Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001381.1 Kokia drynarioides strain JFW-HI SEQ_112853, 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: 41989
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3727 original size:21 final size:21
Alignment explanation
Indices: 3701--3742 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3691 TAAGAATCTT
3701 CTTCATCTTCTTCACAATATA
1 CTTCATCTTCTTCACAATATA
3722 CTTCATCTTCTTCACAATATA
1 CTTCATCTTCTTCACAATATA
3743 GATGGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (21 bp):
CTTCATCTTCTTCACAATATA
Found at i:6919 original size:579 final size:576
Alignment explanation
Indices: 5232--8095 Score: 2821
Period size: 579 Copynumber: 5.0 Consensus size: 576
5222 ATCTAACTCG
5232 TTTAATG-CTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
1 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
* *
5296 ATATTACAAGGACTTAAATAATTAACTCAAATTTTAAATCAATTAATTAACAAATAAATC-AAAA
66 ATATTACAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAATAAATCTAAAA
* * *
5360 ATTCCAAATAACGATCATCGACCATAACAATAACCATATTCAATTTTTT-ATTT--AAAAAATTC
131 ATTCCAAAT-A--A--A--GACCATAACAATAACTATATTCAATTTTTTGTTTTAAAAAAAAATC
* * * *
5422 TAGATCCAATTAAAAAGAAAATGCTAAACTGAAAAA-ATCAGGAAGACCGAAACTAACAGATCAA
189 TAGATCCAATTAAAAAGAAAACGCTAAACTGAAAAATA-AAGAAAGACCGAAACTAACAAATCAA
* * * *
5486 AGCAAAGACATTTGATTAATGCTTATTAGTAAAAGCAAGAATTATAATGAAATA-AAAGAAGTGA
253 AGCAAAGACCTTTGATTAATGCTTTTTTGTAAAAACAAGAATTATAATGAAATAGAAA-AAGTGA
* * * * * *
5550 AAACCCTAAAATTTTACCGATAGAGAAGAGA-TCCGTGAGCAAGAGAGAGCACCGAGGGAGATAG
317 AAACCCTAGAATTTTACCGGTAGAGAAGAGAGT-CGCGAGCGAGAGAGAGCACCAAAGGAGATAG
* ** * *
5614 AGTCAACAACCAAGAACTGAAAGCGGCGAAAAGTAGAGTGAATATTACGCATGACGCCTGTCTTT
381 AGTCAACAACCAAGAATTGAAAGCAACGAAAAGTAGAGTGAATATTACGCACGGCGCCTGTCTTT
* * * * *
5679 TATAATCTCAACTTTTTGCTACATTTTTTCTTTTAATTTCTAAATAAAATATCTTTTCCTACTGT
446 TATAATCCCAACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATATCTTTTCCTACTGT
* * * *
5744 TATTCATATGTCATCTGATTTGTAATTAGTAAAAG-TTT-TACGATTTTGCTTTAATTATAAGGT
511 TATTCATATCTCATCTGATTTGTAATTAGTTAAAGTTTTATACGATTTTAC--TAATTATATGGT
5807 TCA
574 TCA
* * * *
5810 TTTAATGTCTTCTACACAC--ATATTACTAGCACTTAAATAACTAATTCATTTAACGCCTTCTAC
1 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
5873 ATAATT-CAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAATAAATCTAAA
66 AT-ATTACAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAATAAATCTAAA
* * *
5937 AATTCCAAATAAAGATCATCGACCATAACAATAACTATATTCAAATTTTTCTTTTAAAAAAAAAC
130 AATTCCAAAT--A-A--A--GACCATAACAATAACTATATTCAATTTTTTGTTTTAAAAAAAAAT
* * *
6002 CTAGATCCAATTAAAAAGAAAACGCTAAATTGAAAAATCAAGGAAA-ACCGAAACTAACAAATCT
188 CTAGATCCAATTAAAAAGAAAACGCTAAACTGAAAAAT-AAAGAAAGACCGAAACTAACAAATCA
* * *
6066 AAGCAAAGACCTTTGATTAATG-TTTATTTGTAAAAACAAGAATTATAATAAAATAGAAGAGGTG
252 AAGCAAAGACCTTTGATTAATGCTTT-TTTGTAAAAACAAGAATTATAATGAAATAGAAAAAGTG
** * * * * *
6130 AAAACCCTAGAATTTTACCGGTAGAGAAGAGACCCGCGAGCGAGAGAGA-AATCAAGGGAAATCG
316 AAAACCCTAGAATTTTACCGGTAGAGAAGAGAGTCGCGAGCGAGAGAGAGCACCAAAGGAGATAG
* * * * *
6194 AGTCGACAGCCATGAACTGAAAGCAACGAAAAGTAGAGTGAATATTAAGCACGGCGCCTGTCTTT
381 AGTCAACAACCAAGAATTGAAAGCAACGAAAAGTAGAGTGAATATTACGCACGGCGCCTGTCTTT
* * * * *
6259 TATAATCTCAACTTTTTGTTACGTTTTTTCTTTTAATTCTGAAATAAAATATTTTTTCCTACTGT
446 TATAATCCCAACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATATCTTTTCCTACTGT
* *
6324 TATTCGTATCTCATCTGATTTGTAATTAGTTAAAGTTTTATACGATTTTACTAAATATATGGTTC
511 TATTCATATCTCATCTGATTTGTAATTAGTTAAAGTTTTATACGATTTTACTAATTATATGGTTC
6389 A
576 A
* *
6390 TTTAATGCCTTTTACACACACATATATTACAAGCACTTAAATAACTAGCTCATTTAATGCCTTCT
1 TTTAATGCCTTCT--ACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCT
* * * *
6455 ACATATTATAAGGACTTAAATAACTAATTCAAATTTTAAATCAATTAATTAGCAAATAAATCTAA
64 ACATATTACAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAATAAATCTAA
* * *
6520 AAATTCCAAATAAAGATCATAACAATAACTACATTCAATTTTTTGTTTTAAAAAAGAAATCTAGT
129 AAATTCCAAATAAAGACCATAACAATAACTATATTCAATTTTTTGTTTTAAAAAA-AAATCTAGA
** * * * *
6585 TCCAATTAAAAAGAAAACATTAAACTGAAAAATAAAAAAAGACCGAAACTAATATATCAAAACAA
193 TCCAATTAAAAAGAAAACGCTAAACTGAAAAATAAAGAAAGACCGAAACTAACAAATCAAAGCAA
* *
6650 AGAACTTTGATTAATGCTTTTTTGTAAAAACAAAAATTATAATGAAATAGAAAAAGTGAAAACCC
258 AGACCTTTGATTAATGCTTTTTTGTAAAAACAAGAATTATAATGAAATAGAAAAAGTGAAAACCC
* * *
6715 TAGAATTTTACCGGTAGAGAAGAGAGTCGCGAGTGAGAGATAGCACCAAAGGAGATAGAGTTAAC
323 TAGAATTTTACCGGTAGAGAAGAGAGTCGCGAGCGAGAGAGAGCACCAAAGGAGATAGAGTCAAC
* * * * *
6780 AACAAAAAATTGAAAGCAGCGAAAAGTAGAGTGAATATTACGCATGGCACCTGTCTTTTATAATC
388 AACCAAGAATTGAAAGCAACGAAAAGTAGAGTGAATATTACGCACGGCGCCTGTCTTTTATAATC
*
6845 CCAACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATATCTTTTCCTACTGTTATTCTT
453 CCAACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATATCTTTTCCTACTGTTATTCAT
* *
6910 ATCTCATCTGATTTGTAATTAGTTAAA-TTCTGATACAATTTTACTTTAATTATATGGTTCA
518 ATCTCATCTGATTTGTAATTAGTTAAAGTT-TTATACGATTTTAC--TAATTATATGGTTCA
*
6971 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAGCTCA---AAT---TT-TA-
1 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
* * * *
7028 A-A-T-C-A--A-TTAAATAAC-AAAT-AAA-TCT--A--AA--AATT-CCAAATAAAGATC-AT
66 ATATTACAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAAT-AA-ATCTAA
** * ***** ** * *
7075 CGA--CC--ATAAA-A--ATAAC--T-A--A-ATTCATTTTTTTAAAAGAAAACTTAGATCCA-A
129 AAATTCCAAATAAAGACCATAACAATAACTATATTCAATTTTTTGTTTTAAAA-AAAAATCTAGA
* * * * *
7126 T-T----AAAAAGAAAACGCTGAAGTGAAAAATTAAA-AAAGACTGAAACTAACATATCAAAGCA
193 TCCAATTAAAAAGAAAACGCTAAACTGAAAAA-TAAAGAAAGACCGAAACTAACAAATCAAAGCA
* * * *
7185 AAGACCTTTGATTAATACTTATTTGTAAAAGA-AAGAATTATAATGAAATAGAAGAAGTG-AAAT
257 AAGACCTTTGATTAATGCTTTTTTGTAAAA-ACAAGAATTATAATGAAATAGAAAAAGTGAAAAC
* * * * *
7248 CCTAGAATTTTACCGGTAGAGAAAAGAGTCACGAGCGAGAGAGAGCATC-GAGGAAGATCGAGTC
321 CCTAGAATTTTACCGGTAGAGAAGAGAGTCGCGAGCGAGAGAGAGCACCAAAGG-AGATAGAGTC
* * * * * * * *
7312 AACATCCAAGAATTGAAAGCTATGAAAAGTAAAGTGAATA-TATGAACGGTGCTTGTCTTTTATA
385 AACAACCAAGAATTGAAAGCAACGAAAAGTAGAGTGAATATTACGCACGGCGCCTGTCTTTTATA
* * * * *
7376 AT-CCAACCTTTTGCTACG--TT-TCTTTTGATTCCAAAATAAAATATATTTTTCCTACCGTTAT
450 ATCCCAACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATAT-CTTTTCCTACTGTTAT
* * * *
7437 TCATATCTCATCAT-ATTTGTAATTAGTTAATGTTTTATATGGTTTTATTTTAATTATATGGTTC
514 TCATATCTCATC-TGATTTGTAATTAGTTAAAGTTTTATACGATTTTA--CTAATTATATGGTTC
7501 A
576 A
*
7502 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAAAAACTAACTCATTTAATGCCTTCTAC
1 TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
7567 ATATTACAAGCACTTAAATAAACTACATATTACAAGCACTTAAATAATTAACTCAAATTTTAAAT
66 ATATTACAAGCAC-----T----TA-A-A-T---A--AC---------TAACTCAAATTTTAAAT
* *
7632 CAATTAATTAATAAATATATCTAAAAATTCCAAATGAAGATCATCGACCATAACAATAACTATAT
105 CAATTAATTAACAAATAAATCTAAAAATTCCAAAT--A-A--A--GACCATAACAATAACTATAT
* * * * * * *
7697 CCAATTTTGTGTTTAAAAAAAGAAAATCTAAATCCAATTAAAAAGAAAAAGTTAAATTGAAAAAT
163 TCAATTTTTTGTTT-TAAAAA-AAAATCTAGATCCAATTAAAAAGAAAACGCTAAACTGAAAAAT
* * *
7762 CAAGAAAGACCCAAACTAACAAATCAAAGCAAAGACCTTTGATTAATGCTTTTTTTATAAAAACA
226 AAAGAAAGACCGAAACTAACAAATCAAAGCAAAGACCTTTGATTAATGC-TTTTTTGTAAAAACA
* * * * *
7827 AGAATTATAATGAAATAG---GAGTGAAAA-CCTAAAATTTTACCTGTAAAGAAGAAAGTCGCGA
290 AGAATTATAATGAAATAGAAAAAGTGAAAACCCTAGAATTTTACCGGTAGAGAAGAGAGTCGCGA
* * * * * * *
7888 GTGAGAGAGAGCACCAAAAGAGATAGAGTCAACAGCAAAAAATTGAAAGAAACGAAAAGTAAAGT
355 GCGAGAGAGAGCACCAAAGGAGATAGAGTCAACAACCAAGAATTGAAAGCAACGAAAAGTAGAGT
* * * ** * *
7953 AAATATTACGCACGACACCTGT-TTCTTATAATCCCAACTTTTTATTA---TATATTTTTTAATT
420 GAATATTACGCACGGCGCCTGTCTT-TTATAATCCCAACTTTTTGCTACGTTTTATCTTTTAATT
* * ** * *
8014 CCGAAATAGAATATCTTTTTTCTTACCATTAATT-GTATCTCATCTAATTTGTAATTAGTTAAAG
484 CCGAAATAAAATATC--TTTTCCTACTGTT-ATTCATATCTCATCTGATTTGTAATTAGTTAAAG
* * *
8078 TCTGATATGATTTTACTA
546 TTTTATACGATTTTACTA
8096 TGATTCATTT
Statistics
Matches: 1900, Mismatches: 255, Indels: 233
0.80 0.11 0.10
Matches are distributed among these distances:
530 22 0.01
531 115 0.06
532 3 0.00
533 15 0.01
534 26 0.01
535 88 0.05
536 97 0.05
537 7 0.00
538 2 0.00
539 1 0.00
540 1 0.00
541 2 0.00
542 21 0.01
543 2 0.00
545 2 0.00
546 1 0.00
548 5 0.00
550 1 0.00
551 6 0.00
553 2 0.00
554 5 0.00
555 10 0.01
556 4 0.00
557 3 0.00
558 1 0.00
559 1 0.00
561 3 0.00
562 3 0.00
563 5 0.00
564 9 0.00
565 1 0.00
567 1 0.00
569 1 0.00
570 1 0.00
571 1 0.00
572 2 0.00
573 5 0.00
574 3 0.00
575 2 0.00
576 3 0.00
577 138 0.07
578 211 0.11
579 228 0.12
580 187 0.10
581 188 0.10
582 26 0.01
583 6 0.00
584 106 0.06
585 2 0.00
587 1 0.00
588 1 0.00
590 1 0.00
593 1 0.00
595 5 0.00
597 1 0.00
598 1 0.00
600 1 0.00
601 9 0.00
602 9 0.00
603 2 0.00
606 89 0.05
607 28 0.01
608 95 0.05
609 78 0.04
610 3 0.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (576 bp):
TTTAATGCCTTCTACACACATATATTACAAGCACTTAAATAACTAACTCATTTAATGCCTTCTAC
ATATTACAAGCACTTAAATAACTAACTCAAATTTTAAATCAATTAATTAACAAATAAATCTAAAA
ATTCCAAATAAAGACCATAACAATAACTATATTCAATTTTTTGTTTTAAAAAAAAATCTAGATCC
AATTAAAAAGAAAACGCTAAACTGAAAAATAAAGAAAGACCGAAACTAACAAATCAAAGCAAAGA
CCTTTGATTAATGCTTTTTTGTAAAAACAAGAATTATAATGAAATAGAAAAAGTGAAAACCCTAG
AATTTTACCGGTAGAGAAGAGAGTCGCGAGCGAGAGAGAGCACCAAAGGAGATAGAGTCAACAAC
CAAGAATTGAAAGCAACGAAAAGTAGAGTGAATATTACGCACGGCGCCTGTCTTTTATAATCCCA
ACTTTTTGCTACGTTTTATCTTTTAATTCCGAAATAAAATATCTTTTCCTACTGTTATTCATATC
TCATCTGATTTGTAATTAGTTAAAGTTTTATACGATTTTACTAATTATATGGTTCA
Found at i:7592 original size:26 final size:26
Alignment explanation
Indices: 7563--7613 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
7553 TTAATGCCTT
7563 CTACATATTACAAGCACTTAAATAAA
1 CTACATATTACAAGCACTTAAATAAA
7589 CTACATATTACAAGCACTTAAATAA
1 CTACATATTACAAGCACTTAAATAA
7614 TTAACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
CTACATATTACAAGCACTTAAATAAA
Found at i:8154 original size:20 final size:19
Alignment explanation
Indices: 8129--8171 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
8119 ACTCTAATTC
8129 TAAATC-AATTAATTAACAAA
1 TAAATCTAA-TAATT-ACAAA
*
8149 TAAATCTAATAATTCCAAA
1 TAAATCTAATAATTACAAA
8168 TAAA
1 TAAA
8172 GATGGCAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 11 0.52
21 2 0.10
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAATCTAATAATTACAAA
Found at i:16677 original size:8 final size:7
Alignment explanation
Indices: 16660--16691 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
16650 TTGTTTCTAC
16660 TTTTTAT
1 TTTTTAT
16667 TTTTTAT
1 TTTTTAT
16674 TTTTTAT
1 TTTTTAT
16681 TTTCTTAT
1 TTT-TTAT
16689 TTT
1 TTT
16692 GGCTAGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:35555 original size:19 final size:20
Alignment explanation
Indices: 35531--35579 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
35521 TGTGGGTATT
35531 AAGGAAGAAAAAAAAAG-AG
1 AAGGAAGAAAAAAAAAGAAG
* *
35550 AAGGAAG-TAAAAAAGGAAG
1 AAGGAAGAAAAAAAAAGAAG
35569 AAGGAAGAAAA
1 AAGGAAGAAAA
35580 GAGGAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.28
19 16 0.64
20 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (20 bp):
AAGGAAGAAAAAAAAAGAAG
Done.