Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014258.1 Kokia drynarioides strain JFW-HI SEQ_129291, 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: 2309
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Found at i:820 original size:215 final size:216
Alignment explanation
Indices: 73--2309 Score: 2770
Period size: 215 Copynumber: 10.4 Consensus size: 216
63 CAAAAGAGAA
* *
73 AAGTTTTAAATTTAAAGACCAAAAGTTGTTTACAAAATGAAAAACCATTTGGACCAAATGATGCG
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCG
* * * * ** ** * *
138 ATTTCCCAAGAAGGGAATGTTTGAAAAATGGCTTGAAGGAATGGAT-TATCATGAATACTGTAAG
66 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCT-TCTTGAATACTTTAAG
***
202 GAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAA
130 GAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAAA
267 GAGAAACAAGTCTCACTTAAAT
195 GAGAAACAAGTCTCACTTAAAT
* * *
289 AAGTTTTTAATTTAAAAACCAAAAGTTGTTTACAAAATGACAAACTATTTTGGACCAAATGGTGC
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCA-TTTGGACCAAATGATGC
* * *
354 GATTTCCCGAGCATGGAATGCTCAAAAAATTGCTCAAAGGAATGGATCGTT-TTGAATACTTTAA
65 GATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATC-TTCTTGAATACTTTAA
* * * * * ** * ***
418 GGAATCGAAGTTAT-AAAGAACTCGCAACATTTTGA-AGAACTCGTAAAAGTTAAACCAAGAACC
129 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACA-AGTTC--ATAAGTTCGTCCAAGAACC
* * *
481 AAAGGAGGAACAAGTCTCACTTAATT
191 AAAAGAGAAACAAGTCTCACTTAAAT
507 AAGTTTTTTAATTTAAA-ACCCAAAAGTTGTTTAC-AAATGACAAACTC-TTTGGACCAAATGAT
1 AAG-TTTTTAATTTAAAGA-CCAAAAGTTGTTTACAAAATGACAAAC-CATTTGGACCAAATGAT
* *
569 GCGATTTCCCAAGCATGGAAGGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTA
63 GCGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTA
* *
634 AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAATCAA
128 AGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAA
* *
699 AAGAGAAACAA-TCTGA-TGCAAAT
193 AAGAGAAACAAGTCTCACT-TAAAT
* * * *
722 AAGTTTTAAATTCAAAGGCCAAAAGTT-TTTACAAAAATGACAAACCATTTGGAACAAATGATGC
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTAC-AAAATGACAAACCATTTGGACCAAATGATGC
* * * *
786 GATTTCCCGAGCATCGAATGCTCGAAATATTACTCAAAGGAATGGATCGTT-TTGAACACTTTAA
65 GATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATC-TTCTTGAATACTTTAA
* * ** * * **
850 GGAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTATCCAAGAACCAAA
129 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAA
*
915 AGAGAAACAAGTCTCACTTATAT
194 AGAGAAACAAGTCTCACTTAAAT
* * * *
938 AAGTTCTTAATTTAAAAACCAAAAGTTGTTTAC-AAATGACAAACTATTTTGACCAAATGATGCG
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCG
* * * *
1002 ATTTCAC-ACGCATGGAATGTTCGAAAAATTACTCGAAGGAATGAATCGTCTTGAATACTTTAAG
66 ATTTCCCGA-GCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAAG
* *
1066 GAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTAGTCCAAGAACCAAAA
130 GAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAAA
* *
1131 GAGAAACAA-TCTGACGTAAAT
195 GAGAAACAAGTCTCACTTAAAT
* * * * *
1152 AAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAGCATTTGGACCAAATAATACG
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCG
* * * *
1217 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAA-GAATGCATCGTCATGAATACTTTAAGG
66 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAAGG
* * * * ***
1281 AACCAATGTTATAAAATAACTTGAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAG
131 AACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAAAG
* * * *
1346 AGATACAATTCTGACGTAAAT
196 AGAAACAAGTCTCACTTAAAT
* * *
1367 AAGTTTTTAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGC
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTAC-AAAATGACAAACCATTTGGACCAAATGATGC
* * * *
1432 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCACAAAGGAATGGATCGTTC-TGAATACTTTAA
65 GATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATC-TTCTTGAATACTTTAA
* * * ** * * * * *
1496 GGAATCAAAGTTAAAAAAGAACTCATATTATTTTGACAGGCTCGTAAGTTCATCCAAGAACCAAA
129 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAA
1561 AGAGAAACAAGTCTCACTTAAAT
194 AGAGAAACAAGTCTCACTTAAAT
* *
1584 AAGTTTTTTCATTTAAA-ACCAAAAAGTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATG
1 AAG-TTTTTAATTTAAAGACC-AAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATG
* * * *
1647 CGATTTCCCAAGCATGGAAGGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAATACTTTAA
64 CGATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAA
*
1712 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAACCAAA
129 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAA
* *
1777 AGAGAAACAA-TCTGACGTAAAT
194 AGAGAAACAAGTCTCACTTAAAT
* * * *
1799 AAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAGCATTTGGACCAAATGATACG
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCG
* * *
1864 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGG
66 ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAAGG
* * * ***
1929 AACCAAAGTTATAAAATAACTTGAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAG
131 AACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAAAG
* * * *
1994 AGATACAATTCTGACGTAAAT
196 AGAAACAAGTCTCACTTAAAT
* * * *
2015 AAGTTTTTAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGG
1 AAGTTTTTAATTTAAAGACCAAAAGTTGTTTAC-AAAATGACAAACCATTTGGACCAAATGATGC
* * *
2080 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATT-TTGAATACTTTAA
65 GATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATC-TTCTTGAATACTTTAA
* * ** * * * *
2144 GGAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAA
129 GGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAA
2209 AGAGAAACAAGTCTCACTTAAAT
194 AGAGAAACAAGTCTCACTTAAAT
* * * *
2232 AATTTTTTTAATTTAAAAACCAAAAGTTGTTTAC-AAATAACAAACTATTTGGACCAAATGATGC
1 AA-GTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGC
*
2296 GATTTCCCAAGCAT
65 GATTTCCCGAGCAT
Statistics
Matches: 1740, Mismatches: 243, Indels: 76
0.85 0.12 0.04
Matches are distributed among these distances:
213 5 0.00
214 173 0.10
215 578 0.33
216 409 0.24
217 419 0.24
218 126 0.07
219 30 0.02
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (216 bp):
AAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATGCG
ATTTCCCGAGCATGGAATGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAAGG
AACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCATAAGTTCGTCCAAGAACCAAAAG
AGAAACAAGTCTCACTTAAAT
Found at i:2216 original size:648 final size:647
Alignment explanation
Indices: 73--2309 Score: 3360
Period size: 648 Copynumber: 3.5 Consensus size: 647
63 CAAAAGAGAA
* * *
73 AAGTTTTAAATTTAAAGACCAAAAGTTGTTTAC-AAAATGAAAAACCATTTGGACCAAATGATGC
1 AAGTTTTAAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCATTTGGACCAAATGATGC
* * ** * * * ** * ** *
137 GATTTCCCAAGAAGGGAATGTTTGAAAAATGGCTTGAAGGAATGGATTATCATGAATACTGTAAG
66 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
* * ** * * * * *
202 GAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAA
131 GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
267 GAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTTTACAAAATGACAA
196 GAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTTTAC-AAATGACAA
* * * * * *
332 ACTATTTTGGACCAAATGGTGCGATTTCCCGAGCATGGAATGCTCAAAAAATTGCTCAAAGGAAT
260 ACTA-TTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
* * * * * * * **
397 GGATCGTTTTGAATACTTTAAGGAATCGAAGTTAT-AAAGAACTCGCAACATTTTGA-AGAACTC
324 GGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACA-AGTTC
* ** * * * * * * *
460 GTAAAAGTTAAACCAAGAACCAAAGGAGGAACAAGTCTCACTTAATTAAGTTTTTTAATTTAAA-
388 --ATAAGTTAGTCCAAGAACCAAAAGAGAAACAA-TCTGACGTAAATAAG-TTTTAAATTCAAAG
* * *
524 ACCCAAAAGTTGTTTAC-AAATGACAAA-CTCTTTGGACCAAATGATGCGATTTCCCAAGCATGG
449 A-CCAAAAGTTGTTTACAAAATGACAAAGC-ATTTGGACCAAATGATACGATTTCCCGAGCATGG
* * * *
587 AAGGTTCGAAAAATTACTCAAAGGAATGGATCTTCTTGAATACTTTAAGGAACCAAAGTTATAAA
512 AATGTTCGAAAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAAGTTATAAA
* * * * *** * * *
652 AGAACTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAATCAAAAGAGAAACAA-TCTGAT
577 ATAACTTGAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGAC
*
716 GCAAAT
642 GTAAAT
* * *
722 AAGTTTTAAATTCAAAGGCCAAAAGTT-TTTACAAAAATGACAAACCATTTGGAACAAATGATGC
1 AAGTTTTAAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCATTTGGACCAAATGATGC
* * * *
786 GATTTCCCGAGCATCGAATGCTCGAAATATTACTCAAAGGAATGGATCGTTTTGAACACTTTAAG
66 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
* * * *
851 GAATCGAAGTTATAAAAGAACTCGTATTATTTTGACAAGCTCATAAGTTTATCCAAGAACCAAAA
131 GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
* *
916 GAGAAACAAGTCTCACTTATATAAGTTCTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAA
196 GAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAA
* * * *
981 CTATTTTGACCAAATGATGCGATTTCACACGCATGGAATGTTCGAAAAATTACTCGAAGGAATGA
261 CTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGG
1046 ATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATA
326 ATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATA
1111 AGTTAGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAAAGACCAAAA
391 AGTTAGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAAAGACCAAAA
*
1176 GTTGTTTACAAAATGACAAAGCATTTGGACCAAATAATACGATTTCCCGAGCATGGAATGTTCGA
456 GTTGTTTACAAAATGACAAAGCATTTGGACCAAATGATACGATTTCCCGAGCATGGAATGTTCGA
* * *
1241 AAAATTACTCGAA-GAATGCATCGTCATGAATACTTTAAGGAACCAATGTTATAAAATAACTTGA
521 AAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTTGA
1305 AAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTAAAT
586 AAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTAAAT
* *
1367 AAGTTTTTAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGC
1 AAGTTTTAAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCATTTGGACCAAATGATGC
* * *
1432 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCACAAAGGAATGGATCGTTCTGAATACTTTAAG
66 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
* *
1497 GAATCAAAGTTAAAAAAGAACTCATATTATTTTGACAGGCTCGTAAGTTCATCCAAGAACCAAAA
131 GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
*
1562 GAGAAACAAGTCTCACTTAAATAAGTTTTTTCATTT-AAAACCAAAAAGTTGTTTACAAATGACA
196 GAGAAACAAGTCTCACTTAAATAAG-TTTTTAATTTAAAAACC-AAAAGTTGTTTACAAATGACA
*
1626 AACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAAGGTTCGAAAAATTACTCGAAGGAAT
259 AACTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTACTCGAAGGAAT
1691 GGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCA
324 GGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCA
*
1756 TAAGTTCGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAAAGACCAA
389 TAAGTTAGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAAAGACCAA
1821 AAGTTGTTTACAAAATGACAAAGCATTTGGACCAAATGATACGATTTCCCGAGCATGGAATGTTC
454 AAGTTGTTTACAAAATGACAAAGCATTTGGACCAAATGATACGATTTCCCGAGCATGGAATGTTC
1886 GAAAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTT
519 GAAAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTT
1951 GAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTAAAT
584 GAAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTAAAT
* * *
2015 AAGTTTTTAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCGTTTGGACCAAATGATGG
1 AAGTTTTAAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCATTTGGACCAAATGATGC
2080 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
66 GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
2145 GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
131 GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
* *
2210 GAGAAACAAGTCTCACTTAAATAATTTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATAACAA
196 GAGAAACAAGTCTCACTTAAATAA-GTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAA
2275 ACTATTTGGACCAAATGATGCGATTTCCCAAGCAT
260 ACTATTTGGACCAAATGATGCGATTTCCCAAGCAT
Statistics
Matches: 1453, Mismatches: 122, Indels: 27
0.91 0.08 0.02
Matches are distributed among these distances:
644 113 0.08
645 108 0.07
646 211 0.15
647 379 0.26
648 426 0.29
649 216 0.15
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (647 bp):
AAGTTTTAAATTCAAAGACCAAAAGTTGGTTACAAAAATGACAAACCATTTGGACCAAATGATGC
GATTTCCCGAGCATCGAATGCTCGAAAAATTGCTCAAAGGAATGGATCATTTTGAATACTTTAAG
GAATCAAAGTTAAAAAAGAACTCGTATTATTTTGACAAGCTCGTAAGTTCATCCAAGAACCAAAA
GAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAAACCAAAAGTTGTTTACAAATGACAAA
CTATTTGGACCAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTACTCGAAGGAATGG
ATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAGTTCATA
AGTTAGTCCAAGAACCAAAAGAGAAACAATCTGACGTAAATAAGTTTTAAATTCAAAGACCAAAA
GTTGTTTACAAAATGACAAAGCATTTGGACCAAATGATACGATTTCCCGAGCATGGAATGTTCGA
AAAATTACTCGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTTGA
AAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTAAAT
Done.