Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001392.1 Kokia drynarioides strain JFW-HI SEQ_112876, 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, 905
Length: 1509
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Found at i:478 original size:217 final size:217
Alignment explanation
Indices: 1--1509 Score: 1503
Period size: 217 Copynumber: 7.0 Consensus size: 217
** * * *
1 TCCAAGAATC-AAGAGAGAAGTAACTCTCACGTAAATAAATTTTTAACTCATAA-ACCAAAAGTT
1 TCCAAGAA-CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA-AAGACCAAAAGTT
* * * * * * * *
64 GTTAAGAAAATGA-AAATCTATTTTGACCAAATGATGTGATTTC-CTGAGAACGAAAGGTTC-AA
64 GTTTACAAAATGACAAA-CTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCGAA
* ** ** *
126 AAAGTTGCTCGAAGGAATGGATCGTCTTTCATATTCAAAGGAACCGAAGTTATAGAAGAACTCGT
127 AAA-TTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTATAAAAGAACTCGT
* *
191 AAATGTTTTACCAGTTC-GAAAGTTCG
191 AAATGTTTGACAAGTTCGGAAAGTTCG
* * * *
217 TCCAAGAAGAAAGAGAGATACAATTC-CTACGTAAAAAAGTTTTTAATTCAAAGACCGAAAGATT
1 TCCAAGAACAAAGAGAGAAACAATTCTC-ACGTAAATAAGTTTTTAATTCAAAGACCAAAAG-TT
* * * *
281 -TTTATAAAATGACAAACTGTTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTCGGAAA
64 GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAA
* ** *
345 ATTGGTCGAAGGAATAGATCGTCTTGAATATTCTCAGGAATTGAAGTTATAAAAAGAATTCGTAA
129 ATTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTAT-AAAAGAACTCGTAA
* *
410 ATGTCTGACAAATT-GGAAAGTTCG
193 ATGTTTGACAAGTTCGGAAAGTTCG
* * *
434 TCCATGAACAAAGAGAGAAACAATTTTCACGTAAATAAGTTTTTAATTCAAAGATCAAAAGTTGT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
** * * * * * *
499 GAACAAAATGAAAAACTATTTTA-ACCAAATGATGTGATTTCCCGTGAATGGAAGGTTCAGAAAA
66 TTACAAAATGACAAACTA-TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC-GAAAA
* * ** *
563 CTT-GTCGAAGGAATGGGTCGTCTTGAATATTCAAAGGAACCGACGTTATAAAAGAACTCGTAAA
129 ATTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAA
* *
627 TGTTTGACAAGTTCGGGGAAGTTTG
194 TGTTTGACAAGTTC-GGAAAGTTCG
* * * * * * *
652 TCCAAGAAGAAAGAGAGATACAATTCCCACGTAAAAAAGTTTTTAATTTAAACACCAAAAGATTT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAG-TTG
** * ** *
717 TTTGTAAAACGATGAAGTATTTAGACCAAATGATGCGATTT-TCGGAGCATGGAATGTTCGAAAA
65 TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCGAAAA
* * * * * *
781 ATTGGTTGAAGGAATGGATTGTGTTGAATACTCTCAAGAACTGAAGTTATAAAAGAACTCGTAAA
129 ATTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAA
* * * * *
846 TGTTTAACGAGATC-GACAGTTCA
194 TGTTTGACAAGTTCGGAAAGTTCG
* * * * *
869 TCCAAGAACCAAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAAACTCATAGACAAAAAGTTG
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT-AATTCAAAGACCAAAAGTTG
* * * * *
934 TTTACAAAATGACAAATTTTTTAGACCAAATGATGCGATTTC-CTAAGCATGAAATGGTCGAAAA
65 TTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCGAAAA
* * * * * *
998 ATTGCTCGAATGAATGAATCGTCTTGAATACTCTCAAG-ACCTGAAGTTATAAAAGAACTCTTAA
129 ATTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACC-GAAGTTATAAAAGAACTCGT-A
* *
1062 AATATTTGACAAGTTCTG-AAGTTCG
192 AATGTTTGACAAGTTCGGAAAGTTCG
* * * * * *
1087 TCCAAGAACCAAGAGAGAAACAATTCTCTCATAAATAAGTTTTTAACTAAAAGTCCAAAAGTTGT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
* ** * * ** *
1152 TTACAAAATAACAAACTATTTTCACAAAATGATGTGATTTCTTAAGCATGGAATGTTCAAAAAAT
66 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAAT
* * * *
1217 TGGTCG-AGAGAACGGATCGTCTTGAATACTCTCTA--AATCGAAGTTTTAAAAGAACTCGTAAA
131 TGGTCGAAG-GAATGGATCGTCTTGAATATTCTC-AGGAACCGAAGTTATAAAAGAACTCGTAAA
1279 TGTTTGACAAGTTCGG-AAGTTCG
194 TGTTTGACAAGTTCGGAAAGTTCG
* * **
1302 TCCAAGAACGAAGAGAGAAACTATTCTCACGTAAATAAGTTTTTAATTCAAAGAAAAAAAGTTGT
1 TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
* * * * * *
1367 TAACAAAATGAAAAACTATTTTGACCAGATGATGCGATTTCCCGAGAATGGAA-GATTCGAAAAA
66 TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATG-TTCGAAAAA
* * * * ** * *
1431 TTGGTCGGAGGAAGGGATCATCTCGAATATTCAAAGGAACCAAAGTTATAAAAGAACTCATAAAT
130 TTGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAAT
*
1496 GTTTGACTAGTTCG
195 GTTTGACAAGTTCG
Statistics
Matches: 1058, Mismatches: 203, Indels: 64
0.80 0.15 0.05
Matches are distributed among these distances:
214 2 0.00
215 158 0.15
216 217 0.21
217 422 0.40
218 155 0.15
219 104 0.10
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (217 bp):
TCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
TTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAAT
TGGTCGAAGGAATGGATCGTCTTGAATATTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATG
TTTGACAAGTTCGGAAAGTTCG
Found at i:1346 original size:433 final size:428
Alignment explanation
Indices: 25--1509 Score: 1704
Period size: 433 Copynumber: 3.4 Consensus size: 428
15 GAGAAGTAAC
* * * *
25 TCTCACGTAAATAAATTTTTAACTCATAA-ACCAAAAGTTGTTAAGAAAATGAAAATCTATTTTG
1 TCTCACGTAAATAAGTTTTTAACTCA-AAGACAAAAAGTTGTTAACAAAATGAAAAACTATTTTG
* *
89 ACCAAATGATGTGATTTCCTGAGAACGAAAGGTTC-AAAAAGTTGCTCGAAGGAATGGATCGTCT
65 ACCAAATGATGCGATTTCCTGAGAATGAAAGGTTCGAAAAA-TTGCTCGAAGGAATGGATCGTCT
** * * *
153 TTCATATTCAAAGGAACCGAAGTTATAGAAGAACTCGTAAATGTTTTACCAGTTCGAAAGTTCGT
129 TGAATATTCAAAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCG-AAGTTCGT
* *
218 CCAAGAAGAAAGAGAGATACAATTCCTACGTAAAAAAGTTTTTAATTCAAAGACCGAAAGATTTT
193 CCAAGAAGAAAGAGAGATACAATTCCT-CGTAAAAAAGTTTTTAATTAAAAGACCAAAAGATTTT
* * *
283 TATAAAATGACAAACTGTTTAGACCAAATGATGCAATTTCTCGAGCATGGAATGTTCGGAAAATT
257 TATAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATT
* * * * *
348 GGTCGAAGGAATAGATCGTCTTGAATATTCTCAGGAATTGAAGTTATAAAAAGAATTCGTAAATG
322 GGTCGAAGGAATGGATCGTCTTGAATACTCTCA--AATCGAAGTT-TTAAAAGAACTCGTAAATG
* * * *
413 TCTGACAAATT-GGAAAGTTCGTCCATGAACAAAGAGAGAAACAAT
384 TTTGACAAGTTCGG-AAGTTCGTCCAAGAACAAAGAGAGAAACTAT
* * * *
458 TTTCACGTAAATAAGTTTTTAATTCAAAGATC-AAAAGTTGTGAACAAAATGAAAAACTATTTTA
1 TCTCACGTAAATAAGTTTTTAACTCAAAGA-CAAAAAGTTGTTAACAAAATGAAAAACTATTTTG
* * * * * *
522 ACCAAATGATGTGATTTCCCGTGAATGGAAGGTTCAGAAAACTTG-TCGAAGGAATGGGTCGTCT
65 ACCAAATGATGCGATTTCCTGAGAATGAAAGGTTC-GAAAAATTGCTCGAAGGAATGGATCGTCT
* *
586 TGAATATTCAAAGGAACCGACGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGGGGAAGTTT
129 TGAATATTCAAAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTC---GAAGTTC
* * *
651 GTCCAAGAAGAAAGAGAGATACAATTCCCACGTAAAAAAGTTTTTAATTTAAACACCAAAAGATT
191 GTCCAAGAAGAAAGAGAGATACAATT-CCTCGTAAAAAAGTTTTTAATTAAAAGACCAAAAGA-T
* * ** *
716 TTTTGTAAAACGATGAAGTATTTAGACCAAATGATGCGATTT-TCGGAGCATGGAATGTTCGAAA
254 TTTTATAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTC-GAGCATGGAATGTTCGAAA
* * * * *
780 AATTGGTTGAAGGAATGGATTGTGTTGAATACTCTCAAGAACTGAAGTTATAAAAGAACTCGTAA
318 AATTGGTCGAAGGAATGGATCGTCTTGAATACTCTCAA-ATC-GAAGTTTTAAAAGAACTCGTAA
* * * * *
845 ATGTTTAACGAGATC-GACAGTTCATCCAAGAACCAAGAGAGAAA-TAAT
381 ATGTTTGACAAGTTCGGA-AGTTCGTCCAAGAACAAAGAGAGAAACT-AT
* * * *
893 TCTCACGTAAATAAGTTTTTAAACTCATAGACAAAAAGTTGTTTACAAAATGACAAA-TTTTTTA
1 TCTCACGTAAATAAGTTTTT-AACTCAAAGACAAAAAGTTGTTAACAAAATGAAAAACTATTTT-
* * * *
957 GACCAAATGATGCGATTTCCTAAGCATGAAATGG-TCGAAAAATTGCTCGAATGAATGAATCGTC
64 GACCAAATGATGCGATTTCCTGAGAATGAAA-GGTTCGAAAAATTGCTCGAAGGAATGGATCGTC
* *
1021 TTGAATACTCTC-AA-G-ACCTGAAGTTATAAAAGAACTCTTAAAATATTTGACAAGTTCTGAAG
128 TTGAATA-T-TCAAAGGAACC-GAAGTTATAAAAGAACTCGT-AAATGTTTGACAAGTTC-GAAG
** * * * * *
1083 TTCGTCCAAGAACCAAGAGAGAAACAATTCTCTCATAAATAAGTTTTTAACTAAAAGTCCAAAAG
188 TTCGTCCAAGAAGAAAGAGAGATACAATTC-CTCGTAAAAAAGTTTTTAATTAAAAGACCAAAAG
* * ** * * ** *
1148 -TTGTTTACAAAATAACAAACTATTTTCACAAAATGATGTGATTTCTTAAGCATGGAATGTTCAA
252 ATT-TTTATAAAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGA
*
1212 AAAATTGGTCG-AGAGAACGGATCGTCTTGAATACTCTCTAAATCGAAGTTTTAAAAGAACTCGT
316 AAAATTGGTCGAAG-GAATGGATCGTCTTGAATACTCTC-AAATCGAAGTTTTAAAAGAACTCGT
*
1276 AAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACGAAGAGAGAAACTAT
379 AAATGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACTAT
* *
1326 TCTCACGTAAATAAGTTTTTAATTCAAAGAAAAAAAGTTGTTAACAAAATGAAAAACTATTTTGA
1 TCTCACGTAAATAAGTTTTTAACTCAAAGACAAAAAGTTGTTAACAAAATGAAAAACTATTTTGA
* * * * * * * * *
1391 CCAGATGATGCGATTTCCCGAGAATGGAAGATTCGAAAAATTGGTCGGAGGAAGGGATCATCTCG
66 CCAAATGATGCGATTTCCTGAGAATGAAAGGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTG
* * *
1456 AATATTCAAAGGAACCAAAGTTATAAAAGAACTCATAAATGTTTGACTAGTTCG
131 AATATTCAAAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCG
Statistics
Matches: 884, Mismatches: 132, Indels: 75
0.81 0.12 0.07
Matches are distributed among these distances:
430 3 0.00
431 19 0.02
432 108 0.12
433 241 0.27
434 88 0.10
435 211 0.24
436 191 0.22
437 21 0.02
438 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (428 bp):
TCTCACGTAAATAAGTTTTTAACTCAAAGACAAAAAGTTGTTAACAAAATGAAAAACTATTTTGA
CCAAATGATGCGATTTCCTGAGAATGAAAGGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTG
AATATTCAAAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAGTTCGTCCA
AGAAGAAAGAGAGATACAATTCCTCGTAAAAAAGTTTTTAATTAAAAGACCAAAAGATTTTTATA
AAATGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGGTC
GAAGGAATGGATCGTCTTGAATACTCTCAAATCGAAGTTTTAAAAGAACTCGTAAATGTTTGACA
AGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACTAT
Done.