Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3156
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: 21383
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.32
Found at i:4468 original size:15 final size:15
Alignment explanation
Indices: 4429--4506 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
4419 GTATCTTGGG
*
4429 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
4444 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
4459 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
*
4472 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
4487 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
4501 TTTCTT
1 TTTCTT
4507 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
12 2 0.04
13 7 0.13
14 12 0.23
15 30 0.57
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:4495 original size:28 final size:28
Alignment explanation
Indices: 4420--4502 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
4410 CATAGTATCG
* * * *
4420 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GG-TTTCTC
4450 TAT-TCTGGATTTCTTTATTCGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGTTTCTC
4478 TATCTTGGATTTCTTTATTCGGTTT
1 TATCTTGGATTTCTTTATTCGGTTT
4503 TCTTGTTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 27 0.57
29 4 0.09
30 16 0.34
ACGTcount: A:0.11, C:0.17, G:0.16, T:0.57
Consensus pattern (28 bp):
TATCTTGGATTTCTTTATTCGGTTTCTC
Found at i:6966 original size:46 final size:43
Alignment explanation
Indices: 6866--6992 Score: 139
Period size: 46 Copynumber: 2.8 Consensus size: 43
6856 CTAGGATTTG
** *
6866 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
*
6909 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGA-AGATGTAACT
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACAGATG-AA-T
*
6957 AGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
6993 TTATGGGCGG
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
43 1 0.01
44 2 0.03
45 1 0.01
46 60 0.86
47 2 0.03
48 3 0.04
49 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (43 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
Found at i:11736 original size:30 final size:30
Alignment explanation
Indices: 11700--11759 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
11690 TTCCCGAGCC
*
11700 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
11730 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
11760 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:14010 original size:21 final size:21
Alignment explanation
Indices: 13969--14010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13959 TCCCCCACCT
* *
13969 CCCCCGATTCCTCAACTTGTA
1 CCCCCGATGCCTCAACGTGTA
*
13990 CCCCCGATGCCTCAAGGTGTA
1 CCCCCGATGCCTCAACGTGTA
14011 GATCTGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.24
Consensus pattern (21 bp):
CCCCCGATGCCTCAACGTGTA
Found at i:18926 original size:30 final size:29
Alignment explanation
Indices: 18880--18938 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
18870 TTCCCGAGCC
*
18880 TAGGGGAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAATGTAATTATGCAAAAGTT
* *
18909 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGG-AAAAATGTAATTATGCAAAAGTT
18939 CGTATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (29 bp):
TAGGGGAAAAATGTAATTATGCAAAAGTT
Done.