Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004260.1 Kokia drynarioides strain JFW-HI SEQ_117545, 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: 1850
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Found at i:461 original size:211 final size:208
Alignment explanation
Indices: 1--660 Score: 654
Period size: 211 Copynumber: 3.1 Consensus size: 208
* * * *
1 AAGAGAAACAATTCTCACGTAAATGAGTATTTAATTCAAAGACCAAAAGTTTTTTAGAAAATGAC
1 AAGAGAAACAATTCTCACGTAAATAAGT-TTTAATT---AGACCAAAACTTATTTACAAAATGAC
* * * *
66 AAACTATTTAGACCAAATGATGCGACTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGATGGAA
62 AAACTATTTAGACAAAATGATGCGATTTCCCGAG-ATGGAATGTTCAG-AAATTGC-TAAAGGAA
* *
131 TGGATCGTCTTGAATACTGTAAGGAACCAAGTTATATAAGAACTCGTAAAAGTTTGAAAAGTTCA
124 TGGATCGTCTTGAATACTGTAAGGAACCAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCG
*
196 GAAGTTCGTCCAATAGC--C
189 GAAGTTCGTCCAAAAGCAAC
* * * ** * * * *
214 AAGA-AAA-AATTCTCAGGAAAATATGTTCTTGTTTTAATGATCAAAACTCATTTACAAAATTAA
1 AAGAGAAACAATTCTCACGTAAATAAGTT-TT-AATT-A-GACCAAAACTTATTTACAAAATGAC
* * *
277 AAACTATTTAGACTAAATGATGTGATTTCCCGAGAATGGAATGTTCAGAAATTCCTCAAAGGAAT
62 AAACTATTTAGACAAAATGATGCGATTTCCCGAG-ATGGAATGTTCAGAAATTGCT-AAAGGAAT
* * *
342 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAATTCGTAAAAGTTTGAAAAGTTTG
125 GGATCGTCTTGAATACTGTAAGGAACC-AAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCG
* *
407 GAAGTTCATCCAAAAGCAAAG
189 GAAGTTCGTCCAAAAGC-AAC
*
428 AGAGAGAAACAATTCTCACGTAAATAAGTTTTAAATTTAAAGACCAAAACTTGTTTACAAAATGA
1 A-AGAGAAACAATTCTCACGTAAATAAGTTTT-AA-TT--AGACCAAAACTTATTTACAAAATGA
* * *
493 CAAACAATTTAGA-AAAATGATGCGACTTT-TCGAG-T---A---T-A-AAGTTGCTAGAAGGAA
61 CAAACTATTTAGACAAAATGATGCGA-TTTCCCGAGATGGAATGTTCAGAAATTGCTA-AAGGAA
* * * *
547 TGTATCGTCTTGAATACTGAAAGGAACCAAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTC
124 TGGATCGTCTTGAATACTGTAAGGAACC-AAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTC
612 GGAAGTTCGTCC--AAG-AACC
188 GGAAGTTCGTCCAAAAGCAA-C
631 AAGAGAAACAATTCTCACGTAAATAAGTTT
1 AAGAGAAACAATTCTCACGTAAATAAGTTT
661 CTGATTCAAA
Statistics
Matches: 376, Mismatches: 55, Indels: 43
0.79 0.12 0.09
Matches are distributed among these distances:
202 31 0.08
203 1 0.00
204 3 0.01
205 1 0.00
206 80 0.21
207 1 0.00
208 1 0.00
209 1 0.00
210 41 0.11
211 128 0.34
212 5 0.01
213 4 0.01
214 2 0.01
215 3 0.01
216 19 0.05
217 53 0.14
218 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (208 bp):
AAGAGAAACAATTCTCACGTAAATAAGTTTTAATTAGACCAAAACTTATTTACAAAATGACAAAC
TATTTAGACAAAATGATGCGATTTCCCGAGATGGAATGTTCAGAAATTGCTAAAGGAATGGATCG
TCTTGAATACTGTAAGGAACCAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCGGAAGTTC
GTCCAAAAGCAAC
Found at i:718 original size:70 final size:70
Alignment explanation
Indices: 605--744 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
595 AAAAGTTTGA
*
605 CAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTCTGATTCAA
1 CAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTCTGATTCAA
670 AGACC
66 AGACC
* *
675 CAAGTTCGAAAGTTTGTCCAAGAACCAAGCA-AAACAATTCTCACGTAAATAAGTTTTTGATTCA
1 CAAGTTCGAAAGTTCGTCCAAGAACCAAG-AGAAACAATTCTCACGTAAATAAGTTTCTGATTCA
739 AAGACC
65 AAGACC
745 AAAACTTGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 65 0.98
71 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (70 bp):
CAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTCTGATTCAA
AGACC
Found at i:1669 original size:427 final size:429
Alignment explanation
Indices: 706--1850 Score: 1256
Period size: 427 Copynumber: 2.7 Consensus size: 429
696 GAACCAAGCA
* **
706 AAACAATTCTCACGTAAATAAGTTTTTGATTCAAAGACCAAAACTTGTTTTTAAAATGACAAACT
1 AAACAATTCTCACGTAAATAAG-TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * * * * *
771 CTTTAGACCAAATGCTGCCATTTCTCAAGAATTGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAGAAAATTGCTAGAAGGAATGGAT
* * * * *
836 CGTCTTGAATACTTTAAGGAACTGAAGATATGAAAGAACTCGTAAAAGTTTGACTAGTTCGAAAG
130 CGTCTTGAATACTGTAAGGAAC-CAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG-AAG
** * * * *
901 TTCGTCCACGAACAAAGAGAGAAACAATTCTCACGTAAATAAGCTTTTAATTCAAACAACGAAAC
193 TTCAACCAAGAACAAAGAGAGAAACAATCCTCACGAAAATAAGCTTTTAATTCAAACAACAAAAC
* * * * * * *
966 CTTTTAACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAA
258 CGTTTAACAAAATGAAAAACTATTTAGAACAAATGATGCGAATTCCCGAGAATGGAATATTCAAA
* * * *
1031 AAATTGCTCGAAGGAATGGATCATCTTGAATGCTTTACAAAACTAAAATTATAAAAGAACTCGTA
323 AAATTCCTCAAAGGAATGGATCATCTTGAATACATTACAAAACTAAAATTATAAAAGAACTCGTA
* *
1096 AAAATTTGATAAGTTCAGAAGTTCATCCAAGAACCAAAAGAG
388 AAAATTTGAAAAGTTCAGAAGTTCATCCAAGAACAAAAAGAG
* * * *
1138 AAACAATTCTCACGTAAATAAGTATTTAATTCAATGACCAAAAGTTTTTTACACAATGACAAACT
1 AAACAATTCTCACGTAAATAAGT-TTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * *
1203 ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGATGGAATGGAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAGAAAATTGCTAGAAGGAATGGAT
* * * *
1268 CATCTTGAATAGTGCAAGGAACCAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGT
130 CGTCTTGAATACTGTAAGGAACCAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GAAGT
* * * * ** * ** *
1333 TCAACCAAGAGC-CA-AGA-AAA-AATCCTCAGGAAAATATG-TTCTTGTTTTAATGATCAAAAC
194 TCAACCAAGAACAAAGAGAGAAACAATCCTCACGAAAATAAGCTT-TTAATTCAAACAACAAAAC
* * *
1393 TCGTTT-ACAAAATTAAAAACTATTTAGAATAAATGATGCGAATTCTCGAGAATGGAATATT-AA
258 -CGTTTAACAAAATGAAAAACTATTTAGAACAAATGATGCGAATTCCCGAGAATGGAATATTCAA
* * * *
1456 AAAATTCCTCAAAGGAATGGATCGTCTTGAATACATTA-AGGAA-TCGAAGTTATAAAAGAACTC
322 AAAATTCCTCAAAGGAATGGATCATCTTGAATACATTACA-AAACT-AAAATTATAAAAGAACTC
* *
1519 GTAAAAGTTTGAAAAGTTTAGAAGTTCATCCAAGAACAAAGAGAGAG
385 GTAAAAATTTGAAAAGTTCAGAAGTTCATCCAAGAACAAA-A-AGAG
** * * *
1566 AAACAATTCTCATTTAAATAAGTTTTAAATTTAAAGACAAAAACTTGTTTACAAAATGACAAACA
1 AAACAATTCTCACGTAAATAAGTTTT-AATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * * *
1631 ATTTAGA-AAAATGATGCGATTTTTCGAGCATAGAATGTTAAGAAAGTTGCTAGAAGGAATGTAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAGAAAATTGCTAGAAGGAATGGAT
1695 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
130 CGTCTTGAATACTGTAAGGAACC-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GAAG
** * * * * * * *
1760 TTCGTCAAAGAAC-CA-AGAGAAACAATTCTCACGTAAATAAG-TTTCTGATTCAAAGACCAAAA
193 TTCAACCAAGAACAAAGAGAGAAACAATCCTCACGAAAATAAGCTTT-TAATTCAAACAACAAAA
* * * *
1822 CTTGTTT-TCAAAATGACAAACTCTTTAGA
257 C-CGTTTAACAAAATGAAAAACTATTTAGA
Statistics
Matches: 597, Mismatches: 103, Indels: 28
0.82 0.14 0.04
Matches are distributed among these distances:
425 2 0.00
426 90 0.15
427 145 0.24
428 123 0.21
429 7 0.01
430 54 0.09
431 45 0.08
432 131 0.22
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (429 bp):
AAACAATTCTCACGTAAATAAGTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
TTTAGACCAAATGATGCGATTTCTCGAGCATAGAATGTTCAGAAAATTGCTAGAAGGAATGGATC
GTCTTGAATACTGTAAGGAACCAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAGTTC
AACCAAGAACAAAGAGAGAAACAATCCTCACGAAAATAAGCTTTTAATTCAAACAACAAAACCGT
TTAACAAAATGAAAAACTATTTAGAACAAATGATGCGAATTCCCGAGAATGGAATATTCAAAAAA
TTCCTCAAAGGAATGGATCATCTTGAATACATTACAAAACTAAAATTATAAAAGAACTCGTAAAA
ATTTGAAAAGTTCAGAAGTTCATCCAAGAACAAAAAGAG
Found at i:1723 original size:217 final size:214
Alignment explanation
Indices: 706--1850 Score: 1263
Period size: 216 Copynumber: 5.3 Consensus size: 214
696 GAACCAAGCA
* **
706 AAACAATTCTCACGTAAATAAGTTTTTGATTCAAAGACCAAAACTTGTTTTTAAAATGACAAACT
1 AAACAATTCTCACGTAAATAAG-TTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * * * * * *
771 CTTTAGACCAAATGCTGCCATTTCTCAAGAATTGAATGTTCAGAAAATTGCTCGAAGGAATGGAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAGAAAATTGCTAGAAGGAATGGAT
* * * * **
836 CGTCTTGAATACTTTAAGGAACTGAAGATATGAAAGAACTCGTAAAAGTTTGACTAGTTC-GAAA
130 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAG-AA
* *
900 GTTCGTCCACGAACAAAGAGAG
194 GTTCATCCAAGAACAAA-AGAG
* * * *
922 AAACAATTCTCACGTAAATAAGCTTTTAATTCAAACAACGAAACCTT-TTAACAAAATGACAAAC
1 AAACAATTCTCACGTAAATAAG-TTTTAATTCAAA-GACCAAAACTTGTTTACAAAATGACAAAC
* * *
986 TATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT-CGAAAAATTGCTCGAAGGAATGG
64 TATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAG-AAAATTGCTAGAAGGAATGG
* * * * ** * * *
1050 ATCATCTTGAATGCTTTACA-AAACTAAAATTATAAAAGAACTCGTAAAAATTTGATAAGTTCAG
128 ATCGTCTTGAATACTGTA-AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAG
1114 AAGTTCATCCAAGAACCAAAAGAG
192 AAGTTCATCCAAGAA-CAAAAGAG
* * * *
1138 AAACAATTCTCACGTAAATAAGTATTTAATTCAATGACCAAAAGTTTTTTACACAATGACAAACT
1 AAACAATTCTCACGTAAATAAGT-TTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * *
1203 ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGATGGAATGGAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAGAAAATTGCTAGAAGGAATGGAT
* * *
1268 CATCTTGAATAGTGCAAGGAACC-AAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAG
130 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAG
* * *
1332 TTCAACCAAGAGC-CAAGA-
195 TTCATCCAAGAACAAAAGAG
* * * * ** * * * * * *
1350 AAA-AATCCTCAGGAAAATATGTTCTTGTTTTAATGATCAAAACTCGTTTACAAAATTAAAAACT
1 AAACAATTCTCACGTAAATAAGTT-TTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
** * * * *
1414 ATTTAGAATAAATGATGCGAATTCTCGAGAATGGAATATTAA-AAAATTCCTCA-AAGGAATGGA
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAGAAAATTGCT-AGAAGGAATGGA
* *
1477 TCGTCTTGAATACAT-TAAGGAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTTAGA
129 TCGTCTTGAATAC-TGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGA
1541 AGTTCATCCAAGAACAAAGAGAGAG
193 AGTTCATCCAAGAAC-AA-A-AGAG
** * * *
1566 AAACAATTCTCATTTAAATAAGTTTTAAATTTAAAGACAAAAACTTGTTTACAAAATGACAAACA
1 AAACAATTCTCACGTAAATAAGTTTT-AATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
* * * * *
1631 ATTTAGA-AAAATGATGCGATTTTTCGAGCATAGAATGTTAAGAAAGTTGCTAGAAGGAATGTAT
65 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAGAAAATTGCTAGAAGGAATGGAT
* *
1695 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAG
130 CGTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAG
* * *
1760 TTCGTCAAAGAAC-CAAGAG
195 TTCATCCAAGAACAAAAGAG
* *
1779 AAACAATTCTCACGTAAATAAGTTTCTGATTCAAAGACCAAAACTTGTTTTCAAAATGACAAACT
1 AAACAATTCTCACGTAAATAAGTTT-TAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT
*
1844 CTTTAGA
65 ATTTAGA
Statistics
Matches: 785, Mismatches: 120, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
210 36 0.05
211 132 0.17
212 3 0.00
213 70 0.09
214 4 0.01
215 61 0.08
216 326 0.42
217 153 0.19
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (214 bp):
AAACAATTCTCACGTAAATAAGTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTAAGAAAATTGCTAGAAGGAATGGATC
GTCTTGAATACTGTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGT
TCATCCAAGAACAAAAGAG
Done.