Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011184.1 Kokia drynarioides strain JFW-HI SEQ_126160, 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: 13301
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Found at i:862 original size:16 final size:15
Alignment explanation
Indices: 836--865 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
826 TTTTTTTTTT
836 CCTTCTCCTTCTTCC
1 CCTTCTCCTTCTTCC
851 CCTTCTTCCTTCTTC
1 CCTTC-TCCTTCTTC
866 TTTCTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (15 bp):
CCTTCTCCTTCTTCC
Found at i:4252 original size:22 final size:22
Alignment explanation
Indices: 4224--4274 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4214 TTTCACTCAC
*
4224 TCTTGTCTTAGATAACACCAAT
1 TCTTGTCTCAGATAACACCAAT
4246 TCTTGTCTCAGATAACACCAAT
1 TCTTGTCTCAGATAACACCAAT
4268 TCTTGTC
1 TCTTGTC
4275 GCTTTCCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.37
Consensus pattern (22 bp):
TCTTGTCTCAGATAACACCAAT
Found at i:10367 original size:6 final size:6
Alignment explanation
Indices: 10358--10405 Score: 62
Period size: 6 Copynumber: 8.2 Consensus size: 6
10348 ATTTAAATTT
* * *
10358 ATATTA ATATTA ATATTA ACATTA ACATTA ACATTA ATATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
10405 A
1 A
10406 ATAAACATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (6 bp):
ATATTA
Found at i:12564 original size:297 final size:297
Alignment explanation
Indices: 12029--12622 Score: 1116
Period size: 297 Copynumber: 2.0 Consensus size: 297
12019 ACGAACATTC
*
12029 GAGTTAAATATGAATAAGCAGTTGATAATGGATATAAAATAACGCGAAGTAAGATAAATAAGAAG
1 GAGTTAAATATGAATAAGCAGTTGATAATGGATATAAAATAACACGAAGTAAGATAAATAAGAAG
* *
12094 ATAAATGATATGCAAAAATCAAAAATGCAAAATACGAGTGCATAATAATTTAAAATTAAATGCAA
66 ATAAATGATATGCAAAAATAAAAAATGCAAAATACGAGTGCATAATAATTTAAAATTAAATACAA
*
12159 ATATTGATGAGAAAGAAGAATGATGCAATCAGAGTTGAAAATGAGGCTTTTCGGATACCCGAGGG
131 ATATTGATGAGAAAGAAGAATAATGCAATCAGAGTTGAAAATGAGGCTTTTCGGATACCCGAGGG
* *
12224 CGAAATGATAATTTTGGATCCTCGGGGGCAAAATGGCAATTTTGAGAAAATTCGGAGTTAAAAAT
196 CGAAATGATAATTTTGGATCCTCGGGGGAAAAATGACAATTTTGAGAAAATTCGGAGTTAAAAAT
12289 GAAATTTTTAGACATTCGGGGGTAAAAGGGTAATTTT
261 GAAATTTTTAGACATTCGGGGGTAAAAGGGTAATTTT
12326 GAGTTAAATATGAATAAGCAGTTGATAATGGATATAAAATAACACGAAGTAAGATAAATAAGAAG
1 GAGTTAAATATGAATAAGCAGTTGATAATGGATATAAAATAACACGAAGTAAGATAAATAAGAAG
12391 ATAAATGATATGCAAAAATAAAAAATGCAAAATACGAGTGCATAATAATTTAAAATTAAATACAA
66 ATAAATGATATGCAAAAATAAAAAATGCAAAATACGAGTGCATAATAATTTAAAATTAAATACAA
12456 ATATTGATGAGAAAGAAGAATAATGCAATCAGAGTTGAAAATGAGGCTTTTCGGATACCCGAGGG
131 ATATTGATGAGAAAGAAGAATAATGCAATCAGAGTTGAAAATGAGGCTTTTCGGATACCCGAGGG
*
12521 CGAAATGATAATTTTGGATCCTCGGGGGAAAAATGATAATTTTGAGAAAATTCGGAGTTAAAAAT
196 CGAAATGATAATTTTGGATCCTCGGGGGAAAAATGACAATTTTGAGAAAATTCGGAGTTAAAAAT
*
12586 GAAATTTTTAGACATTCGGGGGTAAATGGGTAATTTT
261 GAAATTTTTAGACATTCGGGGGTAAAAGGGTAATTTT
12623 TAGAGTTTCG
Statistics
Matches: 289, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
297 289 1.00
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (297 bp):
GAGTTAAATATGAATAAGCAGTTGATAATGGATATAAAATAACACGAAGTAAGATAAATAAGAAG
ATAAATGATATGCAAAAATAAAAAATGCAAAATACGAGTGCATAATAATTTAAAATTAAATACAA
ATATTGATGAGAAAGAAGAATAATGCAATCAGAGTTGAAAATGAGGCTTTTCGGATACCCGAGGG
CGAAATGATAATTTTGGATCCTCGGGGGAAAAATGACAATTTTGAGAAAATTCGGAGTTAAAAAT
GAAATTTTTAGACATTCGGGGGTAAAAGGGTAATTTT
Found at i:12645 original size:58 final size:56
Alignment explanation
Indices: 12581--13010 Score: 361
Period size: 58 Copynumber: 7.4 Consensus size: 56
12571 TTCGGAGTTA
* *
12581 AAAATGAAATTTTTAGACA-TTCGGGGGTAAATGGGTAATTTTTAG-AGTTTCGAGGTC
1 AAAATGAAATTTTTGGA-AGTTCGGGGGTAAAT-GG-AATTTTTGGAAGTTTCGAGGTC
* *
12638 GAAAATGAAGTTTTTGGACA-TTCGGGGGCAAAATGGTAATTTTTGGAAGTTTC-AGTGTC
1 -AAAATGAAATTTTTGGA-AGTTCGGGGG-TAAATGG-AATTTTTGGAAGTTTCGAG-GTC
*
12697 AAAAATGGAAA-TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
1 -AAAAT-GAAATTTTTGGAAGTTCGGGGGT--AAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * **
12756 AAAATGGAATTTTTTGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTAAGGTC
1 AAAATGAAATTTTTGGAAGTTCGGGGGT--AAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * *
12814 AAAATGGAATTTTTGGAAGTTCGGGGGTTAAATGGAATTTTTGGAATTTTTGGGGTTG
1 AAAATGAAATTTTTGGAAGTTCGGGGG-TAAATGGAATTTTTGGAAGTTTCGAGG-TC
* * *
12872 AAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTGGAAG-CTCGAGGGTC
1 AAAATGAAATTTTTGGAAGTTCGGGGGT--AAATGGAATTTTTGGAAGTTTCGA-GGTC
* * * * * *
12930 AAAATGGAATTTTTGGAAATTTTGGGGTCGTAAATGGAATTTTTAGAAG-TTAGAGGGTA
1 AAAATGAAATTTTTGG-AAGTTCGGGG--GTAAATGGAATTTTTGGAAGTTTCGA-GGTC
*
12989 AAAATGTAATTTTTGGATAGTT
1 AAAATGAAATTTTTGGA-AGTT
13011 TAGGGACCTT
Statistics
Matches: 319, Mismatches: 35, Indels: 35
0.82 0.09 0.09
Matches are distributed among these distances:
57 26 0.08
58 159 0.50
59 121 0.38
60 11 0.03
61 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (56 bp):
AAAATGAAATTTTTGGAAGTTCGGGGGTAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:12680 original size:29 final size:28
Alignment explanation
Indices: 12629--13010 Score: 329
Period size: 29 Copynumber: 13.1 Consensus size: 28
12619 TTTTTAGAGT
*
12629 TTCGAGGTCGAAAAT-GAAGTTTTTGGACA-
1 TTCGGGGTC-AAAATGGAA-TTTTTGGA-AG
*
12658 TTCGGGGGCAAAATGGTAATTTTTGGAAG
1 TTCGGGGTCAAAATGG-AATTTTTGGAAG
* * *
12687 TTTCAGTGTCAAAAATGGAAATTTTGGAAG
1 -TTCGGGGTC-AAAATGGAATTTTTGGAAG
*
12717 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCG-GGGTCAAAATGGAATTTTTGGAAG
* *
12746 TTTCGAGGTCAAAATGGAATTTTTTGAAG
1 -TTCGGGGTCAAAATGGAATTTTTGGAAG
* *
12775 TTCGAGGGTAAAAATGGAATTTTTAGAAG
1 TTCG-GGGTCAAAATGGAATTTTTGGAAG
***
12804 TTTTAAGGTCAAAATGGAATTTTTGGAAG
1 -TTCGGGGTCAAAATGGAATTTTTGGAAG
* *
12833 TTCGGGGGT-TAAATGGAATTTTTGGAATT
1 TTC-GGGGTCAAAATGGAATTTTTGGAA-G
* * *
12862 TTTGGGGTTGAAAATGGAATTTTTGAAAG
1 TTCGGGG-TCAAAATGGAATTTTTGGAAG
*
12891 TTCGGGGGTAAAAATGGAATTTTTGGAAG
1 TTC-GGGGTCAAAATGGAATTTTTGGAAG
* *
12920 CTCGAGGGTCAAAATGGAATTTTTGGAAAT
1 TTCG-GGGTCAAAATGGAATTTTTGG-AAG
* * *
12950 TTTGGGGTCGTAAATGGAATTTTTAGAAG
1 TTCGGGGTC-AAAATGGAATTTTTGGAAG
* * *
12979 TTAGAGGGTAAAAATGTAATTTTTGGATAG
1 TTCG-GGGTCAAAATGGAATTTTTGGA-AG
13009 TT
1 TT
13011 TAGGGACCTT
Statistics
Matches: 288, Mismatches: 46, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
28 34 0.12
29 173 0.60
30 74 0.26
31 7 0.02
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.35
Consensus pattern (28 bp):
TTCGGGGTCAAAATGGAATTTTTGGAAG
Done.