Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009347.1 Kokia drynarioides strain JFW-HI SEQ_124054, 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: 31354
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:9884 original size:41 final size:41
Alignment explanation
Indices: 9839--9916 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
9829 GTTTTTAGGC
** * *
9839 TTTGACTTTTGGATTTTATTTAGATAAAATTATCTTTAAAT
1 TTTGACTTTTCAACTTTAATTAGATAAAATTATCTTTAAAT
*
9880 TTTGACTTTTCAACTTTAATTAGATCAAATTATCTTT
1 TTTGACTTTTCAACTTTAATTAGATAAAATTATCTTT
9917 GTTTTAGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.53
Consensus pattern (41 bp):
TTTGACTTTTCAACTTTAATTAGATAAAATTATCTTTAAAT
Found at i:15285 original size:5 final size:6
Alignment explanation
Indices: 15271--15295 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15261 GGGAAATATT
15271 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
15296 CATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:15354 original size:14 final size:14
Alignment explanation
Indices: 15310--15354 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 14
15300 TATATTTTAT
15310 ATTTTAAAAAATAA
1 ATTTTAAAAAATAA
*
15324 A--TTAAAAAATTAT
1 ATTTTAAAAAA-TAA
15337 ATTTTAAAAAATAA
1 ATTTTAAAAAATAA
15351 ATTT
1 ATTT
15355 GATAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 7 0.27
15 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTTAAAAAATAA
Found at i:18912 original size:746 final size:743
Alignment explanation
Indices: 17648--19769 Score: 2742
Period size: 746 Copynumber: 2.8 Consensus size: 743
17638 GGTTTCCCCA
* * * * *
17648 TCATTCCATTTTGAATGCTGAAAAGGGTCCC-CAAATCCATCAATTCA-TATTATGCGGC-ATTT
1 TCATTCTATTTTGAATGCTGAAGAGGGTCCCTC-AATCCATCAACT-ATTATTACGCGACGA-TT
* *
17710 ATGGTTTT-TTTTT-ATTTAAAATTTAATGTTTAAAATTAAATATTTTTTTGTTATAAATACATC
63 ATGGTTTTCTTTTTAATTTAAAATTTAATATTTAAAATT--AGATTTTTTTGTTATAAATACATC
* * * *
17773 ATCTTAAAAGGAAATACTTAATCTATTTTTCATATTATTAATAAATTATTTAAAAATGAAATTTA
126 ACCTTAAAAGGAAATACATAATCTATTTTTCAGATTATTTATAAATTATTTAAAAATGAAATTTA
* * * *
17838 ATTTTGAGATTATTTAGAAAAGTAATTTAAATTTTTGTTCATGCAAAGTGAAACCGTGGCGACAA
191 ATTTTCAGATTATTTAGAAAAGTAATTTACATTTTTGTTCATGCAAGGTGAAACCGTGGCGACGA
* *
17903 TTTTAATAAAGATGTGACACGTGGTCAAATATGAATTTTAAAAAAAATATTGTTTTAGAATTTAA
256 TTTTAATAAAGATGTGACACGTGGTCAAATATGAA-TTT-AAAAAAATAATGTTTTACAATTTAA
* * **
17968 AAAAAAAACTTTTTAACTTATTGCATCAGATGATAGGTTTAGCCAATGGTTAATACGTGACAACA
319 AAAAAAAAC-TTTGAACTTATTGCATCAGATGATAGGTTTAGTCAATGGTTAATACGTG-GTACA
* * *
18033 TGGGTTGAACAAAAAACTAAAAAGGAATCTTGAAATTATCGTGTGAAATGATGGGTTTAACT-GG
382 TGAGTTGAACAAAAAACTAAAAAGGAATCTTGAAACTATCGTGTCAAATGATGGGTTTAA-TAGG
* * * *
18097 AATATGACACGTTGTAAATCTTTGCAAAAATTACAATAATTGATTACGTCTTGTTAAATGAGAGT
446 AATATGACACGTTGTAAATCTCTGCAAAAATTACAAAAATTGATTACGTCTTGTTAGATGACAGT
* * * *
18162 TTCAACTTTTTAAGATTTCAATTACAAATACAAAATTAAGAAGTAGATTGATGCGAATAAGTGCA
511 TTCAACTTTTCAAGATTCCAATTACAAATACAAAATTAAGAAGTAGATTGATGCTAACAAGTGCA
* ***
18227 TTTAGTTTGAAAAGGGTTTAATTAAAGACTAAATTTGGAATTATTTTGTTTTAGTTAGTTGTCAT
576 TTTAGTTTGAAAAGGGTATAATTAAAGACTAAATTTGGAATTATTTTGTTTTAGTTACCAGTCAT
* * ** * * *
18292 TGC-ATTTTTTTGGTGAATTAGAAGAGGTGGGCAAAACCCTAACAATAAGATGATTAGCACGACT
641 TGCAATTTTCTTGGTGAATTACAAGAGGAAGGCAAAACCATAACAACAAGATGACTAGCACGACT
* * *
18356 CGAACCCAAGCCATCAAATCAACACACGGGGTTCCTTG
706 CGAACCCAAACCATCAAACCAACACACGAGGTTCCTTG
* *
18394 TCATTCTAGTTTGAATGCTGAAGAGGGTCCCTCAATCTATCAACTATTATTACGCGACGATTATG
1 TCATTCTATTTTGAATGCTGAAGAGGGTCCCTCAATCCATCAACTATTATTACGCGACGATTATG
*
18459 ATTTTCTTTTTAATTTAAAATTTAATATTTAAAATTAGATTTTTTT-TTATAAATACATCACCTT
66 GTTTTCTTTTTAATTTAAAATTTAATATTTAAAATTAGATTTTTTTGTTATAAATACATCACCTT
* * *
18523 AAAAGGAAATAGATAATCTATTTTTCAGATTATTTAGAAATTATTTAAACATGAAATTTAATTTT
131 AAAAGGAAATACATAATCTATTTTTCAGATTATTTATAAATTATTTAAAAATGAAATTTAATTTT
*
18588 CAGATTATTTAGAAAAGTAATTTACATTTTTGTTCATGCATGGTGAAACCGTGGCGACGATTTTA
196 CAGATTATTTAGAAAAGTAATTTACATTTTTGTTCATGCAAGGTGAAACCGTGGCGACGATTTTA
* *
18653 ATAAATATGTGTCACGTGGTCAAATATGAATTTAAAATAAATAATGTTTTACAATTTAAAAAAAA
261 ATAAAGATGTGACACGTGGTCAAATATGAATTTAAAA-AAATAATGTTTTACAATTT--AAAAAA
* * * *
18718 AAAACCTTTGAACTTGTCGCATCAGATGATAAGTTTAGTCAATGGTTAACACGTGGTGACATGAG
323 AAAA-CTTTGAACTTATTGCATCAGATGATAGGTTTAGTCAATGGTTAATACGTGGT-ACATGAG
* *
18783 TTGAACAAAAAACTAAAAAGGAATCTTGAAACTATCGTGTCAGATGATGGGTTTAATAGGAATGT
386 TTGAACAAAAAACTAAAAAGGAATCTTGAAACTATCGTGTCAAATGATGGGTTTAATAGGAATAT
* * *
18848 GATATGTTGTAAATCTCTGCAAAAATTACAAAAATTGATTATGTCTTGTTAGATGACAGTTTCAA
451 GACACGTTGTAAATCTCTGCAAAAATTACAAAAATTGATTACGTCTTGTTAGATGACAGTTTCAA
* * *
18913 CTTTTCAAGATTCCAATTACAAATAC-AAATTAAAAAAGTAGATTAATGCTAACAAGAGCATTTA
516 CTTTTCAAGATTCCAATTACAAATACAAAATT-AAGAAGTAGATTGATGCTAACAAGTGCATTTA
* *
18977 GTTT-AACAAGGGGTATAATTGAAGACTAAATTTGGAATTATTTTGTTTTAGTTACCAGTGATTG
580 GTTTGAA-AA-GGGTATAATTAAAGACTAAATTTGGAATTATTTTGTTTTAGTTACCAGTCATTG
* * *
19041 CAATTTTCTTGGTGAATTACAAGAGGAAGGTAAAACCATAACAGCAAGATGACTAGCACGACTTG
643 CAATTTTCTTGGTGAATTACAAGAGGAAGGCAAAACCATAACAACAAGATGACTAGCACGACTCG
* * * *
19106 AATCCAAACCATTATACCGACACACGAGGTTCCTTG
708 AACCCAAACCATCAAACCAACACACGAGGTTCCTTG
* *
19142 TCGTTCTATTTTGAATGCTGAAGAGGGTCCCTCAATCCATCAACTATTATTACACGACGATTATG
1 TCATTCTATTTTGAATGCTGAAGAGGGTCCCTCAATCCATCAACTATTATTACGCGACGATTATG
19207 GTTTTCTTTTTAATTTAAAATATTTCTAATTTAAAATTTAATATTTAAAATTAGATTTTTTTGTT
66 GTTTTC--------------T-TTT-TAATTTAAAATTTAATATTTAAAATTAGATTTTTTTGTT
* * * *
19272 ACAAATACATCACCTTAAAAGGAAACACATAATCTATTTTTCAGATTATTTATAATTTTTTTAAA
115 ATAAATACATCACCTTAAAAGGAAATACATAATCTATTTTTCAGATTATTTATAAATTATTTAAA
*
19337 AATGAAATTTAATTTTCAGATTATTTAGAAAAGTAATTTACATTTTTGTTTATGCAAGGTGAAAC
180 AATGAAATTTAATTTTCAGATTATTTAGAAAAGTAATTTACATTTTTGTTCATGCAAGGTGAAAC
* * * * *
19402 TGTGGCGACGGTTTCAATAAAGATGTGACACGGGGTCAAATATAAATTTAAAAATAATAATGTTT
245 CGTGGCGACGATTTTAATAAAGATGTGACACGTGGTCAAATATGAATTTAAAAA-AATAATGTTT
* * *
19467 TTCAATTTTTTTAAAAAAAAAA--TTGAACTTATTGCATCAGATGATAGGTTTAATCAATGATTA
309 TACAA----TTTAAAAAAAAAACTTTGAACTTATTGCATCAGATGATAGGTTTAGTCAATGGTTA
* *** * *
19530 ATACGTGGATAC-TTAGGTTGAACAAAAAACTAAAAAGGAATCACAAAAACTACCCCATGTCAAA
370 ATACGTGG-TACATGA-GTTGAACAAAAAACTAAAAAGGAATC-TTGAAACTA--TCGTGTCAAA
* ** * * *
19594 TGATGGATTTAGCAGGAATATGACACGTTGTAAATATCTGCAAAAGTTACACAAAAATGATTACG
430 TGATGGGTTTAATAGGAATATGACACGTTGTAAATCTCTGCAAAAATTACA-AAAATTGATTACG
* * * *
19659 T-TGTGTCAGATGACAGTTTCAAATTTTCAAGATTCCAATTACATATACAAAATTAAGATGTAGA
494 TCT-TGTTAGATGACAGTTTCAACTTTTCAAGATTCCAATTACAAATACAAAATTAAGAAGTAGA
* *
19723 TTGATGCTAACAAGTGCATTTAGTTTGACAAGGGGTATAATTGAAGA
558 TTGATGCTAACAAGTGCATTTAGTTTGA-AAAGGGTATAATTAAAGA
19770 TTAGTGCCTT
Statistics
Matches: 1200, Mismatches: 129, Indels: 72
0.86 0.09 0.05
Matches are distributed among these distances:
743 4 0.00
744 20 0.02
745 173 0.14
746 298 0.25
747 57 0.05
748 171 0.14
762 1 0.00
763 5 0.00
764 108 0.09
765 190 0.16
767 61 0.05
768 101 0.08
769 10 0.01
770 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (743 bp):
TCATTCTATTTTGAATGCTGAAGAGGGTCCCTCAATCCATCAACTATTATTACGCGACGATTATG
GTTTTCTTTTTAATTTAAAATTTAATATTTAAAATTAGATTTTTTTGTTATAAATACATCACCTT
AAAAGGAAATACATAATCTATTTTTCAGATTATTTATAAATTATTTAAAAATGAAATTTAATTTT
CAGATTATTTAGAAAAGTAATTTACATTTTTGTTCATGCAAGGTGAAACCGTGGCGACGATTTTA
ATAAAGATGTGACACGTGGTCAAATATGAATTTAAAAAAATAATGTTTTACAATTTAAAAAAAAA
ACTTTGAACTTATTGCATCAGATGATAGGTTTAGTCAATGGTTAATACGTGGTACATGAGTTGAA
CAAAAAACTAAAAAGGAATCTTGAAACTATCGTGTCAAATGATGGGTTTAATAGGAATATGACAC
GTTGTAAATCTCTGCAAAAATTACAAAAATTGATTACGTCTTGTTAGATGACAGTTTCAACTTTT
CAAGATTCCAATTACAAATACAAAATTAAGAAGTAGATTGATGCTAACAAGTGCATTTAGTTTGA
AAAGGGTATAATTAAAGACTAAATTTGGAATTATTTTGTTTTAGTTACCAGTCATTGCAATTTTC
TTGGTGAATTACAAGAGGAAGGCAAAACCATAACAACAAGATGACTAGCACGACTCGAACCCAAA
CCATCAAACCAACACACGAGGTTCCTTG
Found at i:20414 original size:21 final size:21
Alignment explanation
Indices: 20375--20414 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20365 TATTTTTTGT
*
20375 TATTTTAATCTTTATTAAAAA
1 TATTTTAATCTTTACTAAAAA
20396 TATTTTAAT-TATTACTAAA
1 TATTTTAATCT-TTACTAAA
20415 TTAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTTAATCTTTACTAAAAA
Found at i:27945 original size:2 final size:2
Alignment explanation
Indices: 27938--27967 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27928 ATCTATGAAT
27938 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27968 GTGGATTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29442 original size:47 final size:47
Alignment explanation
Indices: 29377--29467 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
29367 GCTCCTTAGA
29377 TAGGTCGAGAAGAGATGGTTGTAAATACATGGGAGTGAAATTGTAGG
1 TAGGTCGAGAAGAGATGGTTGTAAATACATGGGAGTGAAATTGTAGG
29424 TAGGTCGAGAAGAGATGGTTGTAAATACATGGGAGTGAAATTGT
1 TAGGTCGAGAAGAGATGGTTGTAAATACATGGGAGTGAAATTGT
29468 TTTCATTTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.26
Consensus pattern (47 bp):
TAGGTCGAGAAGAGATGGTTGTAAATACATGGGAGTGAAATTGTAGG
Done.