Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003266.1 Kokia drynarioides strain JFW-HI SEQ_115923, 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: 7462
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:553 original size:6 final size:6
Alignment explanation
Indices: 544--636 Score: 72
Period size: 6 Copynumber: 16.2 Consensus size: 6
534 TTTTAGCTTT
* * *
544 ATTTAA ATTTATA A--TAA TTTTAA ATTTGAA A-ATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
* * *
591 A-TTAA ATTTAA ATTCAA A-ATAA ATTTAA ATTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
636 A
1 A
637 ATTTTAAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
4 1 0.01
5 17 0.25
6 45 0.66
7 5 0.07
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:583 original size:18 final size:17
Alignment explanation
Indices: 544--672 Score: 159
Period size: 17 Copynumber: 7.4 Consensus size: 17
534 TTTTAGCTTT
*
544 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
561 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
579 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
*
596 ATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAA
613 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* *
630 ATTTAAAATTTTAAACAA
1 ATTT-AAATTTAAAATAA
*
648 ATTTAATTTTTAAAATAA
1 ATTTAA-ATTTAAAATAA
666 ATTTAAA
1 ATTTAAA
673 GGAAGTTTGG
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
17 51 0.54
18 43 0.46
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:583 original size:35 final size:34
Alignment explanation
Indices: 544--672 Score: 159
Period size: 35 Copynumber: 3.7 Consensus size: 34
534 TTTTAGCTTT
* *
544 ATTTAAATTTATAATAATTTTAAATTTGAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTT-AAAATAA
* * *
579 ATTTAAACTTAAATTAAATTTAAATTCAAAATAA
1 ATTTAAATTTAAAATAAATTTAAATTTAAAATAA
* *
613 ATTTAAATTTAAAATAAATTTAAAATTTTAAACAA
1 ATTTAAATTTAAAATAAATTT-AAATTTAAAATAA
*
648 ATTTAATTTTTAAAATAAATTTAAA
1 ATTTAA-ATTTAAAATAAATTTAAA
673 GGAAGTTTGG
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
34 26 0.32
35 41 0.51
36 14 0.17
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (34 bp):
ATTTAAATTTAAAATAAATTTAAATTTAAAATAA
Found at i:601 original size:11 final size:11
Alignment explanation
Indices: 576--636 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
566 AATTTGAAAA
*
576 TAAATTTAAACT
1 TAAA-TTAAATT
588 TAAATTAAATT
1 TAAATTAAATT
*
599 TAAATTCAAA-A
1 TAAATT-AAATT
610 TAAATTTAAATT
1 TAAA-TTAAATT
*
622 TAAAATAAATT
1 TAAATTAAATT
633 TAAA
1 TAAA
637 ATTTTAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
11 29 0.69
12 13 0.31
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:637 original size:11 final size:11
Alignment explanation
Indices: 564--638 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
554 ATAATAATTT
564 TAAATTTGAAAA
1 TAAATTT-AAAA
*
576 TAAATTTAAACT
1 TAAATTTAAA-A
*
588 TAAA-TTAAATT
1 TAAATTTAAA-A
*
599 TAAATTCAAAA
1 TAAATTTAAAA
610 TAAA-TT----
1 TAAATTTAAAA
616 TAAATTTAAAA
1 TAAATTTAAAA
627 TAAATTTAAAA
1 TAAATTTAAAA
638 T
1 T
639 TTTAAACAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
10 1 0.02
11 29 0.57
12 15 0.29
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:2908 original size:16 final size:16
Alignment explanation
Indices: 2887--2917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2877 AAAAAATTCT
2887 TTGTTTATTTGATTTA
1 TTGTTTATTTGATTTA
*
2903 TTGTTTATTTTATTT
1 TTGTTTATTTGATTT
2918 GATTATTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (16 bp):
TTGTTTATTTGATTTA
Found at i:5282 original size:18 final size:19
Alignment explanation
Indices: 5259--5295 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5249 CCCTCCGATT
5259 TTTTCC-ATTTTTTAAAAA
1 TTTTCCTATTTTTTAAAAA
*
5277 TTTTCCTTTTTTTTAAAAA
1 TTTTCCTATTTTTTAAAAA
5296 AAAACTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTCCTATTTTTTAAAAA
Done.