Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003183.1 Kokia drynarioides strain JFW-HI SEQ_115794, 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: 2182
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Found at i:802 original size:348 final size:348
Alignment explanation
Indices: 1--2182 Score: 3190
Period size: 348 Copynumber: 6.3 Consensus size: 348
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
*
66 TTTCGCAGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* * * *
131 TTTCACAAAATTGCAAACTTAGGATAAATAAAATAATACAAAGAGAAAAAAAAACGAAAAGAGGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
*
196 GTGCAACACGAGGA-ATTCCCAGCAGGTCACCCATCCTAGTACTACTCTCGCCCAA--A--C---
196 GTGCAACACGAGGACA-TCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTA
* * * * * * ***
253 A--GCGGAGTTCTGATGAGATCCGGTGCATCAGTGCTAGTATGACCGCACCCATTATGTTCCAAG
260 ACTACGGAGTTCTGATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCG
* *
316 CAATCTATTTACACAAACGCTACC
325 CAATCTATTTACATAAAGGCTACC
** * *
340 TTTCATCCCATTCGTGTATCGAATTTGAATGTAAATATACCCAAATAATGCTTGAGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
* *
405 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATCTCCCTGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* *
470 TTTCACAAAATTTCAAACTTACGATAAATAAAGTAATACAAAAAGAAAAAAAAACAAAAAGAAGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
* * *
535 GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTGCTACTCTCTCCCAAGCACGCTTGA
196 GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
* * *
600 CTATGGAGTTTTGATGGGATCCGATCCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCGC
261 CTACGGAGTTCTGATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCGC
* *
665 AATCTGTTTACATAAAGGCCACC
326 AATCTATTTACATAAAGGCTACC
* * * * *
688 TTTCATCCCATTCGTGCCTCGAATTTGACTGTAAATATATCTAAATAATGCTCGAGAAGTCGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
* *
753 TTTCGCGGATAAAAATAAAATAAAAACACTCTAATAACGTCCATGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
*
818 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAATAAAAAACAAAAAGAAGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
* * * * *
883 GTGCTACACGAGGACATCCTAGGAGGTCACCCATCCTAGTGCTACTCTTGCCCAAGCACGCTTAG
196 GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
* * * * *
948 CTACAGAGTTCTGATGGGATTCGATGCATTAGTGCTAGTATGATCTCTCCCATTATGTTCTGCGC
261 CTACGGAGTTCTGATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCGC
*
1013 AATCTGTTTACATAAAGGCTACC
326 AATCTATTTACATAAAGGCTACC
*
1036 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCTAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
* *
1101 TTTCGCGGATAAAAAGAAAATAAAAACACGCTAATAATGTCTATGTA-CCCTATGAAGCTTTACT
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCC-ATGAAGCTTTACT
* * *
1165 ATTTCGCAAAATTACAAACTTAAGATAAATAAAATAATAC-AAAAGAAAAAAAAAACAAAAA-AA
130 ATTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAG-AAAAAAAAACAAAAAGAA
* * * * * *
1228 GGGGTGCAACACGAGGACTTCCTAGGAGGTCAACCAACCTAGTACTACTCACGCCTAAGCACGCT
194 -GGGTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCT
* * * *
1293 TAACTGCGGAGTTTTGAAT-GGATCCGTTGCATTAGTGCTGGTATGATCGCACCCATTATGTTTT
258 TAACTACGGAGTTCTG-ATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCT
*
1357 GCGCAATCTTTTTACATAAAGGCTACC
322 GCGCAATCTATTTACATAAAGGCTACC
* *
1384 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAGTATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
* * * *
1449 TTTGGTGGATAAAAATAAAATAAAAACACGCTAATAATTTCCATGTATCCCATGAAGCGTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* * * *
1514 TTTCGCAAAATTGCAAACTTATGATAAATAAAATAGTAC-AAAAGAAAAAAAAACAAAAAGAGGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
* * *
1578 GTGCAACACGAGGACTTTCCAGGAGGTCACCCATCCTGGTACTACTCTCGCCCAAGCACGCTTAA
196 GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
* * * *
1643 CTACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATTATGTTTTACGC
261 CTACGGAGTTCTGATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCGC
1708 AATCTATTTACATAAAGGCTACC
326 AATCTATTTACATAAAGGCTACC
* * *
1731 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAGTATACCCGAATAATGCTCGAGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
* * *
1796 TTTCGTGGATAAAAATAAAATAAAAACACACTAATAATGTCAATGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* *
1861 TTTCACAAAATTGCAAACTTATGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAGGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
** * *
1926 GTGCAACACGAGGATTTCCAAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACACTTAA
196 GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
* * * * * * * *
1991 CTGCGGAGTTCTGTTGGGATCC-AGTCCATTACTGTTGGAATGATCGCACCCATTATGTTATGTG
261 CTACGGAGTTCTGATGGGATCCGA-TGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCG
* *
2055 CAATCTATTTACATAAACGCTAGC
325 CAATCTATTTACATAAAGGCTACC
* * *
2079 TTTCATCCCATTCGTGCCTTGAATTTGAATGGAAGTATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
*
2144 TTTCGTGGATAAAAATAAAATAAAAACACGCTAATAATG
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATG
Statistics
Matches: 1673, Mismatches: 151, Indels: 29
0.90 0.08 0.02
Matches are distributed among these distances:
339 232 0.14
340 1 0.00
341 1 0.00
343 1 0.00
346 3 0.00
347 323 0.19
348 1107 0.66
349 5 0.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (348 bp):
TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAAGG
GTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAA
CTACGGAGTTCTGATGGGATCCGATGCATTAGTGCTGGTATGATCGCACCCATTATGTTCTGCGC
AATCTATTTACATAAAGGCTACC
Found at i:1328 original size:696 final size:694
Alignment explanation
Indices: 1--2182 Score: 3269
Period size: 695 Copynumber: 3.1 Consensus size: 694
*
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAATATACCCAAATAATGCTCGGGAAGACGTAT
*
66 TTTCGCAGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* * *
131 TTTCACAAAATTGCAAACTTAGGATAAATAAAATAATACAAAGAGAAAAAAAAACGAAAAGAGGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAGGG
*
196 GTGCAACACGAGGA-ATTCCCAGCAGGTCACCCATCCTAGTACTACTCTCGCCCAA--A--C--A
196 GTGCAACACGAGGACA-T-CCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTA
* * * * *
254 G---CGGAGTTCTGATGAGATCCGGTGCATCAGTGCTAGTATGACCGCACCCATTATGTTCCAAG
259 GCTACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTAGTATGATCGCACCCATTATGTTCTACG
* * **
316 CAATCTATTTACACAAACGCTACCTTTCATCCCATTCGTGTATCGAATTTGAATGTAAATATACC
324 CAATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACC
* *
381 CAAATAATGCTTGAGAAGACGTATTTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATCTC
389 CAAATAATGCTCGAGAAGACGTATTTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTC
** * * *
446 CCTGTATCCCATGAAGCTTTACTATTTCACAAAATTTCAAACTTACGATAAATAAAGTAATACAA
454 AATGTATCCCATGAAGCTTTACTATTTCACAAAATTACAAACTTAAGATAAATAAAATAATACAA
* *
511 AAAGAAAAAAAAACAAAAAGAA-GGGTGCAACACGAGGACATCCCAGGAGGTCACCCATCCTAGT
519 AAAGAAAAAAAAACAAAAA-AAGGGGTGCAACACGAGGACTTCCAAGGAGGTCACCCATCCTAGT
* * * **
575 GCTACTCTCTCCCAAGCACGCTTGACTATGGAGTTTTGATGGGATCCGATCCATTAGTGCTGGTA
583 ACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTTTGATGGGATCCG-TCCATTAGTGCTGGTA
* * *
640 TGATCGCACCCATTATGTTCTGCGCAATCTGTTTACATAAAGGCCACC
647 TGATCGCACCCATTATGTTATGCGCAATCTATTTACATAAAGGCTACC
* * * * * *
688 TTTCATCCCATTCGTGCCTCGAATTTGACTGTAAATATATCTAAATAATGCTCGAGAAGTCGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAATATACCCAAATAATGCTCGGGAAGACGTAT
* *
753 TTTCGCGGATAAAAATAAAATAAAAACACTCTAATAACGTCCATGTATCCCATGAAGCTTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* *
818 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAATAAAAAACAAAAAGAAGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAGGG
* * *
883 GTGCTACACGAGGACATCCTAGGAGGTCACCCATCCTAGTGCTACTCTTGCCCAAGCACGCTTAG
196 GTGCAACACGAGGACATCC-AGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAG
* * * * * *
948 CTACAGAGTTCTGATGGGATTCGATGCATTAGTGCTAGTATGATCTCTCCCATTATGTTCTGCGC
260 CTACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTAGTATGATCGCACCCATTATGTTCTACGC
* *
1013 AATCTGTTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCT
325 AATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCC
* * *
1078 AAATAATGCTCGGGAAGACGTATTTTCGCGGATAAAAAGAAAATAAAAACACGCTAATAATGTCT
390 AAATAATGCTCGAGAAGACGTATTTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCA
*
1143 ATGTA-CCCTATGAAGCTTTACTATTTCGCAAAATTACAAACTTAAGATAAATAAAATAATAC-A
455 ATGTATCCC-ATGAAGCTTTACTATTTCACAAAATTACAAACTTAAGATAAATAAAATAATACAA
* * *
1206 AAAGAAAAAAAAAACAAAAAAAGGGGTGCAACACGAGGACTTCCTAGGAGGTCAACCAACCTAGT
519 AAAG-AAAAAAAAACAAAAAAAGGGGTGCAACACGAGGACTTCCAAGGAGGTCACCCATCCTAGT
* * *
1271 ACTACTCACGCCTAAGCACGCTTAACTGCGGAGTTTTGAAT-GGATCCGTTGCATTAGTGCTGGT
583 ACTACTCTCGCCCAAGCACGCTTAACTGCGGAGTTTTG-ATGGGATCCG-TCCATTAGTGCTGGT
* *
1335 ATGATCGCACCCATTATGTTTTGCGCAATCTTTTTACATAAAGGCTACC
646 ATGATCGCACCCATTATGTTATGCGCAATCTATTTACATAAAGGCTACC
*
1384 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAGTATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAATATACCCAAATAATGCTCGGGAAGACGTAT
* * * *
1449 TTTGGTGGATAAAAATAAAATAAAAACACGCTAATAATTTCCATGTATCCCATGAAGCGTTACTA
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
* * *
1514 TTTCGCAAAATTGCAAACTTATGATAAATAAAATAGTAC-AAAAGAAAAAAAAACAAAAAGAGGG
131 TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAGGG
* * *
1578 GTGCAACACGAGGACTTTCCAGGAGGTCACCCATCCTGGTACTACTCTCGCCCAAGCACGCTTAA
196 GTGCAACACGAGGAC-ATCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAG
* * *
1643 CTACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTGGTATGATCGCACCAATTATGTTTTACGC
260 CTACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTAGTATGATCGCACCCATTATGTTCTACGC
*
1708 AATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAGTATACCC
325 AATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCC
* * *
1773 GAATAATGCTCGAGAAGACGTATTTTCGTGGATAAAAATAAAATAAAAACACACTAATAATGTCA
390 AAATAATGCTCGAGAAGACGTATTTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCA
* *
1838 ATGTATCCCATGAAGCTTTACTATTTCACAAAATTGCAAACTTATGATAAATAAAATAATACAAA
455 ATGTATCCCATGAAGCTTTACTATTTCACAAAATTACAAACTTAAGATAAATAAAATAATACAAA
* *
1903 AAGAAAAAAAAACAAAAAGAGGGGTGCAACACGAGGATTTCCAAGGAGGTCACCCATCCTAGTAC
520 AAGAAAAAAAAACAAAAAAAGGGGTGCAACACGAGGACTTCCAAGGAGGTCACCCATCCTAGTAC
* * * * * *
1968 TACTCTCGCCCAAGCACACTTAACTGCGGAGTTCTGTTGGGATCCAGTCCATTACTGTTGGAATG
585 TACTCTCGCCCAAGCACGCTTAACTGCGGAGTTTTGATGGGATCC-GTCCATTAGTGCTGGTATG
* * *
2033 ATCGCACCCATTATGTTATGTGCAATCTATTTACATAAACGCTAGC
649 ATCGCACCCATTATGTTATGCGCAATCTATTTACATAAAGGCTACC
* *
2079 TTTCATCCCATTCGTGCCTTGAATTTGAATGGAAGTATACCCAAATAATGCTCGGGAAGACGTAT
1 TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAATATACCCAAATAATGCTCGGGAAGACGTAT
*
2144 TTTCGTGGATAAAAATAAAATAAAAACACGCTAATAATG
66 TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATG
Statistics
Matches: 1348, Mismatches: 127, Indels: 32
0.89 0.08 0.02
Matches are distributed among these distances:
686 2 0.00
687 228 0.17
688 1 0.00
689 1 0.00
691 1 0.00
693 2 0.00
694 1 0.00
695 571 0.42
696 539 0.40
697 2 0.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (694 bp):
TTTCATCCCATTCGTGCCTCGAATTTGAATGGAAATATACCCAAATAATGCTCGGGAAGACGTAT
TTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCCATGTATCCCATGAAGCTTTACTA
TTTCACAAAATTGCAAACTTACGATAAATAAAATAATACAAAAAGAAAAAAAAACAAAAAGAGGG
GTGCAACACGAGGACATCCAGGAGGTCACCCATCCTAGTACTACTCTCGCCCAAGCACGCTTAGC
TACGGAGTTCTGATGGGATCCGGTGCATTAGTGCTAGTATGATCGCACCCATTATGTTCTACGCA
ATCTATTTACATAAAGGCTACCTTTCATCCCATTCGTGCCTCGAATTTGAATGTAAATATACCCA
AATAATGCTCGAGAAGACGTATTTTCGCGGATAAAAATAAAATAAAAACACGCTAATAATGTCAA
TGTATCCCATGAAGCTTTACTATTTCACAAAATTACAAACTTAAGATAAATAAAATAATACAAAA
AGAAAAAAAAACAAAAAAAGGGGTGCAACACGAGGACTTCCAAGGAGGTCACCCATCCTAGTACT
ACTCTCGCCCAAGCACGCTTAACTGCGGAGTTTTGATGGGATCCGTCCATTAGTGCTGGTATGAT
CGCACCCATTATGTTATGCGCAATCTATTTACATAAAGGCTACC
Done.