Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012646.1 Kokia drynarioides strain JFW-HI SEQ_127656, 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: 3115
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Found at i:780 original size:216 final size:216
Alignment explanation
Indices: 12--3084 Score: 2775
Period size: 216 Copynumber: 14.3 Consensus size: 216
2 AGTTTGGCCT
* * * * *
12 AGAACCAAGAGTGAGATAATTATCAC-GTAAATAAGTTTTTAATTCAAAGACCAAAAGTTTTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* ** * * *
76 CAAAAGGATTAATTATTTGGACCAAATGATGTGATTTCTCGAAAATGGAATGTTC-GAAAAATTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAG-AAAATTG
* * *
140 CTCGAAGGAATTGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGTACTCGAAAAAGTT
129 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
**
205 TGACAAGTTCGGAAGTTCGGCCA
194 TGACAAGTTCGGAAGTTCAACCA
* * * * *
228 AGAACC-A-AGAGAAACAATTCCCACATAAATAAATTTATAA-TCAAAAGACCAAAAGTAGTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTC-AAAGACCAAAAGTTGTTTA
* * * * *
290 CAAAATGACAGATTATTTAGACCAAATGATGCAATTT-CCAAGAATGAAATGTTC-GAAAAATTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAG-AAAATTG
* * * ***
353 TTCGAAGAAATGGATCATCTTGAATACTTTAAGGAAAAAAAGTTATAAAAGAACTCGAAAAAGTT
129 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
*** *
418 T-ACAAAG-T---AAGTTTTGCCT
194 TGAC-AAGTTCGGAAGTTCAACCA
* * * * * *
437 AGAA-CAACGAGTGAAATAATTCTTAC-GTAAATAAGTTTTTAATTCAAAGATCGAAAGTTTTTT
1 AGAACCAA-GAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTT
* * * * *
500 GCAAAAGGACTAATTATTTGGACCAAATGATGCGATTTCCCGAGAATAGAATGTTCAAAAAATTG
64 ACAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTG
* ** * * * * *
565 ATCGAAGGAATCAATCGTCTTGAATATTTTAAGGAATCGAAGATATAAAAGTACTCGACAAAGTT
129 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
*
630 TGAAAAGTTCGGAAGTTCAACCA
194 TGACAAGTTCGGAAGTTCAACCA
* * * *
653 AGAACCAAGAAAGAAACAATTCTCACAGAAATTAA-ATTTTAATCCAAAGAGCAAAAGTTGTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAGAAA-TAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * *
717 CAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAATGCTCAGAAAATTGC
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGC
* * * * * *
782 TCGAAGGAATCGATTGTCATGAATACTCTAAGGAACCGAAGCTATAAAAGAACTTGAAAAAGTTT
130 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
* * **
847 GACTAGTTTGGAAGTTCTGCCA
195 GACAAGTTCGGAAGTTCAACCA
* * * * * *
869 AGAACAAAGAGAGAAACATTTCTCACATAAATAATTTTTTAATCCAAAGACAAAAAGTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
** * * * * * *
934 AAAATGACAGCTTATTTGGACCTAATGATGCAATTTCTCGAGAACGGAATGTTCAAAAAATTGTT
66 AAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCT
* * * * *
999 CGAA-AAATTAGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAGCTCGAAACAGTTT
131 CGAAGGAA-TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
* *** *
1063 G-CAAAGTTTGGAAGTTTGGCCT
195 GAC-AAGTTCGGAAGTTCAACCA
* * * * * *
1085 AGAACCAAGAGAGAAATAATTCTTAC-GTAAATAAGTTTTTAATTCAAAAACCGAATGTTTTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * * * * *
1149 CAAAAGGACTAACTATTTGGACCAAATGATGCAATTTCTCGAGAATGTAATGTTC-GAAAAATTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAG-AAAATTG
* * * * * *
1213 CTTGAAGGAAT-CAGTCGTCTTGAATACTTTAAGGAGCTGAAGTTATAAAAAAAACTCAAAAAAG
129 CTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAACCGAAGTTAT-AAAAGAACTCGAAAAAG
* * * *
1277 CTTGGCAAGTTCAGAAGTTCAGCCA
192 TTTGACAAGTTCGGAAGTTCAACCA
* ** *
1302 AGAA--ATA-AGAGAAACAATTCTCACATAAATAAAATTTTAATCCAAAGACCAAAAGTTGTTTA
1 AGAACCA-AGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * **
1364 CAAAATGACAGATTATTTGGACCAAATGATGCGATTTCCCAAGCAA-GGAATGTTTGGAAAATTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAG-AATGGAATGTTCAGAAAATTG
** * * * *
1428 CTCGAAGGAATGGATTATCTTGTATACTTTAAGGATCCGAAGTTATAAAATAACTCGTAAAAGTT
129 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
* * * * *
1493 TGAAAAGTTCGAAAGTACTA-TA
194 TGACAAGTTCGGAAGTTCAACCA
* * * * *
1515 AAAACCAAGGGAGAAACCATTCTCACATAAATAAGTTTTTAATTCTAAGA-CAAAATGTTGTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAA-GTTGTTTA
* * * * * * * *
1579 CAAAATGACAAACTATTTTGACCAAATGATGCGATTTCTCGAGCATGAAATATTCAAAAAATTGG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGC
* * * * *
1644 TGGAAGGAATGGATCGTCCTGAATA-TTGTAAGGAATCGAAGCTATAATAGAACTCGAAAAAGTT
130 TCGAAGGAATGGATCGTCTTGAATACTT-TAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
*
1708 TGA-AATGTTTGGAAGTTCAACCA
194 TGACAA-GTTCGGAAGTTCAACCA
* * **
1731 AGAACCAAGAGAGAAAGAATTCT-A-ATGTTAATAAGTTTTTAATTCAAAGAGTAAAAGTTGTTT
1 AGAACCAAGAGAGAAACAATTCTCACA-G-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTT
* * * * * **** * * *
1794 --AAAATAACAAACTACTTGG-CTAAAATGATGTGATTTTTTTAGCATGAAATGGTCAGAAAATT
64 ACAAAATGACAAATTATTTGGAC-CAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATT
* * * * * * * *
1856 TCTCGAAGGAATGGATCGTCTTGAATACTGTAAAGAACCAAAGTTACAAAAAAACTTGTAAAAGT
128 GCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGT
** ** * *
1921 TTGACATTTTTAGATGTTCAGCCA
193 TTGACAAGTTCGGAAGTTCAACCA
* * * * *
1945 AGAGCCAAGAGAGAAACAGTTCTCAC-GTAAATAAATCTTTATTTCAAAGACCAAAAGTTGTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * * * * ** * ** * *
2009 CGAATTGACTAACTATTTGGACCAAATCATGTAACTTCTTGAGCATGGAATGTTC-GAAATTTTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAA-ATTG
* * * * ** *
2073 CTAGAAGGAATGGATCATCTTGTATACTTTCAAGGGATAGAAGTTA-AAAAGAACTCGTAAAAGT
129 CTCGAAGGAATGGATCGTCTTGAATACTTT-AAGGAACCGAAGTTATAAAAGAACTCGAAAAAGT
* * *
2137 TTGACAAGTTCGAAAGTTTAACTA
193 TTGACAAGTTCGGAAGTTCAACCA
* *
2161 AGAACCAAGAGAGAAATAATTCTCAC-GTAAATAAGTTTTTAATTAAAAGACCAAAAGTT-TTTA
1 AGAACCAAGAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * * * ** *
2224 CAAAATAACAGATTATTTGGACCAAATGATGCAATTTCTCGAGAATCCATTGTTC-GAAAAATTG
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAG-AAAATTG
* * * * * *
2288 CTCGAAGGACTGGATCGTCTTGGATACTTTAAGGAACCAAAGTTACAAAAGAACTTGATAAAGTT
129 CTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTT
2353 TGA-AATGTTCGGAAGTT-AAGCCA
194 TGACAA-GTTCGGAAGTTCAA-CCA
* * * * *
2376 AGAACCAAGAGAGAAATAATTCTTACATAAATAAGTTTTTAATTCAAAGACCGAAAGTTTTTTAC
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
** * * ** * ** *
2441 AAAGGGACAAACTATTTGGACCAAATGGTATGATTTCCTGAGGCTGAAATGTT-AGGAAAATTGC
66 AAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCA-GAAAATTGC
* * ** * * * * * *
2505 TCAAAAGAATCTATCATTTTGAATAATTTAAGGAACTGAAGTTATAAAAGAACTCAAAAAAATTT
130 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
* *
2570 GACAAGTTCGGAAGTTCGGA-GA
195 GACAAGTTCGGAAGTTC-AACCA
* * * * * *
2592 AGAACGAAGAGAGAAACAATTATCACATAATTAAGTTTTTAATTCAAAAACCGAAAGTTGTTTAC
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
* * * * * * ** **
2657 AAAAAGATAAAATATTCGAACCAAATGATGCGATTTCTCGACCATGGAATGTTTGGAAAATTGCT
66 AAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCT
* * * * *
2722 CGAAGGAATGGATTGTCTTTG-ATACTTTAAGGAACCGAAATTATAAAATAACTTGTAAAAGTTT
131 CGAAGGAATGGATCGTC-TTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
* *
2786 GACAATTTCGAAAGCTT--ACTCA
195 GACAAGTTCGGAAG-TTCAAC-CA
* * * * *
2808 AGAACCAAGGGAAAAACTATTCTCAC-GTAAATAAGTTTTTAATTCTAAGACAAAAAGTTGTTTA
1 AGAACCAAGAGAGAAACAATTCTCACAG-AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTA
* * * * * *
2872 CAAAATGACAAACTATTTGGACCAAATGATGAGATTTACCGAGCATGGAATGTTCAGATACTTGC
65 CAAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGC
* * * *
2937 TCGAAGGAATCGATAGTCATGAATACTTTAAGGAACCGAAGTTATAAAAGAACTTGAAAAAGTTT
130 TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTT
* ***
3002 GACAAGTTAGGAAGTTCGGTCA
195 GACAAGTTCGGAAGTTCAACCA
* * * * *
3024 AGAAACAAGAGAGAAACAATTCTCACAAAAATAAATTTTTAATCCAAAGACCATAAGTTGT
1 AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
3085 GACAGATTAT
Statistics
Matches: 2299, Mismatches: 484, Indels: 148
0.78 0.17 0.05
Matches are distributed among these distances:
208 1 0.00
209 13 0.01
211 71 0.03
212 83 0.04
213 93 0.04
214 293 0.13
215 470 0.20
216 1207 0.53
217 66 0.03
218 2 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (216 bp):
AGAACCAAGAGAGAAACAATTCTCACAGAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
AAAATGACAAATTATTTGGACCAAATGATGCGATTTCCCGAGAATGGAATGTTCAGAAAATTGCT
CGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGAAAAAGTTTG
ACAAGTTCGGAAGTTCAACCA
Done.