Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006267.1 Kokia drynarioides strain JFW-HI SEQ_120838, 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: 7569
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:2426 original size:19 final size:19
Alignment explanation
Indices: 2273--2443 Score: 67
Period size: 19 Copynumber: 8.7 Consensus size: 19
2263 TTGGTACGAT
2273 AATTTTTATAATTTTTTTAC
1 AATTTTTAT-ATTTTTTTAC
** *
2293 AAAATTTATATTTCTTTAC
1 AATTTTTATATTTTTTTAC
*
2312 -ATTTTGTATAATTTTTTTAG
1 AATTTT-TAT-ATTTTTTTAC
* * *** *
2332 GA-CTTTATAAAGTTTTAT
1 AATTTTTATATTTTTTTAC
* * * *
2350 AATTTTTTTATGTTTCTATG
1 AATTTTTATATTTTTTTA-C
* *
2370 TATTTTATAATTTTTTTTTAC
1 AATTTT-T-ATATTTTTTTAC
* ***
2391 GATTTTTATAAAATTTTAC
1 AATTTTTATATTTTTTTAC
*
2410 AATTTTTATATTTTTTTATA
1 AATTTTTATATTTTTTTA-C
*
2430 AATTTTAATATTTT
1 AATTTTTATATTTT
2444 AATTTTCACG
Statistics
Matches: 106, Mismatches: 37, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
18 10 0.09
19 46 0.43
20 36 0.34
21 7 0.07
22 7 0.07
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (19 bp):
AATTTTTATATTTTTTTAC
Found at i:3290 original size:19 final size:18
Alignment explanation
Indices: 3268--3312 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3258 AAAAGTTATT
*
3268 AAATTTTAATAAAAATATA
1 AAATTTTAA-AAAAATAGA
*
3287 AAATTATTAAAAAATTAGA
1 AAATT-TTAAAAAAATAGA
3306 AAATTTT
1 AAATTTT
3313 TATTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATTTTAAAAAAATAGA
Found at i:3610 original size:10 final size:10
Alignment explanation
Indices: 3597--3666 Score: 58
Period size: 10 Copynumber: 7.2 Consensus size: 10
3587 CTTTATAAAA
3597 TTTTATAATT
1 TTTTATAATT
3607 TTTT-T-ATGT
1 TTTTATAAT-T
* *
3616 TTCTAT-ATA
1 TTTTATAATT
3625 TTTTATAATT
1 TTTTATAATT
*
3635 TTTTACAA-T
1 TTTTATAATT
3644 TTTTATATATT
1 TTTTATA-ATT
*
3655 TTTTCTAATT
1 TTTTATAATT
3665 TT
1 TT
3667 AATATTTTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 2 0.04
9 17 0.35
10 22 0.46
11 7 0.15
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:3650 original size:28 final size:28
Alignment explanation
Indices: 3596--3656 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3586 ACTTTATAAA
*
3596 ATTTTATAATTTTTTTATGTTTCTATAT
1 ATTTTATAATTTTTTAATGTTTCTATAT
3624 ATTTTATAATTTTTTACAAT-TTT-TATAT
1 ATTTTATAATTTTTT--AATGTTTCTATAT
3652 ATTTT
1 ATTTT
3657 TTCTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 25 0.83
29 3 0.10
30 2 0.07
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (28 bp):
ATTTTATAATTTTTTAATGTTTCTATAT
Found at i:3666 original size:19 final size:19
Alignment explanation
Indices: 3624--3674 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3614 GTTTCTATAT
3624 ATTTTATA-ATTTTTTACA
1 ATTTTATATATTTTTTACA
3642 ATTTTTATATATTTTTT-CTA
1 A-TTTTATATATTTTTTAC-A
3662 ATTTTA-ATATTTT
1 ATTTTATATATTTT
3675 GATTTTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.27
19 13 0.43
20 9 0.30
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTATATATTTTTTACA
Done.