Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000686.1 Kokia drynarioides strain JFW-HI SEQ_111683, 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, 868
Length: 1447
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Found at i:406 original size:216 final size:215
Alignment explanation
Indices: 1--1447 Score: 1619
Period size: 216 Copynumber: 6.8 Consensus size: 215
* * * *
1 ACCAAGAGAGATAAAATTCCCACGTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTAC---
1 ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * **
63 ATGACAAACTATTTGGACCAAAAAATGCGATTTATCGAGCATGGAATGTTCTTGAAAT-TGCTCG
66 ATGAAAAACTATTTGGACCAAAAGATGCGATTT-CCGAGCATGGAATGTTCGGGAAATGT-CTCG
** * *
127 AA-GTTATGATCGTCTTGAATACTTTAAGGAACCAAAAG-TATAAAAGAACTCGTAAAAGTTTGA
129 AAGGAAAGGATCGTCTTGAATACTTTAAGGAACC-GAAGTTATAAAAGAACTCGTAAAAGTTTGA
190 CAAGTTCGGAAGTTCGTCCAGGA
193 CAAGTTCGGAAGTTCGTCCAGGA
* * **
213 ACCAGGAGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGTTTACAAA
1 ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * *
278 ATGAAAAACAATTTGGACCAAAAGATACGACTTCCAGAGCATGGAATGCTCGGGAAATGTCTCGA
66 ATGAAAAACTATTTGGACCAAAAGATGCGATTTCC-GAGCATGGAATGTTCGGGAAATGTCTCGA
* * ** *
343 AGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTTAAATGTTTGACA
130 AGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA
*
408 GGTTC----G-TC--CCA-GA
195 AGTTCGGAAGTTCGTCCAGGA
421 ACCAAGAGAGATACA-ATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTT-CAA
1 ACCAAGAGAGATA-ATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
* * * * * * *
484 AATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATATCTTG
65 AATGAAAAACTATTTGGACCAAAAGATGCGATTTC-CGAGCATGGAATGTTCGGGAAATGTCTCG
* * ** * * *
549 AAGGAATGAATAATCTTGAATACTTTAAGGAACTGAAGTTATAAATGAACTCATAAAAGTTTGAC
129 AAGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAC
* *
614 AAGTTCGAAAGTTCGGCCAGGA
194 AAGTTCGGAAGTTCGTCCAGGA
* * *
636 ACCAGGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGCAAAAGTTGCTTACAAA
1 ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * * * *
701 ATGAAAAACAATTTGGACCAAAATATGCGACTTCCAAAGCATGGAATGCTCGGGAAATGTATCGA
66 ATGAAAAACTATTTGGACCAAAAGATGCGATTTCC-GAGCATGGAATGTTCGGGAAATGTCTCGA
* * * * * * ** * *
766 AGGAAAGGATCATATTGAATACATTAAGGAACCGAAGTTAGAAAAGTAGTTTTACATGTTTGAC-
130 AGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACA
*
830 A-----G--GTTCGTCCAAGA
195 AGTTCGGAAGTTCGTCCAGGA
* * *
844 ACCAAGAGTGATACA-ATTCTCACATAAATAAGTTTTTAATTCACAGACCAAAAGTTGTTTAGAA
1 ACCAAGAGAGATA-ATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAA
* * * * *
908 AATTACAAAA-TATTTGGACCAAATGATGCGATTTCTCGAGCATGAAATGTTCAGAAAATAG-CT
65 AATGA-AAAACTATTTGGACCAAAAGATGCGATTTC-CGAGCATGGAATGTTCGGGAAAT-GTCT
* * * * * *
971 TGAAGGAATGAATCATCTTGAATACTTTAAGGAACTGAAGTTATAAATGAACTCGTAAAAGTTTG
127 CGAAGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTG
* *
1036 ACAAGTTCGGAAGTTTGTCCAAGA
192 ACAAGTTCGGAAGTTCGTCCAGGA
* * * *
1060 ACCAAGAGAGATAAAATTCCCACGTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTAC---
1 ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * **
1122 ATGACAAACTATTTGGACCAAAAAATGCGATTTATCGAGCATGGAATGTTCTTGAAAT-TGCTCG
66 ATGAAAAACTATTTGGACCAAAAGATGCGATTT-CCGAGCATGGAATGTTCGGGAAATGT-CTCG
** * *
1186 AA-GTTATGATCGTCTTGAATACTTTAAGGAACCAAAAG-TATAAAAGAACTCGTAAAAGTTTGA
129 AAGGAAAGGATCGTCTTGAATACTTTAAGGAACC-GAAGTTATAAAAGAACTCGTAAAAGTTTGA
1249 CAAGTTCGGAAGTTCGTCCAGGA
193 CAAGTTCGGAAGTTCGTCCAGGA
* * **
1272 ACCAGGAGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGTTTACAAA
1 ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
* * * *
1337 ATGAAAAACAATTTGGACCAAAAGATACGACTTCCAGAGCATGGAATGCTCGGGAAATGTCTCGA
66 ATGAAAAACTATTTGGACCAAAAGATGCGATTTCC-GAGCATGGAATGTTCGGGAAATGTCTCGA
*
1402 AGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTAGAAAAG
130 AGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
Statistics
Matches: 1022, Mismatches: 168, Indels: 86
0.80 0.13 0.07
Matches are distributed among these distances:
207 114 0.11
208 219 0.21
209 12 0.01
211 3 0.00
212 183 0.18
213 52 0.05
214 7 0.01
215 172 0.17
216 260 0.25
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (215 bp):
ACCAAGAGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAA
ATGAAAAACTATTTGGACCAAAAGATGCGATTTCCGAGCATGGAATGTTCGGGAAATGTCTCGAA
GGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAA
GTTCGGAAGTTCGTCCAGGA
Found at i:1356 original size:636 final size:630
Alignment explanation
Indices: 201--1447 Score: 1756
Period size: 636 Copynumber: 2.0 Consensus size: 630
191 AAGTTCGGAA
* * *
201 GTTCGTCCAGGAACCAGGAGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGAAAAA
1 GTTCGTCCAAGAACCAAGAGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACAAAAA
* *
266 GTTGTTTACAAAATGAAAAACAATTTGGACCAAAAGATACGACTTCCAGAGCATGGAATGCTCGG
66 GTTGTTTACAAAATGAAAAACAATTTGGACCAAAAGATACGACTTCCAGAGCATGAAATGCTCAG
* * * * **
331 GAAATGTCTCGAAGGAAAGGATCGTCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAAGTTTT
131 AAAATGTCTCGAAGGAAAGAATCATCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAACTCGT
* * * *
396 AAATGTTTGACAGGTTCGTCCCAGAACCAAGAGAGATACAATTCTCACATAAATAAGTTTTTAAT
196 AAAAGTTTGACAGGTTCGTCCAAGAACCAAGAGAGATAAAATTCCCACATAAATAAGTTTTTAAT
** *
461 TCAAAGACCAAAAGTTGTTTCAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCA
261 TCAAAGACCAAAAGTTGTTT-AAAATGACAAACTATTTGGACCAAAAAATGCGATTTATCGAGCA
* **
526 TGAAATGTTCAGAAAATATCTTGAAGGAATGAATAATCTTGAATACTTTAAGGAACTGAAGTTAT
325 TGAAATGTTCAGAAAATATCTCGAAGGAATGAATAATCTTGAATACTTTAAGGAACAAAAGTTAT
*
591 AAATGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCGGCCAGGAACCAGGAGAGATAATATTCT
390 AAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCGGCCAGGAACCAGGAGAGATAATATTCT
*
656 CACATAAATAAGTTTTTAATTCAAAGAGCAAAAGTTGCTTACAAAATGAAAAACAATTTGGACCA
455 CACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGCTTACAAAATGAAAAACAATTTGGACCA
* *
721 AAATATGCGACTTCCAAAGCATGGAATGCTCGGGAAATGTATCGAAGGAAAGGATCATATTGAAT
520 AAAGATACGACTTCCAAAGCATGGAATGCTCGGGAAATGTATCGAAGGAAAGGATCATATTGAAT
786 ACATTAAGGAACCGAAGTTAGAAAAGTAGTTTTACATGTTTGACAG
585 ACATTAAGGAACCGAAGTTAGAAAAGTAGTTTTACATGTTTGACAG
* *
832 GTTCGTCCAAGAACCAAGAGTGATACA-ATTCTCACATAAATAAGTTTTTAATTCACAGACCAAA
1 GTTCGTCCAAGAACCAAGAGTGATA-ATATTCTCACATAAATAAGTTTTTAATTCAAAGACAAAA
* * * * * * *
896 AGTTGTTTAGAAAATTACAAAA-TATTTGGACCAAATGATGCGATTTCTC-GAGCATGAAATGTT
65 AGTTGTTTACAAAATGA-AAAACAATTTGGACCAAAAGATACGACTTC-CAGAGCATGAAATGCT
* * * * *
959 CAGAAAATAG-CTTGAAGGAATGAATCATCTTGAATACTTTAAGGAACTGAAGTTATAAATGAAC
128 CAGAAAAT-GTCTCGAAGGAAAGAATCATCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAAC
* *
1023 TCGTAAAAGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGAGAGATAAAATTCCCACGTAAA
192 TCGTAAAAGTTTGAC-A-----G--GTTCGTCCAAGAACCAAGAGAGATAAAATTCCCACATAAA
* *
1088 TAAGTTTTTAATTCAAAGACCAAAATTTGTTT-ACATGACAAACTATTTGGACCAAAAAATGCGA
249 TAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAAAATGACAAACTATTTGGACCAAAAAATGCGA
* * ** **
1152 TTTATCGAGCATGGAATGTTCTTG-AAAT-TGCTCGAAGTTATG-ATCGTCTTGAATACTTTAAG
314 TTTATCGAGCATGAAATGTTC-AGAAAATAT-CTCGAAGGAATGAATAATCTTGAATACTTTAAG
* * *
1214 GAACCAAAAG-TATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAGGAACCAGG
377 GAA-CAAAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCGGCCAGGAACCAGG
* *
1278 AGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGTTTACAAAATGAAA
441 AGAGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGCTTACAAAATGAAA
* *
1343 AACAATTTGGACCAAAAGATACGACTTCCAGAGCATGGAATGCTCGGGAAATGTCTCGAAGGAAA
506 AACAATTTGGACCAAAAGATACGACTTCCAAAGCATGGAATGCTCGGGAAATGTATCGAAGGAAA
* * *
1408 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTAGAAAAG
571 GGATCATATTGAATACATTAAGGAACCGAAGTTAGAAAAG
Statistics
Matches: 542, Mismatches: 59, Indels: 25
0.87 0.09 0.04
Matches are distributed among these distances:
631 169 0.31
632 8 0.01
636 232 0.43
637 66 0.12
638 1 0.00
639 66 0.12
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (630 bp):
GTTCGTCCAAGAACCAAGAGTGATAATATTCTCACATAAATAAGTTTTTAATTCAAAGACAAAAA
GTTGTTTACAAAATGAAAAACAATTTGGACCAAAAGATACGACTTCCAGAGCATGAAATGCTCAG
AAAATGTCTCGAAGGAAAGAATCATCTTGAATACTTTAAGGAACCGAAGTTAGAAAAGAACTCGT
AAAAGTTTGACAGGTTCGTCCAAGAACCAAGAGAGATAAAATTCCCACATAAATAAGTTTTTAAT
TCAAAGACCAAAAGTTGTTTAAAATGACAAACTATTTGGACCAAAAAATGCGATTTATCGAGCAT
GAAATGTTCAGAAAATATCTCGAAGGAATGAATAATCTTGAATACTTTAAGGAACAAAAGTTATA
AAAGAACTCATAAAAGTTTGACAAGTTCGAAAGTTCGGCCAGGAACCAGGAGAGATAATATTCTC
ACATAAATAAGTTTTTAATTCAAAGAGAAAAAGTTGCTTACAAAATGAAAAACAATTTGGACCAA
AAGATACGACTTCCAAAGCATGGAATGCTCGGGAAATGTATCGAAGGAAAGGATCATATTGAATA
CATTAAGGAACCGAAGTTAGAAAAGTAGTTTTACATGTTTGACAG
Done.