Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2448
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: 35929
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:2296 original size:56 final size:56
Alignment explanation
Indices: 2248--2422 Score: 255
Period size: 56 Copynumber: 3.1 Consensus size: 56
2238 TCTTACTGGT
* *
2248 ACACATAAATCAGAATCACATATCGATGCCAACATAATAAACGTGGTCTTACTCAC
1 ACACATATATCAGAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCAC
*
2304 ACACATATATC-GAAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTTAC
1 ACACATATATCAG-AATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCAC
* * * * *
2360 ACACATATATCAAAATCACATATCGATGCCAACGTATTAAATGTGGTTTTACTCGC
1 ACACATATATCAGAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCAC
2416 ACA-ATAT
1 ACACATAT
2423 CGATTCCATT
Statistics
Matches: 108, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
55 5 0.05
56 103 0.95
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (56 bp):
ACACATATATCAGAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCAC
Found at i:4372 original size:27 final size:28
Alignment explanation
Indices: 4334--4389 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
4324 TATGAATATC
4334 ACATACTGGATCAG-TTTCAAAATTTTA
1 ACATACTGGATCAGTTTTCAAAATTTTA
*
4361 ACATATTGGATCAGTTTTCAAAATTTTA
1 ACATACTGGATCAGTTTTCAAAATTTTA
4389 A
1 A
4390 TTTTCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (28 bp):
ACATACTGGATCAGTTTTCAAAATTTTA
Found at i:7438 original size:30 final size:30
Alignment explanation
Indices: 7392--7452 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
7382 ATCCCGAGCC
7392 TAGGGGCAAAAATGTAAATATGCAAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
* * * * *
7422 TAGGGGTAAAATTGTAATTTTGCCAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
7452 T
1 T
7453 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATGCAAAAATT
Found at i:14926 original size:30 final size:30
Alignment explanation
Indices: 14880--14940 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14870 ATCCCGAGCC
14880 TAGGGGCAAAAATGTAAATATGCAAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
* * * * *
14910 TAGGGGTAAAATTGTAATTTTGCCAAAATT
1 TAGGGGCAAAAATGTAAATATGCAAAAATT
14940 T
1 T
14941 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATGCAAAAATT
Found at i:15484 original size:44 final size:46
Alignment explanation
Indices: 15360--15484 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
15350 GGTTGAGCAT
* *
15360 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
15406 CCGAGCTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAA-GC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
*
15450 CCGAGCTCGTTGAGTTGAGT-CGAGTTCGCTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
15485 GCGGGTTCAC
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
43 8 0.11
44 26 0.35
45 12 0.16
46 29 0.39
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGC
Found at i:28462 original size:1 final size:1
Alignment explanation
Indices: 28456--28488 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
28446 GAGGGTGGGC
*
28456 GGGGGGGGGGGGGGGGGGGGGGCGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
28489 TGACGGGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:28478 original size:23 final size:23
Alignment explanation
Indices: 28443--28488 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
28433 GTGAGCATTA
*
28443 GGGGAGGGTGGGCGGGGGGGGGG
1 GGGGAGGGGGGGCGGGGGGGGGG
*
28466 GGGGGGGGGGGGCGGGGGGGGGG
1 GGGGAGGGGGGGCGGGGGGGGGG
28489 TGACGGGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.02, C:0.04, G:0.91, T:0.02
Consensus pattern (23 bp):
GGGGAGGGGGGGCGGGGGGGGGG
Found at i:28496 original size:14 final size:12
Alignment explanation
Indices: 28452--28488 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
28442 AGGGGAGGGT
28452 GGGCGGGGGGGG
1 GGGCGGGGGGGG
28464 GGG-GGGGGGGG
1 GGGCGGGGGGGG
28475 GGGCGGGGGGGG
1 GGGCGGGGGGGG
28487 GG
1 GG
28489 TGACGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.00, C:0.05, G:0.95, T:0.00
Consensus pattern (12 bp):
GGGCGGGGGGGG
Found at i:28496 original size:23 final size:23
Alignment explanation
Indices: 28452--28496 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28442 AGGGGAGGGT
**
28452 GGGCGGGGGGGGGGGGGGGGGGG
1 GGGCGGGGGGGGGGGGACGGGGG
*
28475 GGGCGGGGGGGGGGTGACGGGG
1 GGGCGGGGGGGGGGGGACGGGG
28497 AGGAGTGGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.07, G:0.89, T:0.02
Consensus pattern (23 bp):
GGGCGGGGGGGGGGGGACGGGGG
Found at i:33239 original size:44 final size:44
Alignment explanation
Indices: 33186--33288 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
33176 ATTTGGAACA
*
33186 TTGGCATCGATATATGTGTTTCATGTAAGACCACGTCT-GGGCG
1 TTGGCATCGATATATGTGTTTCATGTAAGACCACGTCTAGGACG
* *
33229 TTGGCAATCGATATATGTGTTTCGTGTAAGACTACGTCTAGGACG
1 TTGGC-ATCGATATATGTGTTTCATGTAAGACCACGTCTAGGACG
33274 TTGGCATC-ATATATG
1 TTGGCATCGATATATG
33289 GTTATGTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
43 12 0.22
44 34 0.62
45 9 0.16
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (44 bp):
TTGGCATCGATATATGTGTTTCATGTAAGACCACGTCTAGGACG
Done.