Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2806
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, 507
Length: 845
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.44
Found at i:522 original size:7 final size:7
Alignment explanation
Indices: 510--548 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
500 TTTACCAGAC
510 TTTATTA
1 TTTATTA
517 TTTATTA
1 TTTATTA
524 TTTATTTA
1 TTTA-TTA
*
532 TTTATTG
1 TTTATTA
*
539 TTTTTTA
1 TTTATTA
546 TTT
1 TTT
549 CATGATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (7 bp):
TTTATTA
Found at i:598 original size:19 final size:17
Alignment explanation
Indices: 574--692 Score: 97
Period size: 15 Copynumber: 6.9 Consensus size: 17
564 TCATTTTCAT
574 TTTTTTTAACTCTCTGTCA
1 TTTTTTTAACTCTC--TCA
* *
593 TTTTTTTAGCTCTCTCT
1 TTTTTTTAACTCTCTCA
*
610 TTTTTTTAA--CTATCA
1 TTTTTTTAACTCTCTCA
*
625 TGTTTTTTAA--CTATCA
1 T-TTTTTTAACTCTCTCA
641 TTTTTTCTAACTCTCTCTA
1 TTTTTT-TAACTCTCTC-A
660 TTTTTTTTTAA--CTCTCA
1 --TTTTTTTAACTCTCTCA
677 TTTTTTTAACTCTCTC
1 TTTTTTTAACTCTCTC
693 TCTCTCTCTC
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
15 19 0.22
16 18 0.21
17 16 0.19
18 9 0.11
19 14 0.16
20 3 0.04
21 6 0.07
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTTTAACTCTCTCA
Found at i:605 original size:17 final size:17
Alignment explanation
Indices: 574--692 Score: 57
Period size: 17 Copynumber: 6.9 Consensus size: 17
564 TCATTTTCAT
*
574 TTTTTTTAACTCTCTGTCA
1 TTTTTTTAGCTCTC--TCA
*
593 TTTTTTTAGCTCTCTCT
1 TTTTTTTAGCTCTCTCA
* *
610 TTTTTTTA--ACTATCA
1 TTTTTTTAGCTCTCTCA
* *
625 TGTTTTTTA--ACTATCA
1 T-TTTTTTAGCTCTCTCA
*
641 TTTTTTCTAACTCTCTCTA
1 TTTTTT-TAGCTCTCTC-A
****
660 TTTTTTTTTAACTCTCA
1 TTTTTTTAGCTCTCTCA
*
677 TTTTTTTAACTCTCTC
1 TTTTTTTAGCTCTCTC
693 TCTCTCTCTC
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
15 10 0.12
16 17 0.21
17 23 0.29
18 10 0.12
19 20 0.25
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTTTAGCTCTCTCA
Found at i:630 original size:16 final size:15
Alignment explanation
Indices: 610--687 Score: 75
Period size: 16 Copynumber: 4.7 Consensus size: 15
600 AGCTCTCTCT
610 TTTTTTTAACTATCA
1 TTTTTTTAACTATCA
625 TGTTTTTTAACTATCA
1 T-TTTTTTAACTATCA
*
641 TTTTTTCTAACTCTCTCTA
1 TTTTTT-TAA--CTATC-A
*
660 TTTTTTTTTAACTCTCA
1 --TTTTTTTAACTATCA
677 TTTTTTTAACT
1 TTTTTTTAACT
688 CTCTCTCTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
15 17 0.31
16 18 0.33
17 1 0.02
18 9 0.16
19 1 0.02
20 3 0.05
21 6 0.11
ACGTcount: A:0.21, C:0.17, G:0.01, T:0.62
Consensus pattern (15 bp):
TTTTTTTAACTATCA
Found at i:631 original size:52 final size:53
Alignment explanation
Indices: 574--691 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 53
564 TCATTTTCAT
* *
574 TTTTTTTAACTCTCTGTCATTTTTT-TAGCTCTCTC-TTTTTTTTAACTATCA
1 TTTTTTTAACTCTCTATCATTTTTTCTAACTCTCTCTTTTTTTTTAACTATCA
*
625 TGTTTTTTAA----CTATCATTTTTTCTAACTCTCTCTATTTTTTTTTAACTCTCA
1 T-TTTTTTAACTCTCTATCATTTTTTCTAACTCTCTC--TTTTTTTTTAACTATCA
677 TTTTTTTAACTCTCT
1 TTTTTTTAACTCTCT
692 CTCTCTCTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
48 11 0.20
49 9 0.16
51 9 0.16
52 24 0.44
55 2 0.04
ACGTcount: A:0.17, C:0.19, G:0.03, T:0.61
Consensus pattern (53 bp):
TTTTTTTAACTCTCTATCATTTTTTCTAACTCTCTCTTTTTTTTTAACTATCA
Found at i:706 original size:51 final size:50
Alignment explanation
Indices: 609--714 Score: 117
Period size: 49 Copynumber: 2.1 Consensus size: 50
599 TAGCTCTCTC
* *
609 TTTTTTTTAACTATCATGTTTTTTAACTATCATTTTTTCTAACTCTCTCTAT
1 TTTTTTTTAACTATCATGTTTTTTAA--ATCATTCTCTCTAACTCTCTCTAT
* * **
661 TTTTTTTTAACTCTCAT-TTTTTTAACTC-TCTCTCTCTCTCTCTCTCTAT
1 TTTTTTTTAACTATCATGTTTTTTAAATCAT-TCTCTCTAACTCTCTCTAT
710 TTTTT
1 TTTTT
715 AACTTTATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
48 1 0.02
49 22 0.47
51 8 0.17
52 16 0.34
ACGTcount: A:0.16, C:0.22, G:0.01, T:0.61
Consensus pattern (50 bp):
TTTTTTTTAACTATCATGTTTTTTAAATCATTCTCTCTAACTCTCTCTAT
Done.