATGCAAAATGACCATTATA
2511 CCC
1 CCC
2514 CTAGGGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (27 bp):
CCCTATGTATGCAAAATGACCATTATA
Found at i:2673 original size:25 final size:27
Alignment explanation
Indices: 2633--2707 Score: 100
Period size: 25 Copynumber: 2.8 Consensus size: 27
2623 GGTGGCTATG
*
2633 CACAAATTATCTGTTCTGGTGG-CTGC
1 CACAAAATATCTGTTCTGGTGGACTGC
*
2659 CAC-ATATATCTGTTCTGGTGGCACTGC
1 CACAAAATATCTGTTCTGGTGG-ACTGC
2686 CACAAAATATCTGTATCTGGTG
1 CACAAAATATCTGT-TCTGGTG
2708 ACTTTGTCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.38
26 3 0.07
27 7 0.17
28 9 0.21
29 7 0.17
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (27 bp):
CACAAAATATCTGTTCTGGTGGACTGC
Found at i:3798 original size:11 final size:10
Alignment explanation
Indices: 3770--3803 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3760 AGCCTGTAAG
3770 TATTCTGAAT
1 TATTCTGAAT
*
3780 TTTTCTGAAT
1 TATTCTGAAT
3790 ATATTCTGAAT
1 -TATTCTGAAT
3801 TAT
1 TAT
3804 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:9992 original size:14 final size:15
Alignment explanation
Indices: 9973--10003 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9963 AGGCTAGATC
9973 GCAAAA-GCCGAAAA
1 GCAAAATGCCGAAAA
9987 GCAAAATGCCGAAAA
1 GCAAAATGCCGAAAA
10002 GC
1 GC
10004 CGGTATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.23, G:0.23, T:0.03
Consensus pattern (15 bp):
GCAAAATGCCGAAAA
Found at i:10282 original size:27 final size:27
Alignment explanation
Indices: 10244--10314 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
10234 TGTACTAGAA
10244 ATACCCTATGTATGCAAAATTACCATT
1 ATACCCTATGTATGCAAAATTACCATT
10271 ATACCCTATGTATGCAAAATTACCATT
1 ATACCCTATGTATGCAAAATTACCATT
10298 ATACCCTATGTATGCAA
1 ATACCCTATGTATGCAA
10315 TGACCTCTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (27 bp):
ATACCCTATGTATGCAAAATTACCATT
Found at i:10532 original size:29 final size:28
Alignment explanation
Indices: 10432--10521 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
10422 AGGAAGCGTC
*
10432 CTGGTGGC-CTG-CACAGAATTATCTGTT
1 CTGGTGGCACTGCCACA-AAATATCTGTT
* *
10459 CTGGTGGCCCTGCCACAATATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
10487 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
10516 CTGGTG
1 CTGGTG
10522 ACTCTGTCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
27 8 0.14
28 37 0.66
29 11 0.20
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Done.