Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001644.1 Kokia drynarioides strain JFW-HI SEQ_113288, 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: 5963
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:1179 original size:30 final size:30
Alignment explanation
Indices: 1113--1180 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1103 TGAAGCTTTT
*
1113 TTATTT-TTAGATATTAATATATCAATTTA
1 TTATTTATTAGATATTAATATATCAATTAA
* * *
1142 TTGTTTATTATATATTAATATA-CTTATTAA
1 TTATTTATTAGATATTAATATATC-AATTAA
1172 TTATTTATT
1 TTATTTATT
1181 TATTTCCTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
TTATTTATTAGATATTAATATATCAATTAA
Found at i:3540 original size:39 final size:39
Alignment explanation
Indices: 3497--3643 Score: 174
Period size: 39 Copynumber: 3.8 Consensus size: 39
3487 TTGCAACCGT
* **
3497 CCAATCTTTTACCCCGAGCTTTAGGCAGATCACCATCAG
1 CCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG
3536 CCAATCTCTTACCCCGAGCTTGGGGCAGACTACAGCCAT---
1 CCAATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAG
* * *
3575 CCGATCTTTTACCCCGAGCTTGGGGAAGATCACCATCAG
1 CCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG
* *
3614 CAAATCTCTTACCTCGAGCTTGGGGCAGAT
1 CCAATCTCTTACCCCGAGCTTGGGGCAGAT
3644 TGCAACTGTT
Statistics
Matches: 91, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
36 4 0.04
37 2 0.02
38 1 0.01
39 77 0.85
40 1 0.01
41 2 0.02
42 4 0.04
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (39 bp):
CCAATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAG
Found at i:3548 original size:78 final size:77
Alignment explanation
Indices: 3417--3649 Score: 261
Period size: 78 Copynumber: 3.0 Consensus size: 77
3407 AAATCACAAT
* * * * * * * * *
3417 CATCAAATCTTTTACCTCGAGC-CTGGACAGATTACCATTAGACAATCTCTTACCCCGAACCTAG
1 CATCCAATCTTTTACCCCGAGCTTTGG-CAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGG
*
3481 GGCAAATTGCAAC
65 GGCAGATTGCAAC
*
3494 CGTCCAATCTTTTACCCCGAGCTTTAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGG
1 CATCCAATCTTTTACCCCGAGCTTT-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGG
* * *
3559 GGCAGACTACAGC
65 GGCAGATTGCAAC
* * * * *
3572 CATCCGATCTTTTACCCCGAGCTTGGGGAAGATCACCATCAGCAAATCTCTTACCTCGAGCTTGG
1 CATCCAATCTTTTACCCCGAGCTT-TGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGG
3637 GGCAGATTGCAAC
65 GGCAGATTGCAAC
3650 TGTTAAAACA
Statistics
Matches: 130, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
77 19 0.15
78 109 0.84
79 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.24
Consensus pattern (77 bp):
CATCCAATCTTTTACCCCGAGCTTTGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGG
GCAGATTGCAAC
Found at i:4569 original size:89 final size:90
Alignment explanation
Indices: 4465--4699 Score: 271
Period size: 89 Copynumber: 2.6 Consensus size: 90
4455 AAGCTTGAGA
* * * *
4465 GTTAAAATGTGATTTTGGAAAAGTTT-AGCGGTTAAAATGTGATTTTGTAAAATGTTT-GGGGTC
1 GTTAAAATGTGATTTTAGAAAAGTTTAAG-GGTTAAAATGTAATTTTGGAAAA-GTTTAAGGGTC
* *
4528 AAAATATGATTTTGGAAAAGTTT-GGG
64 AAAATATAATTTTGGAAAAGTTTAAGG
* * * *
4554 GTTAAAATATAATTTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAA
1 GTTAAAATGTGATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCAA
*
4619 AATGTAATTTTGGAAAAGTTTAAGG
66 AATATAATTTTGGAAAAGTTTAAGG
* * * * *
4644 GTTAAAATGTGATTTTAGAAATGTTT-GGGAGTAAAAATATAATTTTAGAAAAGTTT
1 GTTAAAATGTGATTTTAGAAAAGTTTAAGG-GTTAAAATGTAATTTTGGAAAAGTTT
4700 GGGGACCTCT
Statistics
Matches: 124, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
88 4 0.03
89 71 0.57
90 49 0.40
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (90 bp):
GTTAAAATGTGATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTCAA
AATATAATTTTGGAAAAGTTTAAGG
Found at i:4617 original size:119 final size:120
Alignment explanation
Indices: 4438--4699 Score: 343
Period size: 119 Copynumber: 2.2 Consensus size: 120
4428 ACTCGAGATG
* * * * *
4438 AAAATAAAATTTTA-AAGAAGCTTGAGAGTTAAAATGTGATTTTGGAAAAGTTTAGCGGTTAAAA
1 AAAATATAATTTTAGAA-AAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGCGGTTAAAA
* * * * *
4502 TGTGATTTTGTAAAATGTTT-GGGGTCAAAATATGATTTTGGAAAAGTTTGGG-GTT
65 TGTAATTTTGGAAAA-GTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTGGGAGTA
*
4557 AAAATATAATTTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAG-GGTTAAAA
1 AAAATATAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTT-AGCGGTTAAAA
* * *
4621 TGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTAGAAATGTTTGGGAGTA
65 TGTAATTTTGGAAAAGTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTGGGAGTA
4677 AAAATATAATTTTAGAAAAGTTT
1 AAAATATAATTTTAGAAAAGTTT
4700 GGGGACCTCT
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
118 4 0.03
119 92 0.74
120 28 0.23
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (120 bp):
AAAATATAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAGCGGTTAAAAT
GTAATTTTGGAAAAGTTTAAGGGTCAAAATATGATTTTAGAAAAGTTTGGGAGTA
Found at i:4681 original size:30 final size:30
Alignment explanation
Indices: 4465--4703 Score: 270
Period size: 30 Copynumber: 8.0 Consensus size: 30
4455 AAGCTTGAGA
* *
4465 GTTAAAATGTGATTTTGGAAAAGTTTAGCG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
* *
4495 GTTAAAATGTGATTTTGTAAAATGTTT-GGG
1 GTTAAAATGTAATTTTGGAAAA-GTTTAGGG
* * *
4525 GTCAAAATATGATTTTGGAAAAGTTT-GGG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
4554 GTTAAAATATAATTTTTGAAAAGTTTAAGG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
*
4584 GTTAAAATGTAATTTTGGAAAAGTTTAAGG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
*
4614 GTTAAAATGTAATTTTGGAAAAGTTTAAGG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
4644 GTTAAAATGTGATTTTAGAAATGTTT-GGG
1 GTTAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
4673 AGTAAAAATATAATTTTAGAAAAGTTT-GGG
1 -GTTAAAATGTAATTTTGGAAAAGTTTAGGG
4703 G
1 G
4704 ACCTCTTAAG
Statistics
Matches: 187, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
29 33 0.18
30 150 0.80
31 4 0.02
ACGTcount: A:0.37, C:0.01, G:0.24, T:0.38
Consensus pattern (30 bp):
GTTAAAATGTAATTTTGGAAAAGTTTAGGG
Done.