Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold892
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: 4618
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.28
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:572 original size:17 final size:17
Alignment explanation
Indices: 546--581 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
536 GTGTGTTTTG
*
546 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
563 TTTTGACTGCATGACAT
1 TTTTGACTGCATGACAT
580 TT
1 TT
582 CATCATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:2634 original size:52 final size:52
Alignment explanation
Indices: 2559--2662 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
2549 GCCTAGAAGC
2559 AATAAGGATTTCTTTGTGAAATAGGCTCACGTCTAAACATTATTATTTTAAT
1 AATAAGGATTTCTTTGTGAAATAGGCTCACGTCTAAACATTATTATTTTAAT
*
2611 AATAATGATTTCTTTGTGAAATAGGCTCACGTCTAAACATTATTATTTTAAT
1 AATAAGGATTTCTTTGTGAAATAGGCTCACGTCTAAACATTATTATTTTAAT
2663 GAAATACATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (52 bp):
AATAAGGATTTCTTTGTGAAATAGGCTCACGTCTAAACATTATTATTTTAAT
Found at i:3695 original size:7 final size:7
Alignment explanation
Indices: 3670--3711 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
3660 AGTGATGTGA
3670 AAAAATG
1 AAAAATG
3677 AAAAGATG
1 AAAA-ATG
3685 -AAAATG
1 AAAAATG
3691 AAAAATG
1 AAAAATG
3698 AAAAA-G
1 AAAAATG
3704 TAAAAATG
1 -AAAAATG
3712 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.13
7 23 0.74
8 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:3709 original size:21 final size:21
Alignment explanation
Indices: 3670--3711 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3660 AGTGATGTGA
*
3670 AAAAATGAAAAGATGAAAATG
1 AAAAATGAAAAGATAAAAATG
3691 AAAAATGAAAA-AGTAAAAATG
1 AAAAATGAAAAGA-TAAAAATG
3712 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAGATAAAAATG
Done.