Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003479.1 Kokia drynarioides strain JFW-HI SEQ_116288, 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: 2175
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Found at i:790 original size:214 final size:213
Alignment explanation
Indices: 1--2175 Score: 2090
Period size: 214 Copynumber: 10.2 Consensus size: 213
* * * * * * *
1 TTCCTTCGAGCAATTT-TAAGAAAATTCTATGCTCTAGAAATCGCATCATTAAGTGTAAATAATT
1 TTCCTTCGAGCAATTTCT--GAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTT
* * * * *
65 -TCCATTATGTAAACAACTTTTGGTCTCTGAATTAAAAACTTTTTTAAGTGAGAATAGTTTCTCT
64 GT-CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
* * * * * ** *
129 CTTGTTTCTAGACCAAACTTCCGAAGTTGACAAACTTTTACGTGTTCTTTTATAACTTCAGTTCC
128 CTTGGTTCTCGGCCAAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCA
* * * *
194 TTACAGTAATCAAGACAAACCA
192 TTAAAGTATTCAAGACGATCCA
* * * * ** *
216 TTCCTTCGAGCAATTTTCTGAACTTTCCAAGCAC-AGGGAATCTTATCATTTGGTCTAAATAGTT
1 TTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGA-GAAATCACATCATTAGGTCTAAATAGTT
* * * *
280 GTCATTTTGTAAACAACTTTTGGTCTTCGAATTAAAAAATTATTTATGTGAGAATTGTTTCTTTC
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTC
* ** * *
345 TTGGTTCTCGGCCGAACTTTAAACTTGACAAACATTTACGAGTTCTTTTATAACTTTTGTTCATT
129 TTGGTTCTCGGCCAAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCATT
*
410 AAAGTATTCAAGTCGATCCA
194 AAAGTATTCAAGACGATCCA
* * * *
430 TTCCTTCGAGCAATTTTTTCTGTACAGTCCATGCCTGGA-AAATCACAACATTAGGTC-AAATAG
1 TTCCTTCGAGCAA---TTTCTGAACATTCCATG-CTCGAGAAATCACATCATTAGGTCTAAATAG
** * * *
493 TTGTCATTTTGTAAACAACTTTTATTTTTTTAAATTAAAAACTTATTTAGGTGAGAATTATTTCT
62 TTGTCATTTTGTAAACAACTTTT-GGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCT
* * * * *
558 CTCTTGGTTCTCGGCCAAACTTCCGAACCTAACTAACTTTTAAGAGTTCTTTTATAACTTCGGTT
126 CTCTTGGTTCTCGGCCAAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTT
* * *
623 CTTTAAAGTAATCAAGACGATCTA
190 CATTAAAGTATTCAAGACGATCCA
* * *
647 TTCCTTCGAGCAATTTCTGGAACATTCCATGCTCGAGAAATCGCACCATTTGGTCTAAATAGTTG
1 TTCCTTCGAGCAATTTCT-GAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTG
* * * **
712 TTATTATGTAAACAACTTTTGATCTTTGAATT-AAAACTTATTTAGGTGAGAATAATTTCTCTCT
65 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
* * * * * *
776 TGGTTCTGGGCCAAACTTTCAAAGTTGACAAACTTTTACAATTTCTTTTATAACTTTGGTTCCTT
130 TGGTTCTCGGCCAAAC-TTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCATT
*
841 AAAGTATTTAAGACGATCCA
194 AAAGTATTCAAGACGATCCA
* * * * * * *
861 TTCCGTCGAGCAATTTTCCGAACTTTCCATGCTTG-GAAATCGCATCATTTGGTTTAAATAGTTG
1 TTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTG
* * * * *
925 TCATTTTATAAACAACTTTTGGTCTTTGAATTAAAAAATTCTTTAGGTGAGAGTTGTTTCTTTCT
65 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
* ** * * *
990 TGGTTCTCGGGCAAACTTTAAACTTGATCAAA-TTTT-CAAGTTCTTTTATAAATTTTGTTCATT
130 TGGTTCTCGGCCAAACTTCGAACTTGA-CAAACTTTTACGAGTTCTTTTATAACTTTGGTTCATT
1053 AAAGTATTCAAGACGATCCA
194 AAAGTATTCAAGACGATCCA
* * ** * * *
1073 TTCCTTC-AGCAATATAT-TGTACAGTCTGTGCTTG-GTAAATCACATTATTAGGTCTAAATTGT
1 TTCCTTCGAGCAAT-T-TCTGAACATTCCATGCTCGAG-AAATCACATCATTAGGTCTAAATAGT
* * * * * *
1135 TGTCATTCTAT-AACTACTTTCGGTTTTTCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
63 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
* * * * * *
1199 ATTCGTTCT----C-AGC--CGAACTTGACAAAGTTTTACGAGTACTTTTATAACTTTTGTTCAT
128 CTTGGTTCTCGGCCAAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCAT
* *
1257 TAATGTATTCAAGACGATCGA
193 TAAAGTATTCAAGACGATCCA
* * * * *
1278 TTCCTTCGAGTAATTTTCTGTACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAA-AGTTG
1 TTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTG
* * * * *
1342 TCATTTT-TGAAACTACTTCTGGTCTTCT-AATTAAAAATTTATTTAGTTGAGAATTGTTTCTTT
65 TCATTTTGT-AAACAACTTTTGGTCTT-TGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCT
* * ** * * * * *
1405 TTTGGTTCTTGATCGAACTTTCGAGCTTGAAAAACTTTTACGAGTTAC-TTTATAATTTTGATTC
128 CTTGGTTCTCGGCCAAAC-TTCGAACTTGACAAACTTTTACGAGTT-CTTTTATAACTTTGGTTC
* * *
1469 CTTAAACTATTAAAGACGATCCA
191 ATTAAAGTATTCAAGACGATCCA
** * * * *
1492 TTCCTTCGAGCAATTT-TAAGAGA-ATTGTATGCTCTAGAAATCGA-ATCATTAAGTGTAAATAA
1 TTCCTTCGAGCAATTTCT--GA-ACATTCCATGCTCGAGAAATC-ACATCATTAGGTCTAAATAG
* * * * * *
1554 TTGCCATTATGTAAACAACTTTTGGTCTCTGAATTAAAAACTTTTTTAGGTGAGAGTAGTTTCTC
62 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTC
* * * * **
1619 TCTTGTTTCTAGGCCAAACTTCCGAAGTTGACAAACTTTTACGTGTTCTTTTATAACTTCAGTTC
127 TCTTGGTTCTCGGCCAAACTT-CGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTC
* * * *
1684 CTTACAA-TAATCAAGACAAACCA
191 ATTA-AAGTATTCAAGACGATCCA
* * * * * *
1707 TTCCTTCGAGTAATTTTCTGAACATTCCAAGCAC-AGGGAATCTCATCATTTGGTCTAAATAGTT
1 TTCCTTCGAGCAA-TTTCTGAACATTCCATGCTCGA-GAAATCACATCATTAGGTCTAAATAGTT
* * * * *
1771 GTCATTTTGTAAACAACTGTTGGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTATCTTTC
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTC
* * ** * *
1836 TTGGTTCTAGGCCGAACTTTAAACTTGACAAACATTTACGAGTTCTTTTATAACTTTTGTTCATT
129 TTGGTTCTCGGCCAAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCATT
1901 AAAGTATTCAAGACGATCCA
194 AAAGTATTCAAGACGATCCA
* * * *
1921 TTCCTTCGAGCAATTATCTGTACAGTCCATGCTTG-GAAAATCACAACATTAGGTC-AAATAGTT
1 TTCCTTCGAGCAATT-TCTGAACATTCCATGCTCGAG-AAATCACATCATTAGGTCTAAATAGTT
** * *
1984 GTCATTTTGTAAACAACTTTTATTTTTTGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTC
64 GTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTC
* * * ** * *
2049 TTGGTTCTCGGCCAAACTTCTGAACCTAACTAACTTTTAAAAGTTCTTTTATAACTTCGGTTCTT
129 TTGGTTCTCGGCCAAACTTC-GAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCAT
* *
2114 TAAAGTAATCAAGACGATCTA
193 TAAAGTATTCAAGACGATCCA
*
2135 TTCCTTCGAGCAATTTCTGGAACATTTCATGCTCGAGAAAT
1 TTCCTTCGAGCAATTTCT-GAACATTCCATGCTCGAGAAAT
Statistics
Matches: 1606, Mismatches: 294, Indels: 121
0.79 0.15 0.06
Matches are distributed among these distances:
203 4 0.00
204 12 0.01
205 60 0.04
206 95 0.06
207 4 0.00
210 2 0.00
211 72 0.04
212 81 0.05
213 160 0.10
214 517 0.32
215 412 0.26
216 117 0.07
217 69 0.04
218 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (213 bp):
TTCCTTCGAGCAATTTCTGAACATTCCATGCTCGAGAAATCACATCATTAGGTCTAAATAGTTGT
CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTT
GGTTCTCGGCCAAACTTCGAACTTGACAAACTTTTACGAGTTCTTTTATAACTTTGGTTCATTAA
AGTATTCAAGACGATCCA
Found at i:1950 original size:643 final size:636
Alignment explanation
Indices: 67--2167 Score: 2095
Period size: 643 Copynumber: 3.3 Consensus size: 636
57 AAATAATTTC
* * * * *
67 CATTATGTAAACAACTTTTGGTCTCTGAATTAAAAACTTTTTTAAGTGAGAA-TAGTTTCTCTCT
1 CATTTTGTAAACAAC-TTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAATTA-TTTCTCTCT
* * * * * * * *
131 TGTTTCTAGACCAAACTTCCGAAGTTGACAAACTTTTAC-GTGTTCTTTTATAAC-TTCAGTTCC
64 TGGTTCTGGACCAAACTTTCAAAGTTGAAAAACTTTTACAAT-TACTTTTATAACTTTGA-TTCC
* * * * * * * ** * * ** * *
194 TTACAGTAATCAAGACAAACCATTCCTTCGAGCAATTTTCTGAACTTTCCAAGCACAGGGAATCT
127 TTAAACTATTAAAGACGATCCATTCCGTCGAGCAATTTTAAGAAATTT-CATGCTTA-GAAATCG
* ** *
259 TATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTCGAATTAAAAAATTATT
190 AATCATTAAGTGTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTT-GAATTAAAAAATTATT
* * * *
324 TATGTGAGAATTGTTTCTTTCTTGGTTCTCGGCCGAACTTTAAACTTGACAAACATTTACGAGTT
254 TAGGTGAGAGTTGTTTCTTTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAACTTTTACGAGTT
*
389 CTTTTATAACTTTTGTTCATTAAAGTATTCAAGTCGATCCATTCCTTCGAGCAATTTTTTCTGTA
319 CTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAA--TTTTCTGTA
* *
454 CAGTCCATGCCTGGAAAATCACAACATTAGGTC-AAATAGTTGTCATTTTGTAAACAACTTTTAT
382 CAGTCCATGCCTGGAAAATCACATCATTAGGTCTAAATAGTTGTCATTTTGTAAACAAC-TTTAG
* * * *
518 TTTTTTAAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTCTTGGTTCTCGGCCAAACTTCCG
446 GTTTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTAGGCCGAACTT---
* * * * ** * * *
583 AACCTAACTAACTTTTAAGAGTTCTTTTATAACTTCGGTTCTTTAAAGTAATCAAGACGATCTAT
508 AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCCAT
* * * * * * *
648 TCCTTCGAGCAATTTCTGGAACATTCCATGCTCGAGAAATCGCACCATTTGGTCTAAATAGTTGT
573 TCCTTCGAGCAATTTCT-GTACAGTCCATGCTTGGGAAATCACAACATTAGGTCTAAATAGTTGT
* * *
713 TATTATGTAAACAACTTTTGATCTTTGAATT-AAAACTTATTTAGGTGAGAATAATTTCTCTCTT
1 CATTTTGTAAACAAC-TTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTCTT
* * * *
777 GGTTCTGGGCCAAACTTTCAAAGTTGACAAACTTTTACAATTTCTTTTATAACTTTGGTTCCTTA
65 GGTTCTGGACCAAACTTTCAAAGTTGAAAAACTTTTACAATTACTTTTATAACTTTGATTCCTTA
* * ** * * *
842 AAGTATTTAAGACGATCCATTCCGTCGAGCAATTTTCCGAACTTTCCATGCTTGGAAATCGCATC
130 AACTATTAAAGACGATCCATTCCGTCGAGCAATTTTAAGAAATTT-CATGCTTAGAAATCGAATC
** * * *
907 ATTTGGTTTAAATAGTTGTCATTTTATAAACAACTTTTGGTCTTTGAATTAAAAAATTCTTTAGG
194 ATTAAGTGTAAATAGTTGTCATTTTGTAAACAACTTTTGGTC-TTGAATTAAAAAATTATTTAGG
* *
972 TGAGAGTTGTTTCTTTCTTGGTTCTCGGGCAAACTTTAAACTTGATCAAA-TTTT-CAAGTTCTT
258 TGAGAGTTGTTTCTTTCTTGGTTCTCGGCCAAACTTTAAACTTGA-CAAACTTTTACGAGTTCTT
* *
1035 TTATAAATTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTC-AGCAATATAT-TGTACAGT
322 TTATAACTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT-TTTCTGTACAGT
** * * * * * * * *
1098 CTGTGCTTGGTAAATCACATTATTAGGTCTAAATTGTTGTCATTCTAT-AACTACTTTCGGTTTT
386 CCATGCCTGGAAAATCACATCATTAGGTCTAAATAGTTGTCATTTTGTAAACAACTTTAGGTTTT
* * *
1162 TCAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTATTCGTTCTCA-GCCG-----AACTTGA
451 TAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCT-AGGCCGAACTTAACTTGA
* * * *
1221 CAAAGTTTTACGAGTACTTTTATAACTTTTGTTCATTAATGTATTCAAGACGATCGATTCCTTCG
515 CAAACTTTTACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCG
* *
1286 AGTAATTTTCTGTACAGTCCATGCTTGGGAAATCACATCATTAGGTCTAAA-AGTTGT
580 AGCAA-TTTCTGTACAGTCCATGCTTGGGAAATCACAACATTAGGTCTAAATAGTTGT
* * * * * * *
1343 CATTTT-TGAAACTACTTCTGGTCTTCT-AATTAAAAATTTATTTAGTTGAGAATTGTTTCTTTT
1 CATTTTGT-AAACAACTT-TGATCTT-TGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTC
* * * * * *
1406 TTGGTTCTTGATCGAACTTTC-GAGCTTGAAAAACTTTTACGAGTTAC-TTTATAATTTTGATTC
63 TTGGTTCTGGACCAAACTTTCAAAG-TTGAAAAACTTTTAC-AATTACTTTTATAACTTTGATTC
*
1469 CTTAAACTATTAAAGACGATCCATTCCTTCGAGCAATTTTAAGAGAATTGT-ATGCTCTAGAAAT
126 CTTAAACTATTAAAGACGATCCATTCCGTCGAGCAATTTTAAGA-AATT-TCATGCT-TAGAAAT
* * * * *
1533 CGAATCATTAAGTGTAAATAATTGCCATTATGTAAACAACTTTTGGTCTCTGAATTAAAAACTTT
188 CGAATCATTAAGTGTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCT-TGAATTAAAAAATTA
* * * * ** * *
1598 TTTAGGTGAGAGTAGTTTCTCTCTTGTTTCTAGGCCAAACTTCCGAAGTTGACAAACTTTTACGT
252 TTTAGGTGAGAGTTGTTTCTTTCTTGGTTCTCGGCCAAACTT-TAAACTTGACAAACTTTTACGA
** * * * * *
1663 GTTCTTTTATAACTTCAGTTCCTTACAA-TAATCAAGACAAACCATTCCTTCGAGTAATTTTCTG
316 GTTCTTTTATAACTTTTGTTCATTA-AAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTG
* * * * * * *
1727 AACATTCCAAGCACAGG-GAATCTCATCATTTGGTCTAAATAGTTGTCATTTTGTAAACAACTGT
380 TACAGTCCATGC-CTGGAAAATCACATCATTAGGTCTAAATAGTTGTCATTTTGTAAACAACT-T
* * * * * *
1791 T-GGTCTTTGAATTAAAAAATTATTTATGTGAGAATTGTATCTTTCTTGGTTCTAGGCCGAACTT
443 TAGGTTTTTAAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTAGGCCGAAC-T
*
1855 TAAACTTGACAAACATTTACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCC
507 T-AACTTGACAAACTTTTACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCC
*
1920 ATTCCTTCGAGCAATTATCTGTACAGTCCATGCTTGGAAAATCACAACATTAGGTC-AAATAGTT
571 ATTCCTTCGAGCAATT-TCTGTACAGTCCATGCTTGGGAAATCACAACATTAGGTCTAAATAGTT
1984 GT
635 GT
* *
1986 CATTTTGTAAACAACTTTTATTTTTTGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTCTT
1 CATTTTGTAAACAACTTTGA-TCTTTGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTCTT
* ** * * * *
2051 GGTTCTCGG-CCAAAC-TTCTGAACCT-AACTAACTTTTAAAAGTT-CTTTTATAACTTCGGTTC
65 GGTTCT-GGACCAAACTTTC-AAAGTTGAA-AAACTTTTACAA-TTACTTTTATAACTTTGATTC
* * * * * * *
2112 TTTAAAGTAATCAAGACGATCTATTCCTTCGAGCAATTTCT-GGAACATTTCATGCT
126 CTTAAACTATTAAAGACGATCCATTCCGTCGAGCAATTT-TAAGAA-ATTTCATGCT
2168 CGAGAAAT
Statistics
Matches: 1212, Mismatches: 193, Indels: 103
0.80 0.13 0.07
Matches are distributed among these distances:
629 3 0.00
630 28 0.02
631 213 0.18
632 112 0.09
633 11 0.01
634 44 0.04
635 47 0.04
636 56 0.05
637 2 0.00
639 52 0.04
640 37 0.03
641 17 0.01
642 21 0.02
643 293 0.24
644 115 0.09
645 129 0.11
646 32 0.03
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (636 bp):
CATTTTGTAAACAACTTTGATCTTTGAATTAAAAACTTATTTAGGTGAGAATTATTTCTCTCTTG
GTTCTGGACCAAACTTTCAAAGTTGAAAAACTTTTACAATTACTTTTATAACTTTGATTCCTTAA
ACTATTAAAGACGATCCATTCCGTCGAGCAATTTTAAGAAATTTCATGCTTAGAAATCGAATCAT
TAAGTGTAAATAGTTGTCATTTTGTAAACAACTTTTGGTCTTGAATTAAAAAATTATTTAGGTGA
GAGTTGTTTCTTTCTTGGTTCTCGGCCAAACTTTAAACTTGACAAACTTTTACGAGTTCTTTTAT
AACTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGTACAGTCCATG
CCTGGAAAATCACATCATTAGGTCTAAATAGTTGTCATTTTGTAAACAACTTTAGGTTTTTAAAT
TAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGTTCTAGGCCGAACTTAACTTGACAAACT
TTTACGAGTTCTTTTATAACTTTTGTTCATTAAAGTATTCAAGACGATCCATTCCTTCGAGCAAT
TTCTGTACAGTCCATGCTTGGGAAATCACAACATTAGGTCTAAATAGTTGT
Done.