Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011658.1 Kokia drynarioides strain JFW-HI SEQ_126650, 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, 937
Length: 1562
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Found at i:339 original size:59 final size:58
Alignment explanation
Indices: 288--863 Score: 429
Period size: 59 Copynumber: 10.0 Consensus size: 58
278 TTTGGACATC
*
288 CGAGGGCAAAATGGTAATTTTTTGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
1 CGAGGGCAAAATGG-AATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
* * * * ** *
347 TGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTTAAAATGGAATTTTTGGAAGTT
1 CGAGGG-CAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
* *
406 CGAGGGTACAAATGGAATTTTTGGAAG-TTTCGAGGTCAAAAATGGAATTTTTAGAAGTT
1 CGAGGGCA-AAATGGAATTTTTGGAAGTTTTGGA-GTCAAAAATGGAATTTTTAGAAGTT
** * *
465 CG-GGGTCAAAATGGAATTTTTGGAAGTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTT
1 CGAGGG-CAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAG-TT
** * * * * *
523 TAAGGTCTAAAATGGAA-TTTTGGGAG-TTCGAGGGT----AATGGAA-TTTTAGGAATTT
1 CGAGGGC-AAAATGGAATTTTTGGAAGTTTTG-GAGTCAAAAATGGAATTTTTA-GAAGTT
* * * ** * *
577 TG-GAGTCAAAAATAGAATTTTTGGAAG-TTTGG-GGAAAAAATGAAATTTTTAGAATTT
1 CGAG-GGC-AAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
* * * * * *
634 TG-GGGTTAAAAATGGAATTTTTGGAAGTTTAGGGGT-ACAAATGGAATTTTTGGAAGTT
1 CGAGGG--CAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
* * *
692 CG-GGGTCAAAATGGAATTTTTGGAAG-TTCGGGGT-TAAAATGGAATTTTTAGAAGTT
1 CGAGGG-CAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
** * * *
748 CGAGGTAAAAATGGAATTTTTGGAAG-TTTGGGGTCAAAAATGGAATATTTGGAAGTT
1 CGAGGGCAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
** * * *
805 CGAGAGTAAAAATGGAATTTTT-GAGAG-TTTCGAGGTCAAAAATGGGATTTTTGGAAGTT
1 CGAG-GGCAAAATGGAATTTTTGGA-AGTTTTGGA-GTCAAAAATGGAATTTTTAGAAGTT
864 TTGGGACCTC
Statistics
Matches: 429, Mismatches: 62, Indels: 52
0.79 0.11 0.10
Matches are distributed among these distances:
53 2 0.00
54 19 0.04
55 21 0.05
56 55 0.13
57 101 0.24
58 97 0.23
59 127 0.30
60 7 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (58 bp):
CGAGGGCAAAATGGAATTTTTGGAAGTTTTGGAGTCAAAAATGGAATTTTTAGAAGTT
Found at i:348 original size:29 final size:28
Alignment explanation
Indices: 295--864 Score: 583
Period size: 29 Copynumber: 19.8 Consensus size: 28
285 ATCCGAGGGC
* *
295 AAAATGGTAATTTTTTGAAGTTTTGGAGTCA
1 AAAATGG-AATTTTTGGAAG-TTTGGGGT-A
*
326 AAAATGGAATTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
*
355 AAAATGGAATTTTTGGAAGTTTTGGGGTTT
1 AAAATGGAATTTTTGGAAG-TTTGGGG-TA
*
385 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
* *
414 CAAATGGAATTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTT-GGGGT-A
* * *
444 AAAATGGAATTTTTAGAAGTTCGGGGTC
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
*
472 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTT-TGGGGTA
** *
501 AAAATGGAATTTTTGGAAGTTTTAAGGTCT
1 AAAATGGAATTTTTGGAAG-TTTGGGGT-A
* *
531 AAAATGGAA-TTTTGGGAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
* * *
558 --AATGGAATTTTAGGAATTTTGGAGTCA
1 AAAATGGAATTTTTGGAAGTTTGGGGT-A
* *
585 AAAATAGAATTTTTGGAAGTTTGGGGAA
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
* * *
613 AAAATGAAATTTTTAGAATTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGGGG-TA
642 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GGGGTA
* * *
671 CAAATGGAATTTTTGGAAGTTCGGGGTC
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
* *
699 AAAATGGAATTTTTGGAAGTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
* * *
727 AAAATGGAATTTTTAGAAGTTCGAGGTA
1 AAAATGGAATTTTTGGAAGTTTGGGGTA
755 AAAATGGAATTTTTGGAAGTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGGGGT-A
* * *
784 AAAATGGAATATTTGGAAGTTCGAGAGTA
1 AAAATGGAATTTTTGGAAGTTTG-GGGTA
*
813 AAAATGGAATTTTT-GAGAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGA-AGTTT-GGGGT-A
*
843 AAAATGGGATTTTTGGAAGTTT
1 AAAATGGAATTTTTGGAAGTTT
865 TGGGACCTCT
Statistics
Matches: 454, Mismatches: 62, Indels: 47
0.81 0.11 0.08
Matches are distributed among these distances:
25 10 0.02
26 9 0.02
28 127 0.28
29 199 0.44
30 100 0.22
31 9 0.02
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.35
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTGGGGTA
Done.