Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2814
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: 21592
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2363 original size:12 final size:13
Alignment explanation
Indices: 2346--2374 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2336 TTAAACTAAG
2346 TAAATAAAT-AAA
1 TAAATAAATAAAA
2358 TAAATAAATAAAA
1 TAAATAAATAAAA
2371 TAAA
1 TAAA
2375 ACTTTACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:3185 original size:23 final size:23
Alignment explanation
Indices: 3154--3199 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3144 ATCATTAAAA
*
3154 TTTTTTTATGATATTTT-TTATT
1 TTTTTTTATGAAATTTTCTTATT
3176 TTTTTATTATGAAATTTTCTTATT
1 TTTTT-TTATGAAATTTTCTTATT
3200 ATATGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTTTTATGAAATTTTCTTATT
Found at i:6914 original size:18 final size:17
Alignment explanation
Indices: 6886--6920 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6876 ATTATTAAGA
*
6886 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
6903 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
6921 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:7074 original size:157 final size:157
Alignment explanation
Indices: 6874--7190 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
6864 ATAAGAATAT
6874 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
6939 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
7004 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
*
7031 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTTAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
7096 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
*
7161 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
7188 TAA
1 TAA
7191 GGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:7324 original size:45 final size:44
Alignment explanation
Indices: 7224--7333 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
7214 TTTTCCATTA
7224 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
7263 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
7308 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
7334 CCTCTATTCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:7333 original size:16 final size:16
Alignment explanation
Indices: 7312--7365 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
7302 TTGATTTGCT
7312 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
7328 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
7344 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
7360 AATACA
1 ATTACA
7366 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:12514 original size:4 final size:4
Alignment explanation
Indices: 12505--12554 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
12495 GACACTAAGG
*
12505 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
12553 AC
1 AC
12555 CCCAATTCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Done.