Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006324.1 Kokia drynarioides strain JFW-HI SEQ_120899, 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: 4077
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Found at i:483 original size:49 final size:49
Alignment explanation
Indices: 387--498 Score: 188
Period size: 49 Copynumber: 2.3 Consensus size: 49
377 GACTGTTAAC
* *
387 CATTGACAGTTGACCATTGACCGTTAACCGTTGACAGTTGACCGTTGAT
1 CATTGATAGTTGACCATTGACCGTTAACCGTTGACAGTTGACAGTTGAT
*
436 CATTGATAGTTGACCATTGACCGTTGACCGTTGACAGTTGACAGTTGAT
1 CATTGATAGTTGACCATTGACCGTTAACCGTTGACAGTTGACAGTTGAT
*
485 CATTGATCGTTGAC
1 CATTGATAGTTGAC
499 TGTTGACTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (49 bp):
CATTGATAGTTGACCATTGACCGTTAACCGTTGACAGTTGACAGTTGAT
Found at i:523 original size:7 final size:7
Alignment explanation
Indices: 344--505 Score: 108
Period size: 7 Copynumber: 23.1 Consensus size: 7
334 CAAACCCGGC
344 CCGTTGA
1 CCGTTGA
351 CCGTTGA
1 CCGTTGA
**
358 TAGTTGA
1 CCGTTGA
*
365 TCGTTGA
1 CCGTTGA
***
372 TTATTGA
1 CCGTTGA
* *
379 CTGTTAA
1 CCGTTGA
*
386 CCATTGA
1 CCGTTGA
*
393 CAGTTGA
1 CCGTTGA
*
400 CCATTGA
1 CCGTTGA
*
407 CCGTTAA
1 CCGTTGA
414 CCGTTGA
1 CCGTTGA
*
421 CAGTTGA
1 CCGTTGA
428 CCGTTGA
1 CCGTTGA
* *
435 TCATTGA
1 CCGTTGA
**
442 TAGTTGA
1 CCGTTGA
*
449 CCATTGA
1 CCGTTGA
456 CCGTTGA
1 CCGTTGA
463 CCGTTGA
1 CCGTTGA
*
470 CAGTTGA
1 CCGTTGA
*
477 CAGTTGA
1 CCGTTGA
* *
484 TCATTGA
1 CCGTTGA
*
491 TCGTTGA
1 CCGTTGA
*
498 CTGTTGA
1 CCGTTGA
505 C
1 C
506 TTTTGGGTTG
Statistics
Matches: 120, Mismatches: 35, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 120 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (7 bp):
CCGTTGA
Found at i:2584 original size:6 final size:6
Alignment explanation
Indices: 2575--2673 Score: 75
Period size: 6 Copynumber: 17.2 Consensus size: 6
2565 TTAAATTGGT
**
2575 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
* * * **
2622 TCT-AT TTTGAA TTTAAA TTT-GC TTTAAA TTTAAA -TTAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
2666 TTTGAAA T
1 TTT-AAA T
2674 GGTTTTAAAC
Statistics
Matches: 73, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
4 2 0.03
5 18 0.25
6 47 0.64
7 6 0.08
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:2584 original size:17 final size:15
Alignment explanation
Indices: 2559--2618 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 15
2549 TGATTTTAAA
*
2559 TTAAGTTTAAATTGGTT
1 TTAAATTTAAATT--TT
2576 TTAAATTT--A-TTT
1 TTAAATTTAAATTTT
2588 TTAAATTTAAATTTAT
1 TTAAATTTAAATTT-T
2604 CTTAAATTTAAATTT
1 -TTAAATTTAAATTT
2619 AAATCTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 10 0.27
14 2 0.05
15 3 0.08
16 1 0.03
17 21 0.57
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (15 bp):
TTAAATTTAAATTTT
Found at i:2588 original size:11 final size:11
Alignment explanation
Indices: 2551--2636 Score: 54
Period size: 11 Copynumber: 8.1 Consensus size: 11
2541 CAAACTTTTG
*
2551 ATTTTAAATTA
1 ATTTTAAATTT
* *
2562 AGTTTAAATTG
1 ATTTTAAATTT
*
2573 GTTTTAAATTT
1 ATTTTAAATTT
*
2584 ATTTTTAA---
1 ATTTTAAATTT
2592 A-TTTAAATTT
1 ATTTTAAATTT
*
2602 ATCTTAAATTT
1 ATTTTAAATTT
* *
2613 AAATTTAAATCT
1 -ATTTTAAATTT
*
2625 ATTTTGAATTT
1 ATTTTAAATTT
2636 A
1 A
2637 AATTTGCTTT
Statistics
Matches: 55, Mismatches: 15, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
7 5 0.09
8 1 0.02
10 1 0.02
11 40 0.73
12 8 0.15
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:2613 original size:23 final size:23
Alignment explanation
Indices: 2587--2641 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
2577 TAAATTTATT
*
2587 TTTAAATTTAAATTTATCTTAAA
1 TTTAAATTTAAATCTATCTTAAA
* *
2610 TTTAAATTTAAATCTATTTTGAA
1 TTTAAATTTAAATCTATCTTAAA
2633 TTTAAATTT
1 TTTAAATTT
2642 GCTTTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAAATTTAAATCTATCTTAAA
Found at i:2619 original size:17 final size:18
Alignment explanation
Indices: 2575--2619 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
2565 TTAAATTGGT
*
2575 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTCTTAAA
2593 TTTAAATTTA-TCTTAAA
1 TTTAAATTTATTCTTAAA
2610 TTTAAATTTA
1 TTTAAATTTA
2620 AATCTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTCTTAAA
Found at i:2651 original size:17 final size:17
Alignment explanation
Indices: 2610--2657 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2600 TTATCTTAAA
* *
2610 TTTAAATTTAAATCTAT
1 TTTAAATTTAAATTTAC
* *
2627 TTTGAATTTAAATTTGC
1 TTTAAATTTAAATTTAC
2644 TTTAAATTTAAATT
1 TTTAAATTTAAATT
2658 AAATTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Done.