Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001368.1 Kokia drynarioides strain JFW-HI SEQ_112827, 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, 651
Length: 1086
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Found at i:464 original size:203 final size:204
Alignment explanation
Indices: 106--1086 Score: 901
Period size: 203 Copynumber: 4.6 Consensus size: 204
96 GCATGGAATG
** * ** *
106 TTCGAAAAATTACTCAAAGGAATAAATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAA
1 TTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAA
* * * * * *
171 CTCGTAAAAGTTTCACAAGTTCATAAGTTCGTCCAAGAAACAAAAGAGAAACAATTCTAACGTAA
66 CTCGTAAAAGTTTGACAAGTTTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAA
*
236 ATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATG
131 ATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATG
301 CGATTTCC-
196 CGATTTCCA
* * * * *
309 TTCGAAAAATGGTTTGAAGGAATGGATCATCATGAATACTTTAAGGAACCAAGGTTATAAAAAAA
1 TTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAA
* *
374 CTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACTTAA
66 CTCGTAAAAGTTTGACAAGTTTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAA
* * * *
439 ATAAGTTTTTAATTTAAAAACCAAAAGTTGTTTACAAAATGACAAACTATTTTGGACCAAATGGT
131 ATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACCA-TTTGGACCAAATGAT
504 GCGATTTCCCGAGCATGGAA
195 GCGATTT--C---C-----A
* * * ** ***
524 TGCTCAAAAAATTGCTCAAAGGAATGGATCGTTTTGAATACTTTAAGGAATTGAAGTTATAAAAG
1 T--TCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAG
** * * * * * * *** * *
589 AACTCACAACATTTTGAAGAACTCGTAAAAGTTAAACCAAGAACCAAAGGAGGAACAAGTCTCAC
64 AACTCGTAAAAGTTTG-ACAAGT-TTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCAC
* * * *
654 TTAAATAAGTTTTTTAATT-TAAAACTCAAAAGTTGTTTAC-AAATGACAAACTATTTGGACCAA
127 GTAAATAAG-TTTTAAATTCAAAAAC-CAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAA
717 ATGATGCGATTTTCCGAGAATGGAA
190 ATGATGCGA-TTTCC---------A
** * * *
742 TGTTCGAAAAATTACTCGAAAGAATGAATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAG
1 --TTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAG
* * * * *
807 AACTCGTAAAAGTTTCACAAGTTCATAAGTTAGTCCAAGAACCAAAAGAGAAACAA-TCTGACGT
64 AACTCGTAAAAGTTTGACAAGTTTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACGT
* *
871 AAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAGCATTTGGACCAAATGA
129 AAATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGA
*
936 TACGATTTCCCGAGCATGGAA
194 TGCGATTT--C---C-----A
* ** * *
957 TGTTTGAAAAATTACTCGAATGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAT
1 --TTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAG
* * * * * *
1022 AACTTGAAAAAG-TTGACAAGTTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGT
64 AACTCGTAAAAGTTTGACAAGTTTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACGT
1086 A
129 A
Statistics
Matches: 648, Mismatches: 97, Indels: 54
0.81 0.12 0.07
Matches are distributed among these distances:
203 156 0.24
204 21 0.03
206 1 0.00
209 1 0.00
214 63 0.10
215 132 0.20
216 28 0.04
217 66 0.10
218 92 0.14
219 64 0.10
220 24 0.04
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (204 bp):
TTCGAAAAATGGCTCGAAGGAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAAGAA
CTCGTAAAAGTTTGACAAGTTTAGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAA
ATAAGTTTTAAATTCAAAAACCAAAAGTTGTTTACAAAATGACAAACCATTTGGACCAAATGATG
CGATTTCCA
Found at i:968 original size:215 final size:215
Alignment explanation
Indices: 328--1086 Score: 945
Period size: 215 Copynumber: 3.5 Consensus size: 215
318 TGGTTTGAAG
* * * *
328 GAATGGATCATCATGAATACTTTAAGGAACCAAGGTTATAAAAAAACTCGTAAAAGTTTGACAAG
1 GAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
** * *
393 TTTGGAAGTTCGTCCAAGAACCAAAAGAGAAACAAGTCTCACTTAAATAAGTTTTTAATTTAAAA
66 TTCAGAAGTTAGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGTTTTTAATTT-AAA
*
458 ACCAAAAGTTGTTTACAAAATGACAAACTATTTTGGACCAAATGGTGCGATTTCCCGAGCATGGA
130 ACCAAAAGTTGTTTACAAAATGACAAACTA-TTTGGACCAAATGATGCGATTTCCCGAGCATGGA
* * *
523 ATGCTCAAAAAATTGCTC-AAA
194 ATGTTCGAAAAATTACTCGAAA
* *** ** * *
544 GGAATGGATCGTTTTGAATACTTTAAGGAATTGAAGTTATAAAAGAACTCACAACATTTTGA-AG
1 -GAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACA-
** * ** * * *
608 AACTCGTAAAAGTTAAACCAAGAACCAAAGGAGGAACAAGTCTCACTTAAATAAGTTTTTTAATT
64 AGTTC--AGAAGTTAGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAG-TTTTTAATT
* *
673 TAAAACTCAAAAGTTGTTTAC-AAATGACAAACTATTTGGACCAAATGATGCGATTTTCCGAGAA
126 TAAAAC-CAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCGAGCA
737 TGGAATGTTCGAAAAATTACTCGAAA
190 TGGAATGTTCGAAAAATTACTCGAAA
* *
763 GAATGAATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTCACAAG
1 GAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
* * * *
828 TTCATAAGTTAGTCCAAGAACCAAAAGAGAAACAA-TCTGACGTAAATAAGTTTTAAATTCAAAG
66 TTCAGAAGTTAGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGTTTTTAATTTAAA-
*
892 ACCAAAAGTTGTTTACAAAATGACAAAGC-ATTTGGACCAAATGATACGATTTCCCGAGCATGGA
130 ACCAAAAGTTGTTTACAAAATGACAAA-CTATTTGGACCAAATGATGCGATTTCCCGAGCATGGA
* *
956 ATGTTTGAAAAATTACTCGAAT
194 ATGTTCGAAAAATTACTCGAAA
* * * *
978 GAATGGATCGTCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTTGAAAAAG-TTGACAAG
1 GAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
** * * * *
1042 TTTGGAAGTTCGTCCAAGAACCAAAAGAGATACAATTCTGACGTA
66 TTCAGAAGTTAGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTA
Statistics
Matches: 466, Mismatches: 65, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
214 62 0.13
215 137 0.29
216 29 0.06
217 51 0.11
218 100 0.21
219 63 0.14
220 24 0.05
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (215 bp):
GAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
TTCAGAAGTTAGTCCAAGAACCAAAAGAGAAACAAGTCTCACGTAAATAAGTTTTTAATTTAAAA
CCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCGAGCATGGAAT
GTTCGAAAAATTACTCGAAA
Done.