Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1237
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: 9655
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.35
Found at i:3318 original size:13 final size:14
Alignment explanation
Indices: 3288--3319 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3278 ATATTATTTA
3288 ATAAATTTAAAATT
1 ATAAATTTAAAATT
3302 -TAAATTT-AAATT
1 ATAAATTTAAAATT
3314 ATAAAT
1 ATAAAT
3320 ATTTATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAAATTTAAAATT
Found at i:3414 original size:15 final size:16
Alignment explanation
Indices: 3387--3421 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
3377 TTTAATAAAA
3387 ATAAAAAATTATTTTT
1 ATAAAAAATTATTTTT
3403 ATAAAAAA-TATTTTT
1 ATAAAAAATTATTTTT
3418 ATAA
1 ATAA
3422 TTAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAAAAAATTATTTTT
Found at i:3436 original size:27 final size:27
Alignment explanation
Indices: 3406--3457 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3396 TATTTTTATA
3406 AAAAATA-TTTTTATAATTAATATAAAT
1 AAAAATATTTTTTATAATTAA-ATAAAT
* *
3433 AAAATTATTTTTTATTATTAAATAA
1 AAAAATATTTTTTATAATTAAATAA
3458 TAATTTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAAAATATTTTTTATAATTAAATAAAT
Found at i:3456 original size:44 final size:45
Alignment explanation
Indices: 3359--3456 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
3349 GATTTAAAAT
3359 TTAAATTATTATTTATAATTTAATAAAAATAAAAAATTATTTTTATA
1 TTAAA-TATTATTTATAATTTAATAAAAAT-AAAAATTATTTTTATA
** *
3406 AAAAATATT-TTTATAA-TTAATATAAAT-AAAATTATTTTTTATTA
1 TTAAATATTATTTATAATTTAATAAAAATAAAAATTA-TTTTTA-TA
3450 TTAAATA
1 TTAAATA
3457 ATAATTTGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
42 7 0.16
43 6 0.14
44 17 0.39
45 7 0.16
46 4 0.09
47 3 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (45 bp):
TTAAATATTATTTATAATTTAATAAAAATAAAAATTATTTTTATA
Found at i:3989 original size:23 final size:23
Alignment explanation
Indices: 3949--4034 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 23
3939 ATTATTATTC
3949 ATTTTAT-ATT-AATTTAAATAT
1 ATTTTATAATTAAATTTAAATAT
*
3970 ATTTTATAATTAAATTTAAATAA
1 ATTTTATAATTAAATTTAAATAT
* * * *
3993 AATATATTATTTTAATTTAATATATT
1 ATTTTA-TAATTAAATTTAA-ATA-T
4019 ATTTTA-AATTAAATTT
1 ATTTTATAATTAAATTT
4035 TTTAAAATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
21 7 0.14
22 3 0.06
23 14 0.28
24 19 0.38
25 3 0.06
26 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTTATAATTAAATTTAAATAT
Found at i:4014 original size:18 final size:18
Alignment explanation
Indices: 3993--4030 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3983 ATTTAAATAA
*
3993 AATATATTATTTTAATTT
1 AATATATTATTTTAAATT
4011 AATATATTATTTTAAATT
1 AATATATTATTTTAAATT
4029 AA
1 AA
4031 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATATTATTTTAAATT
Found at i:4263 original size:2 final size:2
Alignment explanation
Indices: 4256--4307 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
4246 TCAGCAAAAG
*
4256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4298 AT AT AT AT AT
1 AT AT AT AT AT
4308 TGAGACATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4600 original size:13 final size:13
Alignment explanation
Indices: 4582--4607 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4572 ATATTTATAT
4582 TTAAATATAAATA
1 TTAAATATAAATA
4595 TTAAATATAAATA
1 TTAAATATAAATA
4608 AAAAATCTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:4860 original size:19 final size:19
Alignment explanation
Indices: 4838--4874 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4828 ATTAAAAAAT
*
4838 TATATTATATATATTTTAA
1 TATATCATATATATTTTAA
4857 TATATCATATATATTTTA
1 TATATCATATATATTTTA
4875 TCGAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATCATATATATTTTAA
Found at i:8367 original size:16 final size:17
Alignment explanation
Indices: 8346--8378 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8336 AACTGGTAAA
8346 TTTAAAT-TAAAATAAT
1 TTTAAATGTAAAATAAT
*
8362 TTTAAATGTTAAATAAT
1 TTTAAATGTAAAATAAT
8379 ATATATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATGTAAAATAAT
Found at i:9471 original size:22 final size:20
Alignment explanation
Indices: 9441--9493 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
9431 AGTATTTAAA
*
9441 ATTTAAATTTATTTATTATT
1 ATTTAAATTTATATATTATT
9461 CATATTAAATTTATATATTATT
1 -AT-TTAAATTTATATATTATT
9483 ATTTAAATTTA
1 ATTTAAATTTA
9494 AATTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 9 0.30
21 4 0.13
22 17 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTAAATTTATATATTATT
Done.