Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012605.1 Kokia drynarioides strain JFW-HI SEQ_127614, 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: 13476
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.33
Warning! 354 characters in sequence are not A, C, G, or T
Found at i:280 original size:96 final size:96
Alignment explanation
Indices: 101--287 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 96
91 TGTAAAACGA
** * *
101 TATTCGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAATC
1 TATTCGATTATCTTGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCAGAATC
*
166 GAAAATAAGGAAACATTGCCTCGATTAAGGG
66 GAAAATAAAGAAACATTGCCTCGATTAAGGG
* **
197 TATTCGATTAT-TTCGATTTGAAGAAAAATTACACCTAGTGAGTTAAGGCACAA-ATTTTTGAAA
1 TATTCGATTATCTT-GATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCAG-AA
*
260 CTCGAAACA-AAAG-AATATTGCCTCGATT
64 -TCGAAA-ATAAAGAAACATTGCCTCGATT
288 TTTGAAGCTT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
95 7 0.09
96 61 0.78
97 9 0.12
98 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
TATTCGATTATCTTGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCAGAATC
GAAAATAAAGAAACATTGCCTCGATTAAGGG
Found at i:864 original size:59 final size:59
Alignment explanation
Indices: 602--1061 Score: 675
Period size: 58 Copynumber: 7.9 Consensus size: 59
592 TTCGAGGTCG
* *
602 AAAATGGGATTTTTGGAAGTTCG-GAGGTGAAATGGTAATTTTTGGAAGGTTCGGGG-TC
1 AAAATGGGATTTTTGGAAGTTCGAG-GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
*
660 AAAATGGGATTTTTGGAAGTTCG-GGAGTAAAATGGTAATTTTTGGAAGGTTCAGGGTTA
1 AAAATGGGATTTTTGGAAGTTCGAGG-GTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* * * *
719 AAAATGGGA-ATTTGGAAGTTCGAGGGTAAATTGGTAATTTTAGGAAGGTTTGGGGTT-
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
776 AAAATGAGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGATGGTTCGGGGTTA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* ** *
835 AAAATGGGATTTTTGGAAGTT-AAGGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTCA
1 AAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
* *
894 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGCAATTTTTGAAAGGTTCGGGGTTA
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
*
953 AAAATGGGATTTTTGGAAGTTC-AGGGGTAAAATGGTAATTTTTGGAAGGTTC-GGGTCA
1 AAAATGGGATTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
*
1011 AAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGGAAGGTT
1 AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTT
1062 TAGGGACCTC
Statistics
Matches: 363, Mismatches: 30, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
57 9 0.02
58 190 0.52
59 163 0.45
60 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTTA
Found at i:1066 original size:29 final size:29
Alignment explanation
Indices: 602--1066 Score: 399
Period size: 29 Copynumber: 16.0 Consensus size: 29
592 TTCGAGGTCG
* *
602 AAAATGG-GATTTTTGGAA-GTTCGGAGGT
1 AAAATGGTAATTTTTGGAAGGTTCAG-GGT
* *
630 GAAATGGTAATTTTTGGAAGGTTCGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGT
* *
659 CAAAATGG-GATTTTTGGAA-GTTCGGGAGT
1 -AAAATGGTAATTTTTGGAAGGTTCAGG-GT
688 AAAATGGTAATTTTTGGAAGGTTCAGGGTT
1 AAAATGGTAATTTTTGGAAGGTTCAGGG-T
*
718 AAAAATGGGAA--TTTGGAA-GTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGGTTC-AGGGT
* * **
746 AAATTGGTAATTTTAGGAAGGTTTGGGGTT
1 AAAATGGTAATTTTTGGAAGGTTCAGGG-T
776 AAAAT-G-AGATTTTTGGAA-GTTCGAGGGT
1 AAAATGGTA-ATTTTTGGAAGGTTC-AGGGT
* *
804 AAAATGGTAATTTTTGGATGGTTCGGGGTT
1 AAAATGGTAATTTTTGGAAGGTTCAGGG-T
* *
834 AAAAATGG-GATTTTTGGAA-GTTAAGGGGT
1 -AAAATGGTAATTTTTGGAAGGTTCA-GGGT
*
863 AAAATGGTAATTTTTGGAAGGTTCAAGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGT
*
892 CAAAAATGG-GATTTTTGGAA-GTTCGAGGGT
1 --AAAATGGTAATTTTTGGAAGGTTC-AGGGT
* * *
922 AAAATGGCAATTTTTGAAAGGTTCGGGGTT
1 AAAATGGTAATTTTTGGAAGGTTCAGGG-T
*
952 AAAAATGG-GATTTTTGGAA-GTTCAGGGGT
1 -AAAATGGTAATTTTTGGAAGGTTCA-GGGT
981 AAAATGGTAATTTTTGGAAGGTTC-GGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGT
* * *
1009 CAAAAATGG-GATTTTTGGAAGTTTGAGGGT
1 --AAAATGGTAATTTTTGGAAGGTTCAGGGT
*
1039 AAAATGGTAATTTTTGGAAGGTTTAGGG
1 AAAATGGTAATTTTTGGAAGGTTCAGGG
1067 ACCTCCATGG
Statistics
Matches: 360, Mismatches: 40, Indels: 73
0.76 0.08 0.15
Matches are distributed among these distances:
27 8 0.02
28 67 0.19
29 160 0.44
30 95 0.26
31 30 0.08
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGGTTCAGGGT
Found at i:2710 original size:17 final size:16
Alignment explanation
Indices: 2690--2766 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
2680 AAATAAACTT
2690 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
2707 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
*
2724 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
2741 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
2758 TAAATTTAA
1 TAAATTTAA
2767 GCTGATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 1 0.02
17 47 0.94
18 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:2763 original size:34 final size:34
Alignment explanation
Indices: 2690--2766 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 34
2680 AAATAAACTT
* * * *
2690 TAAATTTAAATTTATAATAAATTTAAATTTCAAC
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
* *
2724 CAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
2758 TAAATTTAA
1 TAAATTTAA
2767 GCTGATTGGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Done.