Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003408.1 Kokia drynarioides strain JFW-HI SEQ_116159, 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, 887
Length: 1479
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:872 original size:298 final size:297
Alignment explanation
Indices: 1--1479 Score: 2011
Period size: 298 Copynumber: 5.0 Consensus size: 297
* * *
1 AATTATGAAAAATGAGAATACATGTGAAAGATT-TCATATGAGATATATGCATGATTCAAGAAAT
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCT-ATATGAGATATATGCATGATTCAAGAAAT
* * *
65 GATCATTGACAAGCTGTGAAATGATCCAAATTTTTTGAATGATATATAGTCGAATATGCAGCCTG
65 GAGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTGCA-CCTG
* * * * * * *
130 AATAATACATGATTGACCGTACCGCTTGAGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTT
129 AATAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTT
* * *
195 AACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTTTTAGGTCCTTTGTAGTGGGTGCATT
194 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATT
* * * *
260 AGGTTCGTCGAA-TTTCCAACAGCCTTTATATCGCTAGAG
259 GGGCTCGTC-AAGTTTCCAACAACCTTTATGTCGCTAGAG
* * *
299 AATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATGATTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCTATATGAGATATATGCATGATTCAAGAAATG
* *
364 AGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCT--AAC--AA
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTGCACCTGAA
*
425 TGAT---T-G--GGCC-TACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAA
131 TAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAA
483 CCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGG
196 CCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGG
*
548 GCTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAG
261 GCTCGTCAAGTTTCCAACAACCTTTATGTCGCTAGAG
* * * *
585 AATTATGCAAAACAAGAACACATATCAAAGATTCTATATGAGATATATGCATGGTTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCTATATGAGATATATGCATGATTCAAGAAATG
* * * * *
650 AGCATTGACAAGATGTGAAATAATCTAAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGA
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTG-CACCTGA
* * * * *
715 ATAATACATGGTTGGCCTTCCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTA
130 ATAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTA
* * * **
780 ACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCCTAGGTCCTCTGTAGTTGGTGTGTTG
195 ACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTG
* * * * *
845 AGCTTGTCGAGTTTCCAACAGCCTTTATGTCGCTAGAA
260 GGCTCGTCAAGTTTCCAACAACCTTTATGTCGCTAGAG
* * *
883 AATTATGAAAAATGAGAATACATGTGAAAGATT-TCATATGAGATATATGCATGATTCAAGAAAT
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCT-ATATGAGATATATGCATGATTCAAGAAAT
* * *
947 GATCATTGACAAGCTGTGAAATGATCCAAATTTTTTGAATGATATATAGTCGAATATGCAGCCTG
65 GAGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTGCA-CCTG
* * * * * * *
1012 AATAATACATGATTGACCGTACCGCTTGAGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTT
129 AATAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTT
* *
1077 AACCGACTTCATAGAGTTGGTGTAACATTACTTATAGGTCTTAGGTCCTTTGTAGTGGGTGCATT
194 AACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATT
* * * * *
1142 GGGTTCGTCGAA-TTTCTAATAGCCTTTATATCGCTAGAG
259 GGGCTCGTC-AAGTTTCCAACAACCTTTATGTCGCTAGAG
* * *
1181 AATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATGATTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCTATATGAGATATATGCATGATTCAAGAAATG
* *
1246 AGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCT--AAC--AA
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTGCACCTGAA
*
1307 TGAT---T-G--GG-CTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAA
131 TAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAA
1365 CCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGG
196 CCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGG
*
1430 GCTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAG
261 GCTCGTCAAGTTTCCAACAACCTTTATGTCGCTAGAG
1467 AATTATGCAAAAC
1 AATTATGCAAAAC
Statistics
Matches: 1039, Mismatches: 123, Indels: 50
0.86 0.10 0.04
Matches are distributed among these distances:
285 4 0.00
286 392 0.38
287 4 0.00
289 2 0.00
290 2 0.00
291 5 0.00
293 10 0.01
294 1 0.00
295 3 0.00
296 2 0.00
297 7 0.01
298 606 0.58
299 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (297 bp):
AATTATGCAAAACGAGAATACATGTCAAAGATTCTATATGAGATATATGCATGATTCAAGAAATG
AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTGCACCTGAA
TAATACATGGTTGGCCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAA
CCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGG
GCTCGTCAAGTTTCCAACAACCTTTATGTCGCTAGAG
Found at i:1328 original size:584 final size:572
Alignment explanation
Indices: 1--1479 Score: 1940
Period size: 584 Copynumber: 2.5 Consensus size: 572
* * * *
1 AATTATGAAAAATGAGAATACATGTGAAAGATTTCATATGAGATATATGCATGATTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGATTCAAGAAATG
* *
66 ATCATTGACAAGCTGTGAAATGATCCAAATTTTTTGAATGATATATAGTCGAATATGCAGCCTGA
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCG-A-AT-----C---
* ** * * * *
131 ATAATACATGATTGACCGTACCGCTTGAGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTTA
121 -TAACA-ATGATTGGGCTTACCGCCTGAGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTA
* *
196 ACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTTTTAGGTCCTTTGTAGTGGGTGCATT-
184 ACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTG
* * *
260 AGGTTCGTCGAATTTCCAACAGCCTTTATATCGCTAGAGAATTATGCAAAACGAGAATACATGTC
249 AGCTT-GTCGAGTTTCCAACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTC
325 AAAAATTCCATATAAGATATATGCATGATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCC
313 AAAAATTCCATATAAGATATATGCATGATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCC
*
390 AAATTTTCTGAATGATATATAGTCGAATCTAACAATGATTGGGCCTACCGCCTGAGTATTATAGT
378 AAATTTTCTGAATGATATATAGTCGAATCTAACAATGATTGGACCTACCGCCTGAGTATTATAGT
* *
455 GCACTAAACTTAGAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTACTTCTAGGT
443 GCACTAAACTTAAAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTACTTATAGGT
*
520 CTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGTTTTCAACAACCTTTATGTCGCTAGAG
508 CTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGTTTTCAACAACCTTTATATCGCTAGAG
* * * * *
585 AATTATGCAAAACAAGAACACATATCAAAGATTCTATATGAGATATATGCATGGTTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGATTCAAGAAATG
* * * * * *
650 AGCATTGACAAGATGTGAAATAATCTAAATTTTCTAAATGATATATAGTGGAATCTGCCACCTGA
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCT---AAC--A
* * * * *
715 ATAATACATGGTTGGCCTTCCCCCCTGAGTATTATAGTGTACCAAAGTTAGAAAATAAAAGGTTA
126 ATGAT---T-G--GG-CTTACCGCCTGAGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTA
* * **
780 ACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCCTAGGTCCTCTGTAGTTGGTGTGTTG
184 ACCGACTTCATAGAGTTGGTGTAACATTACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTG
* * * *
845 AGCTTGTCGAGTTTCCAACAGCCTTTATGTCGCTAGAAAATTATGAAAAATGAGAATACATGTGA
249 AGCTTGTCGAGTTTCCAACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCA
* * * * *
910 AAGATTTCATATGAGATATATGCATGATTCAAGAAATGATCATTGACAAGCTGTGAAATGATCCA
314 AAAATTCCATATAAGATATATGCATGATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCA
* * *
975 AATTTTTTGAATGATATATAGTCGAATATGCAGCCTGAATAATACATGATT-GACCGTACCGCTT
379 AATTTTCTGAATGATATATAGTCG-A-AT-----C----TAACA-ATGATTGGACC-TACCGCCT
* *
1039 GAGTATTATAGTGCATTAAAGTTAAAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACA
431 GAGTATTATAGTGCACTAAACTTAAAAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACA
* * * *
1104 TTACTTATAGGTCTTAGGTCCTTTGTAGTGGGTGCATTGGGTTCGTCGAA--TTTCTAATAGCCT
496 TTACTTATAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTC-AAGTTTTC-AACAACCT
1167 TTATATCGCTAGAG
559 TTATATCGCTAGAG
* *
1181 AATTATGCAAAACGAGAATACATGTCAAAAATTCCATATAAGATATATGCATGATTCAAGAAATG
1 AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGATTCAAGAAATG
*
1246 AGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTAACAATGAT
66 AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTAACAATGAT
*
1311 TGGGCTTACCGCCTGAGTATTATAGTGCACTAAACTTAGAAAATAAAAGGTTAACCGACTTCATA
131 TGGGCTTACCGCCTGAGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATA
* * * *
1376 GAGTTGGTGTAACATTACTTCTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGGGCTCGTCAAGT
196 GAGTTGGTGTAACATTACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGAGCTTGTCGAGT
* *
1441 TTTCAACAACCTTTATGTCGCTAGAGAATTATGCAAAAC
261 TTCCAACAGCCTTTATGTCGCTAGAGAATTATGCAAAAC
Statistics
Matches: 774, Mismatches: 93, Indels: 56
0.84 0.10 0.06
Matches are distributed among these distances:
573 1 0.00
576 1 0.00
577 5 0.01
578 1 0.00
580 1 0.00
581 1 0.00
582 2 0.00
583 1 0.00
584 483 0.62
585 7 0.01
586 2 0.00
587 1 0.00
588 1 0.00
591 6 0.01
593 2 0.00
595 11 0.01
596 246 0.32
597 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (572 bp):
AATTATGCAAAACGAGAATACATGTCAAAGATTCCATATGAGATATATGCATGATTCAAGAAATG
AGCATTGACAAGCTGTGAAATGATCCAAATTTTCTGAATGATATATAGTCGAATCTAACAATGAT
TGGGCTTACCGCCTGAGTATTATAGTGCACTAAAGTTAGAAAATAAAAGGTTAACCGACTTCATA
GAGTTGGTGTAACATTACTTGTAGGTCTTAGGTCCTCTGTAGTGGGTGCATTGAGCTTGTCGAGT
TTCCAACAGCCTTTATGTCGCTAGAGAATTATGCAAAACGAGAATACATGTCAAAAATTCCATAT
AAGATATATGCATGATTCAAGAAATGAGCATTGACAAGCCGTGAAATGATCCAAATTTTCTGAAT
GATATATAGTCGAATCTAACAATGATTGGACCTACCGCCTGAGTATTATAGTGCACTAAACTTAA
AAAATAAAAGGTTAACCGACTTCATAGAGTTGGTGTAACATTACTTATAGGTCTTAGGTCCTCTG
TAGTGGGTGCATTGGGCTCGTCAAGTTTTCAACAACCTTTATATCGCTAGAG
Done.