Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008537.1 Kokia drynarioides strain JFW-HI SEQ_123214, 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, 852
Length: 1420
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Found at i:785 original size:215 final size:215
Alignment explanation
Indices: 339--951 Score: 791
Period size: 215 Copynumber: 2.8 Consensus size: 215
329 TGGAATTTTC
* * * * ** * *
339 GAATGGATCGTCTTCAATACTTTAAGGAACCTAAGTTTTTCAAGAACTCGTAAGACTTTGACAAG
1 GAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
* * * * *
404 TTTGGTAGCTCGGCCAAGAACC-ATGAGACAAACAATTCTCACGTAAATAAGTTTTTAACTCAAA
66 TTTGGAAGTTCGGCCAAGAACCAAT-AGAAAAATAATTCTCACGTAAATAAGTTTTT-ATTCAAA
* * * * * *
468 GACAAAAAGTTGTTTACAAAATGAGAAACTATTTAGACCAAATGATGCGAATTCGCGAGCATGGA
129 GACAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGAATGGA
533 ATGTTCGAGAAATTCCTCGAAG
194 ATGTTCGAGAAATTCCTCGAAG
* * *
555 GAATGGATAATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
1 GAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
* *
620 TTTGGAAGTTTGGCCAAGGACCAATAGAAAAATAATTCTCACGTAAATAAGTTTTTATTCAAAGA
66 TTTGGAAGTTCGGCCAAGAACCAATAGAAAAATAATTCTCACGTAAATAAGTTTTTATTCAAAGA
*
685 CAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATAATGCGATTTCCCAAGAATGGAAT
131 CAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAAT
* *
750 GTTTG-GAGAATTCCTTGAAG
196 GTTCGAGA-AATTCCTCGAAG
*
770 GAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAGGTTAT-ACAA
1 GAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTT-TGACAA
** * * * *
834 GTTCAGAAGTTCGACCAAGAACCAGTAGAAAATTAATTCTCACGTAAATAAGTTTTAAATTCAAA
65 GTTTGGAAGTTCGGCCAAGAACCAATAGAAAAATAATTCTCACGTAAATAAGTTTT-TATTCAAA
* * * * * * *
899 CACCAAAAGTTGTTTACAAAATGATATACTATTTGTACCTAATGATACGATTT
129 GACAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTT
952 TGGAATTTCT
Statistics
Matches: 347, Mismatches: 46, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
214 2 0.01
215 188 0.54
216 155 0.45
217 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (215 bp):
GAATGGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
TTTGGAAGTTCGGCCAAGAACCAATAGAAAAATAATTCTCACGTAAATAAGTTTTTATTCAAAGA
CAAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCCAAGAATGGAAT
GTTCGAGAAATTCCTCGAAG
Found at i:1228 original size:331 final size:330
Alignment explanation
Indices: 649--1251 Score: 826
Period size: 331 Copynumber: 1.8 Consensus size: 330
639 ACCAATAGAA
649 AAATAATTCTCACGTAAATAAGTTTTTATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTA
1 AAATAATTCTCACGTAAATAAGTTTTTATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTA
** * * *
714 TTTGGACCAAATAATGCGATTTCCCAAGAATGGAATGTTTGGAGAATTCCTTGAAGGAATGGATC
66 TTTAAACAAAATAATGCGATTTCCCAAGAATGGAATGTTCGGAGAATTCCTCGAAGGAATGGATC
* *
779 ATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAGGTTATACAAGTTCAGAAGT
131 ATCTTGAATACTTTAAGGAACCAAACTTATAAAAGAACTCGTAAAGATTATACAAGTTCAGAAGT
* * **
844 TCGACCAAGAACCAGTAGAAAATTAATTCTCACGTAAATAAGTTTTAAATTCAAACACCAAAA-G
196 TCGACCAAGAACCAATAGAAAATCAATTCTCACCAAAATAAGTTTTAAATTCAAACA-CAAAATG
908 T-TGTTTACAAAATGATATACTATTTGTACCTAATGATACGATTTTGGAATTTCTTCCAAGGACA
260 TGT-TTTACAAAATGATATACTATTTGTACCTAATGATACGATTTTGGAATTTCTTCCAAGGACA
972 ATGAGGC
324 ATGAGGC
* * * *
979 AAATGATTCTCACGTAAATAAGTTTTTAATTTAAAGATAAAAAGTTGTTTACAAAATGAGAAACT
1 AAATAATTCTCACGTAAATAAGTTTTT-ATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACT
* * * * *
1044 ATTTAAAGAAAATGATGCGATTTTCCGAGCATGGAATGTTCGG-GAATTTCCTCGAAGGAATGGA
65 ATTTAAACAAAATAATGCGATTTCCCAAGAATGGAATGTTCGGAGAA-TTCCTCGAAGGAATGGA
* * *
1108 TCATCTTTAATACTTTAAGGAACCGAACTTATTAAAA-AACTCGTAAA-A-TATTGACAGGTTC-
129 TCATCTTGAATACTTTAAGGAACCAAACTTA-TAAAAGAACTCGTAAAGATTA-T-ACAAGTTCA
* * * *
1169 GAAAGTTCGGCCAAGGACCAATAGACAAA-CAATTCTCACCAAAATAAGTTTTTAATTCAAAGAC
191 G-AAGTTCGACCAAGAACCAATAGA-AAATCAATTCTCACCAAAATAAGTTTTAAATTCAAACAC
1233 AAAATGTGTTTTACAAAAT
254 AAAATGTGTTTTACAAAAT
1252 AACAAACTAT
Statistics
Matches: 237, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
329 2 0.01
330 36 0.15
331 190 0.80
332 9 0.04
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (330 bp):
AAATAATTCTCACGTAAATAAGTTTTTATTCAAAGACAAAAAGTTGTTTACAAAATGACAAACTA
TTTAAACAAAATAATGCGATTTCCCAAGAATGGAATGTTCGGAGAATTCCTCGAAGGAATGGATC
ATCTTGAATACTTTAAGGAACCAAACTTATAAAAGAACTCGTAAAGATTATACAAGTTCAGAAGT
TCGACCAAGAACCAATAGAAAATCAATTCTCACCAAAATAAGTTTTAAATTCAAACACAAAATGT
GTTTTACAAAATGATATACTATTTGTACCTAATGATACGATTTTGGAATTTCTTCCAAGGACAAT
GAGGC
Found at i:1367 original size:216 final size:216
Alignment explanation
Indices: 984--1420 Score: 535
Period size: 216 Copynumber: 2.0 Consensus size: 216
974 GAGGCAAATG
** * * * * *
984 ATTCTCACGTAAATAAGTTTTTAATTTAAAGATAAAAAGTTGTTTACAAAATGAGAAACTATTTA
1 ATTCTCACCAAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATAACAAACTATATA
* * ** *
1049 AAGAAAATGATGCGATTTTCCGAGCATGGAATGTTCGGGAATTTCCTCGAAGGAATGGATCATCT
66 AACAAAATGATGCGATTTTCCGAGAATGGAATGTTCGAAAATTTCCTCGAAGGAATGCATCATCT
*
1114 TTAATACTTTAAGGAACCGAACTTATTAAAAAACTCGTAAAA-TATTGACAGGTTCGAAAGTTCG
131 TTAATAATTTAAGGAACCGAACTTATTAAAAAACTCGTAAAAGT-TTGACAGGTTCGAAAGTTCG
* *
1178 GCCAAGGACCAATAGACAAACA
195 GCCAAGAACCAAGAGACAAACA
*
1200 ATTCTCACCAAAATAAGTTTTTAATTCAAAGACAAAATG-TGTTTTACAAAATAACAAACTATAT
1 ATTCTCACCAAAATAAGTTTTTAATTCAAAGACAAAAAGTTG-TTTACAAAATAACAAACTATAT
** *
1264 GGACCAAATGATGCGA-TTTCTCGAGAATGGAATGTTCGAAAAATTT-CTCGAAGGAATGCATCA
65 AAACAAAATGATGCGATTTTC-CGAGAATGGAATGTTCG-AAAATTTCCTCGAAGGAATGCATCA
* * * * * *
1327 T-TTTGAATAATTTAAGTAACCTAAGTTA-TAAAAGAACTCGTAAAAGTTTTACCGGTTCGAATG
128 TCTTT-AATAATTTAAGGAACCGAACTTATTAAAA-AACTCGTAAAAGTTTGACAGGTTCGAAAG
* *
1390 TTCGTCCAAGAACCAGGAGACAAACA
191 TTCGGCCAAGAACCAAGAGACAAACA
1416 ATTCT
1 ATTCT
Statistics
Matches: 188, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
215 14 0.07
216 168 0.89
217 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (216 bp):
ATTCTCACCAAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATAACAAACTATATA
AACAAAATGATGCGATTTTCCGAGAATGGAATGTTCGAAAATTTCCTCGAAGGAATGCATCATCT
TTAATAATTTAAGGAACCGAACTTATTAAAAAACTCGTAAAAGTTTGACAGGTTCGAAAGTTCGG
CCAAGAACCAAGAGACAAACA
Done.