Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2376
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: 37604
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Found at i:6499 original size:23 final size:23
Alignment explanation
Indices: 6473--6548 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
6463 ATAAGTGCCA
6473 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
6496 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
6519 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
6542 CACTGAT
1 CACTGAT
6549 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:6648 original size:8 final size:8
Alignment explanation
Indices: 6635--6663 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
6625 ACCCGGGACT
6635 CACTGTAA
1 CACTGTAA
6643 CACTGTAA
1 CACTGTAA
6651 CACTGTAA
1 CACTGTAA
6659 CACTG
1 CACTG
6664 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:6792 original size:18 final size:17
Alignment explanation
Indices: 6766--6804 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
6756 ATTTTCCTTC
6766 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
6783 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
6801 CACA
1 CACA
6805 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:9649 original size:16 final size:18
Alignment explanation
Indices: 9630--9662 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
9620 CATACGAATT
9630 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
9646 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
9663 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:10296 original size:42 final size:43
Alignment explanation
Indices: 10229--10349 Score: 192
Period size: 42 Copynumber: 2.8 Consensus size: 43
10219 CTGAACTCAT
*
10229 TCACCGGCATTA-CGCCTGCTAGGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
*
10271 TCACTGGCATTATAGCCTGCT-GGCTCGAAGCCCGATATTAAC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
*
10313 TCACCGACATTATAGCCTGCTAGGCTCGAAGGCCCGA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAA-GCCCGA
10350 ATAGTACCGT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
42 51 0.71
43 15 0.21
44 6 0.08
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (43 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGCCCGATATTAAC
Found at i:17854 original size:13 final size:13
Alignment explanation
Indices: 17836--17862 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17826 CTTTCTCCTT
17836 TCCCTTATCCAAC
1 TCCCTTATCCAAC
17849 TCCCTTATCCAAC
1 TCCCTTATCCAAC
17862 T
1 T
17863 TTGGTCCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.33
Consensus pattern (13 bp):
TCCCTTATCCAAC
Found at i:23487 original size:20 final size:20
Alignment explanation
Indices: 23464--23509 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
23454 GTGTAGTCAC
*
23464 ACACGCCCGTGTGGCTAGGG
1 ACACGCCAGTGTGGCTAGGG
23484 ACACGCCAGTGTGGCTAGGG
1 ACACGCCAGTGTGGCTAGGG
23504 ACACGC
1 ACACGC
23510 TCGGTGCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.30, G:0.37, T:0.13
Consensus pattern (20 bp):
ACACGCCAGTGTGGCTAGGG
Found at i:37084 original size:45 final size:45
Alignment explanation
Indices: 36967--37090 Score: 167
Period size: 45 Copynumber: 2.8 Consensus size: 45
36957 TCGATGTCCC
* * * * * *
36967 AGACATGGTCTTACACGTAACCACATAGATCAATTCCAACGTCCT
1 AGACATGGTCTTACACGAAAACACATATATCGATGCCAACCTCCT
*
37012 AGACGTGGTCTTACACGAAAACACATATATCGATGCCAACCTCCT
1 AGACATGGTCTTACACGAAAACACATATATCGATGCCAACCTCCT
* *
37057 AGACCTGGTCTTACACGAAAACACATATCTCGAT
1 AGACATGGTCTTACACGAAAACACATATATCGAT
37091 CCTATGGTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (45 bp):
AGACATGGTCTTACACGAAAACACATATATCGATGCCAACCTCCT
Done.