Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014097.1 Kokia drynarioides strain JFW-HI SEQ_129128, 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: 4660
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Warning! 15 characters in sequence are not A, C, G, or T
Found at i:1026 original size:216 final size:215
Alignment explanation
Indices: 4--4645 Score: 4369
Period size: 216 Copynumber: 21.6 Consensus size: 215
1 AGG
* * *
4 GAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAATTTGTTTACAAAATCACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * *
69 TATTTAGACCAAAAGACGCGATTTTTGGAGCATGGAATG-TTCAGAAAA-TGGCTCAAAGGAATG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGA-AAAATTGG-TCGAAGGAATG
* * * * * *
132 GATAGTCTTCAATACTTTGAGGAACCAAAGTTATAAAAGAACTCGTAAAAAGTTCGACCAGTTCG
129 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGTTCG
* *
197 TATGTTCGTCCTAGAACCACA-AGA
193 -AAGTTCGTCCAAGAACCA-AGAGA
* * * * *
221 GAAACAATTCTCACGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACAAAG
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * *
286 TTTTTAGACCGAATGATACGA-TTCCCGAGCATGGAAAGTTCGAAAAATTGGTCGAAGGAATGGA
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGA
* * * ** * * ** * * * *
350 TCGTCTTTAATACTCTCAGGAACTTAAGTTACAAAAGAGCTATTAAATGTTCCG-CTAGTACGGA
131 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTT-TGACAAGTTC-GA
* * *
414 AGTTCGTCCAAAAACCATGAGT
194 AGTTCGTCCAAGAACCAAGAGA
* * * * * *
436 GAAACAATTCTCACGTAAACAAGTTTTTAATTCAAAGACGAAAAATTGTTTAGAAAATGATAACC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * ** *
501 TATTTAGACCAAATGATGTC-ATTTCTCGGGCATGGAATGCTTGAAAAATTGCACAAAGGAATGG
66 TATTTAGACCAAATGATG-CGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
** * * *
565 ATCACCTTGAATAGTTTAAGGAACCGAAGTTATAAAGGAACT-GATAAAAAGTTTGACAAGTTTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCG-T-AAAAGTTTGACAAG-TTC
629 GAAGTTCGTCCAAGAACCAAGAGA
192 GAAGTTCGTCCAAGAACCAAGAGA
* * * *
653 GAAACAATTGTCATGTAAAT-A-TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGA-AAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * * * * *
715 TATTTAGACCAAACGATGCGATTTCCCAAGCGTAGAATGTTCGGAAAATTGCTTGAAGGAATGGA
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGA
* * * * *
780 TCATCTTGAATACTTGAAGGAACTGAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAT
131 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA-
*
845 GTTCAG-CCAAGAACAAAGAGA
195 GTTC-GTCCAAGAACCAAGAGA
* * *
866 GAAACAGTTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTGTTTACGAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * ** * *
931 TATTTAGACCAAATAATGCGATTTTTCGGGCATTAAATGTTTTAAAAACTGGTCGAAGG-ATAGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAAT-GG
* * * *
995 ATCGGCATGAATAATTTAAGGAACCGAAGTTATAAAAGAACTGGTAAAAGTTTGACAAGTTCGGA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GA
* *
1060 AGTTCATCCAAAAACCAAGAGA
194 AGTTCGTCCAAGAACCAAGAGA
* * * *
1082 GAAACAATCCTCACGTAAATAAGTTTTCAATTCAAAGACCAAAAGTTGTTTACAAAATTAAAAAA
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGACAAA
* *
1147 C-ATTTAGACCGAAA-GATGCGATTT-TCGGAGCATGGAATG-TTCATAAAA-TGGCTCAAAGGA
65 CTATTTAGACC-AAATGATGCGATTTCTC-GAGCATGGAATGTTTGA-AAAATTGG-TCGAAGGA
* * * * * * *
1207 ATGGATAGTCTTGAATACTTTGAGGAACCAAAGTTATAAAAGAACCCGTAAATGTTCGACCAGTT
126 ATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTT
*
1272 CGTAAGTTCGTCCTAGAACCACA-AGA
191 CG-AAGTTCGTCCAAGAACCA-AGAGA
* * * * *
1298 GAAACAATTCTCACGTAAATAGGTTTTTAATTCGAAGACTAAAAGTTGTTTACATAATGACAAAG
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * * * * * *
1363 TTTTTAGACCGAATGATACGA-TTCGCGAGCATAGAAAGTTYGAAMAATTGGTCDAAGGAATGRA
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGA
* * * ** * * * ** ** * * **
1427 TCGTCTTKAATACTCTCAGGAACTTAAGTYACAAAAGAGCTAYTAAATRTTCHG-CWAGWACGGA
131 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTT-TGACAAGTTC-GA
** * * *
1491 AGTTCGWMCAAAAACCATGAGW
194 AGTTCGTCCAAGAACCAAGAGA
* * * * * *
1513 GAAACAATTCTCACGTAAAYAAGTTTTTAATTCAAAGACGAAAAATTGTTTAGAAAATGATAACC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * ** *
1578 TATTTAGACCAAATGATGTC-ATTTCTCGGGCATGGAATGCTTGAAAAATTGCACAAAGGAATGG
66 TATTTAGACCAAATGATG-CGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
** * * * *
1642 ATCACCTTGAATAGTTTAAGGAACCGAAGTTATAAAGGAAAT-GATAAAAAGTTTGACAAGTTTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCG-T-AAAAGTTTGACAAG-TTC
1706 GAAGTTCGTCCAAGAACCAAGAGA
192 GAAGTTCGTCCAAGAACCAAGAGA
* * * *
1730 GAAACAATTGTCATGTAAAT-A-TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGA-AAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * * * ** *
1792 TATTTAGACCAAACGATGCGATTTCCCAAGCGTAGAATGTTCGGAAAATTACTTGAAGGAATGGA
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGA
* * * * *
1857 TCATCTTGAATACTTGAAGGAACTGAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAAA
131 TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-AA
* *
1922 GTTCAG-CTAAGAACAAAGAGA
195 GTTC-GTCCAAGAACCAAGAGA
* * *
1943 GAAACAGTTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAAAGTTGTTTACGAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * *
2008 TATTTAGACCAAATAATTCAATTTTTCGAGCATTGAAT-TTTCGAAAAATTGGTCGAAGGAAAGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTT-GAAAAATTGGTCGAAGGAATGG
* * * *
2072 ATCGGCTTGAATAATTTAAGGAACCGAAGTTATAAAAGAACTCTTAAAAGTTTGACAAGTTTGGA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-TTCGA
* *
2137 AGTTCATCCAAAAACCAAGAGA
194 AGTTCGTCCAAGAACCAAGAGA
* * *
2159 GAAACAATTCTCACGTAAATAAGTTTTCAATTCAAAGACCAAAAGTTGTTTACAAAATTAAAAAA
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGACAAA
*** * * *
2224 C-ATTTAGAATGAATGATGCGATTTC-CTGAGCATGGAATGCTCGAAAAATTAGTCGAAGGAATG
65 CTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATG
* * * * * * * *
2287 GGTCATCTTTAATGCTCTCAGAAACCGAAGTTATAAAAGAACTGGTAAATA-TTTGACAAGTTCT
129 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAA-AGTTTGACAAGTTC-
2351 GAAGTTCGTCCAAGAACCAAGAGA
192 GAAGTTCGTCCAAGAACCAAGAGA
* * *
2375 GAAACAGTCCTCATGTAAATAAGTTTTTAATTCAAAGACCAAAAGGTT-TTTACAAAATGACAAA
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA-GTTGTTTACAAAATGACAAA
* * * * * ** *
2439 CTATTTTATACCCAATGATGCAATTTCCCGAGCATGGAATGTTTAAAAAATTGCACAAAGGAATG
65 CTA-TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATG
* * ** * * *
2504 GATCGTCTTTAATACTCTCAA-GAACTAAAGTTATAATAAAAGAACTTGT-AAATTATTGAAAAG
129 GATCGTCTTGAATACT-TTAAGGAACCGAAG-T-T-ATAAAAGAACTCGTAAAAGT-TTGACAAG
* ** *
2567 TTTGAAAGTTAATCCAAGAACAAAGAGA
189 TTCG-AAGTTCGTCCAAGAACCAAGAGA
* * * * * * * * *
2595 GAAA-ATATTCACATGCAAATAAATTTTAAATTCAAACACCAAAAGCTGTTTACCATATGACAAA
1 GAAACA-ATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAA
* * * * * * * * * * *
2659 CTATTTTGGCCAAATGATGCAATTTTTTGAGAATGGAATGTTCGGAAAATTGATTGAAGGAATGC
65 CTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
* * * * ** *
2724 ATCTTCTTAAATACTATT-AGGAACCAAAGTTATAAAAGAACTTGTAAATTTTTGAAAAGTTCGG
130 ATCGTCTTGAATACT-TTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-G
* * *
2788 AAGTTCATCCAAGAACTAGGAGA
193 AAGTTCGTCCAAGAACCAAGAGA
2811 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* *
2876 TATTTAGACCAAATGAGGCGATTTCTCGAGCATGGAATGTTCGAAAAA-TGGCTC-----AA---
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGG-TCGAAGGAATGG
* * * *
2932 A--------AATACTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGGCTAGTTCGTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-A
* *
2989 AGTTCATCCGAGAACCAAGAGA
194 AGTTCGTCCAAGAACCAAGAGA
*
3011 GAAACAATTCTCACGAAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * *
3076 TATTTAGACCAAATGATGCGATTTCTCGTGCATGGAATGTTCGGAAAA-TGGCTCAAATGAATGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGG-TCGAAGGAATGG
* * * * *
3140 ATAGTCTTGAATACTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGACTAGTTTGTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-A
* *
3205 AGTTTGTCCGAGAACCAAGAGA
194 AGTTCGTCCAAGAACCAAGAGA
*
3227 GAAACAATTATCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * *
3292 TATTTAGACCAATTGATGCGATTTCTCGAGCATGGAATGTTAGGAAAA-TGGCTCAAATGAATGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGG-TCGAAGGAATGG
* * * *
3356 ATAGTCTTGAATACTTTAAGGAACCAAAGTTGTAAAAGAACTCGTAAAAGTTTGACTAGTTCGTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-A
* * * *
3421 AGTTTGTCTGAA-AACGAAGTGA
194 AGTTCGTC-CAAGAACCAAGAGA
* * * * *
3443 GAAACAATTCTCATGTAAATAAGTTTTTAATGT-AAAGATCAAAATTTGTTTTCAAAATCACAAA
1 GAAACAATTCTCACGTAAATAAGTTTTTAAT-TCAAAGACCAAAAGTTGTTTACAAAATGACAAA
* * *
3507 CTATTTAGACCAAATGATGCGATATC-CGGAGCATGAAATGTTT-AGAAAA-TGGCTCAAAGGAA
65 CTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTTGA-AAAATTGG-TCGAAGGAA
* * * * * *
3569 TGGATAGTCTTGAATACTTTGATGAACCAAAGTTATAAAATAACTCGTAAAAGTTTGACTAGTTC
127 TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
*
3634 GTAAGTTCGTCCGAGAACCACA-AGA
192 G-AAGTTCGTCCAAGAACCA-AGAGA
* * * * **
3659 GAAATAATTCTCACGTAAATAGGTTTTTGAATTCGAAGACTAAAAGTTGTTTACATTATGACAAA
1 GAAACAATTCTCACGTAAATAAGTTTTT-AATTCAAAGACCAAAAGTTGTTTACAAAATGACAAA
* * * * * * *
3724 GTTTTTAGACCGAATGATACGA-TTCGCGAGCATGGAAAGTTTGAAAAATTGGTCGAATGAATGG
65 CTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
* * ** * * ** * * *
3788 ATCGTCTTGAATACTCTCAGGAACTTAAGTCACAAAAGAGGTAC-TAAATGTTCCG-CAAGTACG
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACT-CGTAAAAGTT-TGACAAGTTC-
* *
3851 GAAGTTCGTCCAAAAACCATGAGA
192 GAAGTTCGTCCAAGAACCAAGAGA
* * * * * *
3875 GACACAATTCTCACGTAAATAAGTTTTTAATTCGAAGACCAAAAATTGTTTAGAAAATGATAACC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * ***
3940 TATTTAGACCAAATGATGTC-ATTTCTTGAGCATGGAATGCTTGAAAAATTCCACGAAGGAATGG
66 TATTTAGACCAAATGATG-CGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
** * * * *
4004 ATCACCTT---T--TTTAAGGAATCGAAGTTGTAAAGGAACT-GATAAAAAGTTTGACAAGTTTA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCG-T-AAAAGTTTGACAAG-TTC
*
4063 GAAGTTTGTCCAAGAACCAAGAGA
192 GAAGTTCGTCCAAGAACCAAGAGA
* * * * * *
4087 GAAACAATTGTCATGTAAA-AA-TTTTTAATTCAAAGACGAAAAGTTGATTACAAAATGAAAAAT
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * *
4150 TATTTAGACCAAACGATGCGATTTCTCAAGCGTAGAATGTTT-AGAAAATTGCTCGAAGGAATGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGA-AAAATTGGTCGAAGGAATGG
* * *
4214 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCATAAAAGCTTGACAAGTTCGAA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-A
* *
4279 AGTTCAG-CTAAGAACAAAGAGA
194 AGTTC-GTCCAAGAACCAAGAGA
* * * * * * *
4301 GAAACAGTCCTCACGTAAATAAATTTTTAATTCAAAGAGCAAAAATAGTTTACGAAATGACAAAC
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* ** * * * *
4366 TATTTAGACAAAAAAATGCGATTTTTCGAGCATTGAATGTTCGAAAAACTGGTCGAAGG-ATAGG
66 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAAT-GG
* *
4430 ATCGGCTTGAATAATTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGA
130 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GA
* * *
4495 AGTTCATCCAAAAATCAAGAGA
194 AGTTCGTCCAAGAACCAAGAGA
* ** * ** * *
4517 TAAACAATTCTCACGTAAATAAGTTTACAATTCAAAGAACAAAAGTTACTTACAAAATTTAAAAA
1 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-TGACAAA
*** * * * * * *
4582 C-ATTTAGAATGAATGATGTGATTTCTCAAACATGGAATGCTCGAAAAATTAGTCGAAGGAATGG
65 CTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGG
4646 GTCATCTTTA
Statistics
Matches: 3626, Mismatches: 665, Indels: 269
0.80 0.15 0.06
Matches are distributed among these distances:
199 3 0.00
200 178 0.05
205 2 0.00
208 2 0.00
209 2 0.00
210 92 0.03
211 23 0.01
212 55 0.02
213 105 0.03
214 230 0.06
215 496 0.14
216 1925 0.53
217 336 0.09
218 7 0.00
219 76 0.02
220 94 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (215 bp):
GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGAAAAATTGGTCGAAGGAATGGA
TCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAG
TTCGTCCAAGAACCAAGAGA
Done.