Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009387.1 Kokia drynarioides strain JFW-HI SEQ_124094, 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: 10458
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Found at i:611 original size:17 final size:18
Alignment explanation
Indices: 577--612 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
567 TGAATTTCTA
577 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
595 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
612 T
1 T
613 AACTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:2510 original size:20 final size:21
Alignment explanation
Indices: 2468--2513 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
2458 TTTGAATTGT
* *
2468 TAATTATTTACAATTTTTTAA
1 TAATTATTTACAAGTTTTAAA
2489 TAATTATTTA-AAGTTTTAAA
1 TAATTATTTACAAGTTTTAAA
2509 TAATT
1 TAATT
2514 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATTATTTACAAGTTTTAAA
Found at i:2565 original size:20 final size:20
Alignment explanation
Indices: 2483--2579 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 20
2473 ATTTACAATT
*
2483 TTTTAATAA-TTATTTA-AA
1 TTTTAATAATTTTTTTACAA
*
2501 GTTTTAAATAATTTTTTTTAAAA
1 -TTTT-AATAA-TTTTTTTACAA
* * *
2524 ATTAAATAA-TTTTCTATC-A
1 TTTTAATAATTTTTTTA-CAA
2543 TTTTAATAATTTTTTTACAA
1 TTTTAATAATTTTTTTACAA
2563 TTTTAA-AATATTTTTTA
1 TTTTAATAAT-TTTTTTA
2580 ATAATTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
19 22 0.35
20 25 0.40
21 5 0.08
22 8 0.13
23 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTTAATAATTTTTTTACAA
Found at i:2575 original size:21 final size:21
Alignment explanation
Indices: 2542--2599 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
2532 ATTTTCTATC
*
2542 ATTTTAATA-ATTTTTTTACA
1 ATTTTAAAATATTTTTTTACA
* *
2562 ATTTTAAAATATTTTTTAATA
1 ATTTTAAAATATTTTTTTACA
*
2583 A-TTT-AAATGTTTTTTTA
1 ATTTTAAAATATTTTTTTA
2600 ATAATTTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 11 0.34
20 11 0.34
21 10 0.31
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAAAATATTTTTTTACA
Found at i:2619 original size:20 final size:19
Alignment explanation
Indices: 2514--2621 Score: 76
Period size: 20 Copynumber: 5.5 Consensus size: 19
2504 TTAAATAATT
*
2514 TTTTTTAA-AAATTAAATAA
1 TTTTTTAATAATTTAAAT-A
* * *
2533 TTTTCT-ATCATTTTAATAA
1 TTTTTTAATAATTTAAAT-A
* *
2552 TTTTTTTACAATTTTAAAATA
1 TTTTTTAATAA-TTT-AAATA
*
2573 TTTTTTAATAATTTAAATGT
1 TTTTTTAATAATTTAAAT-A
*
2593 TTTTTTAATAATTTATATA
1 TTTTTTAATAATTTAAATA
2612 TATTTTTAAT
1 T-TTTTTAAT
2622 TTTTTTACTA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
19 23 0.33
20 30 0.43
21 13 0.19
22 3 0.04
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTTTTAATAATTTAAATA
Found at i:5692 original size:18 final size:18
Alignment explanation
Indices: 5652--5695 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5642 AATTCATATA
* * *
5652 ATATTTATTCTTCAGAAT
1 ATATTTCTTCTTCAAAAC
*
5670 TTATTTCTTCTTCAAAAC
1 ATATTTCTTCTTCAAAAC
5688 ATATTTCT
1 ATATTTCT
5696 AGATTTTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (18 bp):
ATATTTCTTCTTCAAAAC
Found at i:9035 original size:28 final size:27
Alignment explanation
Indices: 8986--9053 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
8976 AGAGGATTTT
*** *
8986 TTTTTTTTTAAATTTCAGAGGAAAGGG
1 TTTTTTTTTAAATGAAAGAGGAAAGGA
*
9013 TTTTTTTTTAAATGAAAGAAGGAAATGA
1 TTTTTTTTTAAATGAAAG-AGGAAAGGA
9041 TTTTTTTTCTAAA
1 TTTTTTTT-TAAA
9054 AGAGGTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.44
28 15 0.44
29 4 0.12
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (27 bp):
TTTTTTTTTAAATGAAAGAGGAAAGGA
Found at i:9639 original size:59 final size:59
Alignment explanation
Indices: 9547--9808 Score: 323
Period size: 59 Copynumber: 4.4 Consensus size: 59
9537 TAAACTGTCC
* * *
9547 AAAAATTCTATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGA-CACCGAAATTTCT
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCA-CGAAATTTCT
* * *
9606 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCAATTTTT-ACCCCCGAACTTTC-
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAA-TCCCATTTTTGA-CCACGAAATTTCT
**
9665 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCATAAAATTTCT
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCACGAAATTTCT
* * * * *
9724 AAAAATTCCATTTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCTCGAAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCACGAAATTTCT
* * * *
9783 CAAACTTCTATTTTTACCCCCGAACT
1 AAAAATTCCATTTTTACCCTCGAACT
9809 CTCAAAATTA
Statistics
Matches: 177, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
58 17 0.10
59 142 0.80
60 17 0.10
61 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCACGAAATTTCT
Found at i:9755 original size:118 final size:118
Alignment explanation
Indices: 9538--9808 Score: 368
Period size: 118 Copynumber: 2.3 Consensus size: 118
9528 GGAGGTCCCT
* * *
9538 AAACTGTCCAAAAATTCTATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACACCGAAATT
1 AAACT-TCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAAATT
* *
9603 TCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCAATTTTT-ACCCCCG
65 TCTAAAAATTCCATTTTTACCCCCGAACTCCCAAAAA-TCCAATTTTTGA-CCCCG
* * *
9658 -AACTTTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC-CATAAAATT
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACAC-CAAAATT
* *
9721 TCTAAAAATTCCATTTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCTCG
65 TCTAAAAATTCCATTTTTACCCCCGAACTCCCAAAAATCCAATTTTTGACCCCG
* * *
9775 AAACTTCCCAAACTTCTATTTTTACCCCCGAACT
1 AAACTTCCAAAAATTCTATTTTTACCCTCGAACT
9809 CTCAAAATTA
Statistics
Matches: 133, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
117 14 0.11
118 115 0.86
119 4 0.03
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (118 bp):
AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACACCAAAATTT
CTAAAAATTCCATTTTTACCCCCGAACTCCCAAAAATCCAATTTTTGACCCCG
Found at i:9808 original size:29 final size:29
Alignment explanation
Indices: 9539--9808 Score: 265
Period size: 30 Copynumber: 9.1 Consensus size: 29
9529 GAGGTCCCTA
* *
9539 AACTGTCCAAAAATTCTATTTTTACCCTCA
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
* * *
9569 AACTTCTAAAAATCCCATTTTTGACAC-CG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
9598 AAATTTCTAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
*
9628 AACTTCCAAAAATTCCAATTTTTACCCCCG
1 AACTTCCAAAAATTCC-ATTTTTACCCTCG
*
9658 AACTTTCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* * **
9687 AACTTCCAAAAATCCCATTTTTGACCATAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
9717 AATTTCTAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
9746 AACTCCCAAAAATCCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* * * *
9775 AAACTTCCCAAACTTCTATTTTTACCCCCG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
9805 AACT
1 AACT
9809 CTCAAAATTA
Statistics
Matches: 196, Mismatches: 36, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
29 95 0.48
30 101 0.52
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:10214 original size:33 final size:32
Alignment explanation
Indices: 10157--10226 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
10147 GACGAGAGGA
*** *
10157 TTTTTTTTTTTAAATTTCAGAGGAAAGGGTTT
1 TTTTTTTTTTTAAATGAAAGAGGAAAGGATTT
*
10189 TTTTTTTTTTTAAATGAAAGAAGGAAATGATTT
1 TTTTTTTTTTTAAATGAAAG-AGGAAAGGATTT
10222 TTTTT
1 TTTTT
10227 CTAAAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (32 bp):
TTTTTTTTTTTAAATGAAAGAGGAAAGGATTT
Done.