Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004448.1 Kokia drynarioides strain JFW-HI SEQ_117850, 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, 711
Length: 1186
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.29
Found at i:241 original size:29 final size:29
Alignment explanation
Indices: 208--953 Score: 429
Period size: 29 Copynumber: 25.4 Consensus size: 29
198 AAAAAAAGGG
208 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
** * *
237 ATTTTTCAAAGGTTCGAGGTTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTA
*
267 GTTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * *
296 ATTTTTAGAAGGTTCG-GGGCCAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGG--TAAAATGGTA
* *
326 ATTTTTGGAAGTTTGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * * *
355 TTTTTTTGAAAGTTCG-GGGTAAAAAAAGG-G
1 -ATTTTTGGAAGTTCGAGGGT--AAAATGGTA
* * *
385 ATTTTTGGAAGTTTGGGGGTAAAATAGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
*
414 ATTTTTGGAAAGTTCG-GGGTCAAAAATGG-G
1 ATTTTTGG-AAGTTCGAGGGT--AAAATGGTA
* * * *
444 ATTTTTAGAAGTTTGGGGGTAATATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
473 ATTTTTGGAAAATTCGA-GGTCAAAATGG-G
1 ATTTTTGG-AAGTTCGAGGGT-AAAATGGTA
* *
502 ATTTTTGGAAATT-TAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGA-GGGTAAAATGGTA
*
531 ATTTTTAGAAGGTTC-AGGGTCAAAAAT-G-A
1 ATTTTTGGAA-GTTCGAGGGT--AAAATGGTA
*
560 GATTTTTGGAAGTTTGAGGGTAAAATGGTA
1 -ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* *
590 ATTTTTAGAAAGTT-TAGGGTCAAAAATGG--
1 ATTTTT-GGAAGTTCGAGGGT--AAAATGGTA
* *
619 GTTTTT-GAAATTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* ** * *
647 ATTTTTAGAAGGTTCGAGATTAAAAAAGG-G
1 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTA
* * *
677 ATTTTCT-AAAGTTTGGGGGTAAAATGGTA
1 ATTTT-TGGAAGTTCGAGGGTAAAATGGTA
*
706 A-TTTTGGAAAGTTCGA-GGTCAAAAATGG-G
1 ATTTTTGG-AAGTTCGAGGGT--AAAATGGTA
*
735 ATTTTTGGAAGTTTGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
* * *
764 ATTTTAGGAAAGTTTG-GGGTCAAAAAAGG--
1 ATTTTTGG-AAGTTCGAGGGT--AAAATGGTA
* *
793 ATTTTTTGAAGTT-TAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGA-GGGTAAAATGGTA
* *
822 ATTTTTAGAAGGTTCG-GGGTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGGT-AAAATGGTA
* *
851 ATTTTTAGAAGGTT-TAGGGTAAAATGGTA
1 ATTTTTGGAA-GTTCGAGGGTAAAATGGTA
* * *
880 ATTTTTAGAAGGTT-TAGGGTTAAAAATGG-G
1 ATTTTTGGAA-GTTCGAGGG-T-AAAATGGTA
*
910 ATTTTTGGAAATTCGAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGA-GGGTAAAATGGTA
940 ATTTTTGGAGAGTT
1 ATTTTTGGA-AGTT
954 AAAGGACCTC
Statistics
Matches: 561, Mismatches: 89, Indels: 132
0.72 0.11 0.17
Matches are distributed among these distances:
26 7 0.01
27 12 0.02
28 83 0.15
29 225 0.40
30 170 0.30
31 64 0.11
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGTAAAATGGTA
Found at i:272 original size:59 final size:59
Alignment explanation
Indices: 199--946 Score: 802
Period size: 59 Copynumber: 12.8 Consensus size: 59
189 GAAGGTTCGA
* * * *
199 AAAAAAGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTCAAAGGTTCGAGGTT
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAGGTTCGAGGTC
* * * *
258 AAAAATGGGGTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTT-AGAAGGTTCGGGGCC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGA-AAGGTTCGAGGTC
* * * *
317 AAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTATTTTTTTGAAA-GTTCGGGGTA
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTA-ATTTTTGAAAGGTTCGAGGTC
* * * *
376 AAAAAAGGGATTTTTGGAAGTTTGGGGGTAAAATAGTAATTTTTGGAAA-GTTCGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAGGTTCGAGGTC
* * * *
435 AAAAATGGGATTTTTAGAAGTTTGGGGGTAATATGGTAATTTTTGGAAA-ATTCGAGGTC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAGGTTCGAGGTC
*
494 -AAAATGGGATTTTTGGAAATTT-AGGGGTAAAATGGTAATTTTT-AGAAGGTTC-AGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGA-GGGTAAAATGGTAATTTTTGA-AAGGTTCGA-GGTC
* * *
552 AAAAATGAGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTAGAAAGTTTAG-GGTC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-GAAAGGTTCGAGGTC
* * * *
611 AAAAATGGG-TTTTT-GAAATTCGAGGGTAAAATGGTAATTTTT-AGAAGGTTCGAGATT
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGA-AAGGTTCGAGGTC
* * * *
668 AAAAAAGGGATTTTCT-AAAGTTTGGGGGTAAAATGGTAATTTTGGAAA-GTTCGAGGTC
1 AAAAATGGGATTTT-TGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAGGTTCGAGGTC
* * *
726 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTAGGAAA-GTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTT-TGAAAGGTTCGAGGTC
* * *
785 AAAAA-AGGATTTTTTGAAGTTT-AGGGGTAAAATGGTAATTTTT-AGAAGGTTCGGGGT-
1 AAAAATGGGATTTTTGGAAGTTTGA-GGGTAAAATGGTAATTTTTGA-AAGGTTCGAGGTC
* * *
842 AAAAATGGGATTTTTAGAAGGTTT-AGGGTAAAATGGTAATTTTT-AGAAGGTT-TAGGGTT
1 AAAAATGGGATTTTTGGAA-GTTTGAGGGTAAAATGGTAATTTTTGA-AAGGTTCGA-GGTC
* *
901 AAAAATGGGATTTTTGGAAATTCGAGGGGTAAAATGGTAATTTTTG
1 AAAAATGGGATTTTTGGAAGTTTGA-GGGTAAAATGGTAATTTTTG
947 GAGAGTTAAA
Statistics
Matches: 598, Mismatches: 61, Indels: 58
0.83 0.09 0.08
Matches are distributed among these distances:
55 1 0.00
56 8 0.01
57 48 0.08
58 190 0.32
59 316 0.53
60 33 0.06
61 2 0.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
AAAAATGGGATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAGGTTCGAGGTC
Done.