Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold900
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: 5102
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Found at i:2281 original size:31 final size:32
Alignment explanation
Indices: 2233--2296 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
2223 GGGGTACCTA
2233 TTTCTATCGTGTGTCGGATAGAGATCCGAGATT
1 TTTCTATCG-GTGTCGGATAGAGATCCGAGATT
2266 TTTCTATC-GTGTCGGATAGAGATCCGAGATT
1 TTTCTATCGGTGTCGGATAGAGATCCGAGATT
2297 CACCTCGCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 23 0.74
33 8 0.26
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (32 bp):
TTTCTATCGGTGTCGGATAGAGATCCGAGATT
Found at i:5008 original size:51 final size:55
Alignment explanation
Indices: 4948--5100 Score: 167
Period size: 51 Copynumber: 2.9 Consensus size: 55
4938 TGTATTTGCT
*
4948 ATGTAGCACTAAGTGTGCGATTTGA-CATGTTGC-CTAAGTGTGCGA-AATGA-A
1 ATGTAGCACTAAGTGTGCGATTTGACCATGTCGCACTAAGTGTGCGAGAATGACA
* ** *
4999 ATG-ATGCACTAAGT-TGCGAATTGACCATG-CGCACTAAGTGTGCGAGTTTGACT
1 ATGTA-GCACTAAGTGTGCGATTTGACCATGTCGCACTAAGTGTGCGAGAATGACA
** *
5052 ATGTAGCACTAAGTGTGCGAGTTTGATTATGTGGCACTAAGTGTGCGAG
1 ATGTAGCACTAAGTGTGCGA-TTTGACCATGTCGCACTAAGTGTGCGAG
5101 TT
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
50 12 0.14
51 28 0.33
52 3 0.04
53 12 0.14
54 6 0.07
55 7 0.08
56 16 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (55 bp):
ATGTAGCACTAAGTGTGCGATTTGACCATGTCGCACTAAGTGTGCGAGAATGACA
Found at i:5062 original size:28 final size:27
Alignment explanation
Indices: 4929--5099 Score: 164
Period size: 28 Copynumber: 6.6 Consensus size: 27
4919 GTAATTGTAC
4929 AGCACTAAGTGT---ATTTG-CTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
4952 AGCACTAAGTGTGCGATTTGAC-ATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
4978 TGC-CTAAGTGTGCGAAATGA-AATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
5002 ATGCACTAAGT-TGCGAATTGACCATG-
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5028 CGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
5056 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
5084 GGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
5100 GTT
Statistics
Matches: 125, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
23 12 0.10
25 38 0.30
26 25 0.20
27 9 0.07
28 41 0.33
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Done.