Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001895.1 Kokia drynarioides strain JFW-HI SEQ_113679, 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: 4600
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Found at i:648 original size:18 final size:17
Alignment explanation
Indices: 622--719 Score: 97
Period size: 18 Copynumber: 5.5 Consensus size: 17
612 GTATTTATTT
622 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* * *
641 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
658 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
*
676 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TTTAAAA
* * *
694 CAAATTCAATTTTAAAA
1 TAAATTTAAATTTAAAA
711 TAAATTTAA
1 TAAATTTAA
720 GGAGAGTATG
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
17 25 0.38
18 37 0.57
19 3 0.05
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:669 original size:24 final size:24
Alignment explanation
Indices: 642--688 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
632 ATTTGAAAAT
*
642 AATTTTAAACTTAAA-TTAAATTTA
1 AATTTTAAA-ATAAATTTAAATTTA
666 AATTTTAAAATAAATTTAAATTT
1 AATTTTAAAATAAATTTAAATTT
689 TTAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTTAAAATAAATTTAAATTTA
Found at i:674 original size:7 final size:6
Alignment explanation
Indices: 620--688 Score: 54
Period size: 6 Copynumber: 11.5 Consensus size: 6
610 TCGTATTTAT
* * *
620 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
668 TTTTAAA -ATAAA TTTAAA TTT
1 -TTTAAA TTTAAA TTTAAA TTT
689 TTAAACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
5 11 0.22
6 24 0.48
7 15 0.30
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:706 original size:17 final size:17
Alignment explanation
Indices: 666--716 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
656 ATTAAATTTA
* *
666 AATTTTAAAATAAATTTA
1 AATTTTAAAACAAA-TTC
*
684 AATTTTTAAACAAATTC
1 AATTTTAAAACAAATTC
*
701 AATTTTAAAATAAATT
1 AATTTTAAAACAAATT
717 TAAGGAGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTTAAAACAAATTC
Found at i:2704 original size:43 final size:43
Alignment explanation
Indices: 2643--2748 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 43
2633 AAGTGTTCTT
* * * *
2643 AGTGCCAACTCGGTTGAAAGCTAATCCAGCTAGAAGCGTTTTC
1 AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
* * *
2686 AGTGCCAACTCAGTTGAAAGCGCATCCAATTGGAAGAGTTTTC
1 AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
* *
2729 AATGCCAACTCAGCTGAAAG
1 AGTGCCAACTCAGTTGAAAG
2749 AACTTCCAGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (43 bp):
AGTGCCAACTCAGTTGAAAGCGAATCCAACTAGAAGAGTTTTC
Found at i:2762 original size:43 final size:43
Alignment explanation
Indices: 2675--2762 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
2665 AATCCAGCTA
* * * **
2675 GAAGCGTTTTCAGTGCCAACTCAGTTGAAAGCGCATCCAATTG
1 GAAGAGTTTTCAATGCCAACTCAGCTGAAAGAACATCCAATTG
* *
2718 GAAGAGTTTTCAATGCCAACTCAGCTGAAAGAACTTCCAGTTG
1 GAAGAGTTTTCAATGCCAACTCAGCTGAAAGAACATCCAATTG
2761 GA
1 GA
2763 CGCGCTTTCA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
GAAGAGTTTTCAATGCCAACTCAGCTGAAAGAACATCCAATTG
Found at i:2772 original size:43 final size:43
Alignment explanation
Indices: 2682--2772 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
2672 CTAGAAGCGT
* * ** *
2682 TTTCAGTGCCAACTCAGTTGAAAGCGCATCCAATTGGAAGAGT
1 TTTCAATGCCAACTCAGCTGAAAGAACATCCAATTGGAAGAGC
* * * *
2725 TTTCAATGCCAACTCAGCTGAAAGAACTTCCAGTTGGACGCGC
1 TTTCAATGCCAACTCAGCTGAAAGAACATCCAATTGGAAGAGC
2768 TTTCA
1 TTTCA
2773 GTACTTTTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (43 bp):
TTTCAATGCCAACTCAGCTGAAAGAACATCCAATTGGAAGAGC
Found at i:3507 original size:8 final size:9
Alignment explanation
Indices: 3494--3675 Score: 61
Period size: 9 Copynumber: 19.6 Consensus size: 9
3484 TTATTAGAAT
3494 TTTTTAT-A
1 TTTTTATAA
3502 TTTTTATAA
1 TTTTTATAA
3511 TTTTTTATGAA
1 -TTTTTAT-AA
* *
3522 TTCTTACAA
1 TTTTTATAA
3531 GTTTTTATAAA
1 -TTTTTAT-AA
*
3542 ATTTTA-AA
1 TTTTTATAA
3550 TGTTTTATAA
1 T-TTTTATAA
3560 TTTATTACT-A
1 TTT-TTA-TAA
* *** *
3570 GTAGAAT-T
1 TTTTTATAA
3578 TTTTTATAA
1 TTTTTATAA
*
3587 GTTTTTTATGAT
1 --TTTTTAT-AA
3599 TTTTTATAA
1 TTTTTATAA
*
3608 GTTTTATAA
1 TTTTTATAA
**
3617 TTGGTATAA
1 TTTTTATAA
*
3626 TTTTATATTA
1 TTTT-TATAA
*
3636 GTTTTA-ATA
1 TTTTTATA-A
*
3645 TTTTTAT-T
1 TTTTTATAA
3653 TTTTTATAA
1 TTTTTATAA
* *
3662 TTTATATGA
1 TTTTTATAA
3671 TTTTT
1 TTTTT
3676 TATGAGAAAA
Statistics
Matches: 124, Mismatches: 33, Indels: 33
0.65 0.17 0.17
Matches are distributed among these distances:
8 20 0.16
9 47 0.38
10 44 0.35
11 12 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3512 original size:18 final size:20
Alignment explanation
Indices: 3475--3518 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
3465 ATTTTCTAAC
3475 TTTTATATCTTATTAGAATT
1 TTTTATATCTTATTAGAATT
*
3495 TTTTATAT-TT-TTATAATT
1 TTTTATATCTTATTAGAATT
3513 TTTTAT
1 TTTTAT
3519 GAATTCTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 2 0.09
20 8 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTATATCTTATTAGAATT
Found at i:3515 original size:10 final size:10
Alignment explanation
Indices: 3491--3678 Score: 74
Period size: 10 Copynumber: 19.0 Consensus size: 10
3481 ATCTTATTAG
3491 AATTTTTTAT
1 AATTTTTTAT
3501 -A-TTTTTAT
1 AATTTTTTAT
3509 AATTTTTTAT
1 AATTTTTTAT
* *
3519 GAA-TTCTTAC
1 -AATTTTTTAT
*
3529 AAGTTTTTAT
1 AATTTTTTAT
**
3539 AAAATTTTA-
1 AATTTTTTAT
*
3548 AATGTTTTAT
1 AATTTTTTAT
3558 AATTTATTACTAGT
1 AATTT-TT--TA-T
3572 AGAATTTTTTTAT
1 --AA-TTTTTTAT
3585 AAGTTTTTTAT
1 AA-TTTTTTAT
*
3596 GATTTTTTAT
1 AATTTTTTAT
*
3606 AA-GTTTTAT
1 AATTTTTTAT
**
3615 AA-TTGGTAT
1 AATTTTTTAT
*
3624 AATTTTATAT
1 AATTTTTTAT
* * *
3634 TAGTTTTAAT
1 AATTTTTTAT
3644 -A-TTTTTAT
1 AATTTTTTAT
3652 --TTTTTTAT
1 AATTTTTTAT
*
3660 AA-TTTATAT
1 AATTTTTTAT
*
3669 GATTTTTTAT
1 AATTTTTTAT
3679 GAGAAAAATA
Statistics
Matches: 135, Mismatches: 26, Indels: 34
0.69 0.13 0.17
Matches are distributed among these distances:
8 20 0.15
9 33 0.24
10 54 0.40
11 15 0.11
13 3 0.02
14 3 0.02
16 4 0.03
17 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (10 bp):
AATTTTTTAT
Found at i:3593 original size:11 final size:11
Alignment explanation
Indices: 3577--3612 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
3567 CTAGTAGAAT
3577 TTTTTTATAAG
1 TTTTTTATAAG
*
3588 TTTTTTATGA-
1 TTTTTTATAAG
3598 TTTTTTATAAG
1 TTTTTTATAAG
3609 TTTT
1 TTTT
3613 ATAATTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTTTATAAG
Done.