Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005030.1 Kokia drynarioides strain JFW-HI SEQ_118793, whole genome shotgun sequence
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: 11060
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3610 original size:11 final size:11
Alignment explanation
Indices: 3596--3659 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
3586 AGCCCTTTTT
*
3596 AATTTATTTTA
1 AATTTAATTTA
*
3607 AATTTAAATT-
1 AATTTAATTTA
3617 AATCTTAAATTTA
1 AAT-TT-AATTTA
3630 AATTTAATTTA
1 AATTTAATTTA
3641 AATTTAAATTTA
1 AATTT-AATTTA
*
3653 ATTTTAA
1 AATTTAA
3660 AATTAAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.07
11 23 0.51
12 16 0.36
13 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:3614 original size:6 final size:6
Alignment explanation
Indices: 3603--3666 Score: 80
Period size: 6 Copynumber: 11.0 Consensus size: 6
3593 TTTAATTTAT
3603 TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
3649 TTTAAT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA
3667 AAGTCCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.14
6 39 0.76
7 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:3624 original size:17 final size:17
Alignment explanation
Indices: 3596--3666 Score: 99
Period size: 17 Copynumber: 4.1 Consensus size: 17
3586 AGCCCTTTTT
*
3596 AATTTATTTTAAATTTA
1 AATTTAATTTAAATTTA
3613 AA-TTAATCTTAAATTTA
1 AATTTAAT-TTAAATTTA
3630 AATTTAATTTAAATTTA
1 AATTTAATTTAAATTTA
*
3647 AATTTAATTTTAAAATTA
1 AATTTAA-TTTAAATTTA
3665 AA
1 AA
3667 AAGTCCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
16 4 0.08
17 29 0.59
18 16 0.33
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTA
Found at i:3630 original size:23 final size:22
Alignment explanation
Indices: 3594--3665 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
3584 CGAGCCCTTT
*
3594 TTAATTT-ATTTTAAATTTAAA
1 TTAATTTAAATTTAAATTTAAA
*
3615 TTAATCTTAAATTTAAATTTAAT
1 TTAAT-TTAAATTTAAATTTAAA
*
3638 TTAAATTTAAATTTAATTTTAAAA
1 TT-AATTTAAATTTAAATTT-AAA
3662 TTAA
1 TTAA
3666 AAAGTCCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 29 0.67
24 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTTAAATTTAAATTTAAA
Found at i:4498 original size:3 final size:3
Alignment explanation
Indices: 4438--4480 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
4428 ATAAATGTGC
*
4438 TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA GTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
4481 CTGCCTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5616 original size:30 final size:30
Alignment explanation
Indices: 5551--5720 Score: 133
Period size: 29 Copynumber: 5.8 Consensus size: 30
5541 GAGGGTCCTT
*
5551 AAACTGTCCAAAAATCTCATTTTTACCCCCG
1 AAACT-TCCAAAAATCCCATTTTTACCCCCG
5582 -AACTTCCAAAAATCCCATTTTTGA-CCCCG
1 AAACTTCCAAAAATCCCATTTTT-ACCCCCG
* * * *
5611 AAACTTCTAAAAATTCCA-TTTTGCCCTCG
1 AAACTTCCAAAAATCCCATTTTTACCCCCG
* *
5640 AAATTTCC--AAATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCCG
* *
5668 AAAC-TCTCGAAATTACCC-TTTTTACCCCCG
1 AAACTTC-CAAAAAT-CCCATTTTTACCCCCG
* *
5698 -AA-TATCTAAAAATTCCATTTTTA
1 AAACT-TCCAAAAATCCCATTTTTA
5721 AACCCCATAT
Statistics
Matches: 112, Mismatches: 16, Indels: 24
0.74 0.11 0.16
Matches are distributed among these distances:
27 10 0.09
28 15 0.13
29 48 0.43
30 37 0.33
31 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATCCCATTTTTACCCCCG
Found at i:11036 original size:50 final size:49
Alignment explanation
Indices: 10927--11058 Score: 137
Period size: 50 Copynumber: 2.7 Consensus size: 49
10917 GAACTAATGG
*
10927 ATTACTAAATGCATGACT-TGATTTAATGATGC-ATTTAACTAACAAGGGA
1 ATTACTTAATGCATGA-TATGATTT-ATGATGCAATTTAACTAACAAGGGA
* * * *
10976 ATTACATAATGCATGATAGGATTTATGATGCATATTTAACTAAC-ATGTA
1 ATTACTTAATGCATGATATGATTTATGATGCA-ATTTAACTAACAAGGGA
*
11025 AGTTACTTAATGCATG-TCATTATTTATGATGCAA
1 A-TTACTTAATGCATGAT-ATGATTTATGATGCAA
11059 AC
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
48 8 0.11
49 25 0.36
50 37 0.53
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (49 bp):
ATTACTTAATGCATGATATGATTTATGATGCAATTTAACTAACAAGGGA
Done.