Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000268.1 Kokia drynarioides strain JFW-HI SEQ_111012, 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, 862
Length: 1437
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Found at i:904 original size:214 final size:213
Alignment explanation
Indices: 3--1437 Score: 1474
Period size: 215 Copynumber: 6.8 Consensus size: 213
1 TC
* * * * * * * * *
3 CCGAGCATGGAAAGTTCGAGAAATTGCTCAAAGGAATGGATCGTCTAGAACACCTTATGGAACAA
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCA
* * * * *
68 AAATTATAAAAGAACTCGTAAAATTTTGACAAGTTCGGAAGTTCATCCAAGAACTAAAAGAGAAA
66 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAAC-CAAAGAGAAA
* * * * *
133 CAATTGTCACGTAAATAAGTATTTAATTCAAAGATCAAAATTTGTTTATAAAATGACAAACTATT
130 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CCAAACTTGTTTACAAAATGACAAACTATT
198 TAGACCAAATGATGCGATTT
194 TAGACCAAATGATGCGATTT
* * * * * *
218 CTCGAGCATTGAATGCTCAAAAAATTGCT----TGAA-GG----TCTTGAATACTCTAAGAAACC
1 C-CGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACC
* * * *
274 GAAGTTATAAAAGAACTCGTAAGAGTTTGAAAAGTTCGAAAGTTCGTCCAAGAGCC-AAGAGAAA
65 AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAGAGAAA
* *** * * *
338 CAATTCTCACGTAAATAAGATTTCGTTTTAAAGACCAAAACTTGTTTACAAAATGAAAAACTGTT
130 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC-AAACTTGTTTACAAAATGACAAACTATT
* *
403 TAGACTAAATGATCCGATTT
194 TAGACCAAATGATGCGATTT
* *
423 TCGAAG-AAGAGAATGTTC-AAAAATTGCTC-AATGGAATGGATCATCTTGAATACTTTAAGGAA
1 CCG-AGCATG-GAATGTTCGAAAAATTGCTCGAA-GGAATGGATCATCTTGAATACTTTAAGGAA
* * * * *
485 CCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCGAGAGTG
63 CCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-AAAGAG
* * * *
550 AAACAATTCTCACG-GAATAAGTTTTTAATGCAAAGACCAATACTTGTTTACAAAGTGACAAACA
127 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA-ACTTGTTTACAAAATGACAAACT
* * * *
614 ATTTAGACCGAATTATACAATTT
191 ATTTAGACCAAATGATGCGATTT
* * ** * * * * * *
637 CCCGAGCATGGAATGTT-TAGAAAATTGCTTGAATTAAAGGATCGTCCTGAATACTTTATGTAAT
1 -CCGAGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAAC
* * *
701 CAAAGTTATAAAAGAACTCGTAAAAGTTGGA-AAGGTTCGGAAGTTCGTCCAAGAACC-AAGACA
64 CAAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-GTTCGAAAGTTCGTCCAAGAACCAAAGAGA
* * * *
764 AATAATTCTCAAGTAAATAAGTTTTTAATTCAAACAACAAACTTGTTTTACAAAATGACAAACTA
128 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAACTTG-TTTACAAAATGACAAACTA
*
829 TTTAGACCAAATGATGCGATATA
192 TTTAGACCAAATGATGCGAT-TT
* * * *
852 CCGAGCATTGAATGTTCGAAAAATTACTCGAAGGAATGAATCATCTTGAATACTTTAAGGAACCG
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCA
*
917 AAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAA
66 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAA-AGAGAAA
* * * *
982 CAATTATCACGTAAATAAGTTTTTAATTTAAACAACCAAACCTT-TTTACAAAATG-CATACTAT
130 CAATTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAA-CTTGTTTACAAAATGACAAACTAT
*
1045 TTAGACCAAATGATGTGATTT
193 TTAGACCAAATGATGCGATTT
* * * * *
1066 CCCGAGCATGGAAAGTTCGGAAAATTGCTCAAAGGAATGGATCGA-CTAGAATACTTTATGGAAC
1 -CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATC-ATCTTGAATACTTTAAGGAAC
* * * * * * *
1130 AAAAATTATAAAAGAACTCGTAAAATTTTTACAGGTTCAAAAGTTCATCCAAGAACCAAAGGAGA
64 CAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAA-GAGA
* * *
1195 AACAATTCTCACGTAAATAAATATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
128 AACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC-AAACTTGTTTACAAAATGACAAACTA
*
1260 TTTAGACCAAGTGATGCGATTT
192 TTTAGACCAAATGATGCGATTT
* * *
1282 CTCGAGCATGGAATGTTCAAAAAATTGCTC----GAA-GG----TCTTGAATACTCTAAGAAACC
1 C-CGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACC
* * * * *
1338 GAAGTTATAAAAGAATTCGT-AGAGTTTGAAAAGTTCGAAAGTTCGTCAAAGAACCAAAAGAGAA
65 AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACC-AAAGAGAA
* * *
1402 ACGATTCTCACGT-AATAAGTGTTTAATCCAAAGACC
129 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
Statistics
Matches: 1008, Mismatches: 172, Indels: 90
0.79 0.14 0.07
Matches are distributed among these distances:
204 14 0.01
205 106 0.11
206 44 0.04
207 96 0.10
208 3 0.00
209 2 0.00
211 4 0.00
212 6 0.01
213 91 0.09
214 226 0.22
215 287 0.28
216 121 0.12
217 5 0.00
218 3 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (213 bp):
CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCA
AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAGAGAAAC
AATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAACTTGTTTACAAAATGACAAACTATTTA
GACCAAATGATGCGATTT
Found at i:1068 original size:429 final size:424
Alignment explanation
Indices: 3--1437 Score: 1606
Period size: 429 Copynumber: 3.4 Consensus size: 424
1 TC
* * * * * * * * **
3 CCGAGCATGGAAAGTTCGAGAAATTGCTCAAAGGAATGGATCGTCTAGAACACCTTATGGAACAA
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCG
* * * * *
68 AAATTATAAAAGAACTCGTAAAATTTTGACAAGTTCGGAAGTTCATCCAAGAACTAAAAGAGAAA
66 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAA
* * * * *
133 CAATTGTCACGTAAATAAGTATTTAATTCAAAGATCAAAATTTGTTTATAAAATGACAAACTATT
131 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGA-CCAAACTTGTTTACAAAATGACAAACTATT
* * * *
198 TAGACCAAATGATGCGATTTCTCGAGCATTGAATGCTCAAAAAATTGCTTG---AAGG-TC-T-T
195 TAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGAAAAAGGATCGTCT
* * * * *
257 GAATACTCTAAGAAACCGAAGTTATAAAAGAACTCGTAAGAGTTTGAAAAGTTCGAAAGTTCGTC
260 GAATACTTTATGAAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGGTTCGAAAGTTCGTC
* * *** *
322 CAAGAGCCAAGAGAAACAATTCTCACGTAAATAAGATTTCGTTTTAAAGACCAAAACTTGTTTAC
324 CAAGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTAC
* * * *
387 AAAATGAAAAACTGTTTAGACTAAATGATCCGATTT
389 AAAATGACAAACTATTTAGACCAAATGATGCGATTT
* *
423 TCGAAG-AAGAGAATGTTC-AAAAATTGCTC-AATGGAATGGATCATCTTGAATACTTTAAGGAA
1 CCG-AGCATG-GAATGTTCGAAAAATTGCTCGAA-GGAATGGATCATCTTGAATACTTTAAGGAA
* * * * *
485 CCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAAGAACCGAGAGTG
63 CCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAG
* * * *
550 AAACAATTCTCACG-GAATAAGTTTTTAATGCAAAGACCAATACTTGTTTACAAAGTGACAAACA
128 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA-ACTTGTTTACAAAATGACAAACT
* * * * *
614 ATTTAGACCGAATTATACAATTTCCCGAGCATGGAATGTTTAGAAAATTGCTTGAATTAAAGGAT
192 ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGAA--AAAGGAT
* * *
679 CGTCCTGAATACTTTATGTAATCAAAGTTATAAAAGAACTCGTAAAAGTTGGAAAGGTTCGGAAG
255 CGT-CTGAATACTTTATG-AAACAAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGGTTCGAAAG
* * * * *
744 TTCGTCCAAGAACCAAGACAAATAATTCTCAAGTAAATAAGTTTTTAATTCAAACAAC-AAACTT
318 TTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTT
*
808 GTTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATA
383 G-TTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT-TT
* * *
852 CCGAGCATTGAATGTTCGAAAAATTACTCGAAGGAATGAATCATCTTGAATACTTTAAGGAACCG
1 CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCG
* *
917 AAGTTATGAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAA
66 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAA
* * * *
982 CAATTATCACGTAAATAAGTTTTTAATTTAAACAACCAAACCTT-TTTACAAAATG-CATACTAT
131 CAATTCTCACGTAAATAAGTTTTTAATTCAAA-GACCAAA-CTTGTTTACAAAATGACAAACTAT
* * * *
1045 TTAGACCAAATGATGTGATTTCCCGAGCATGGAAAGTTCGGAAAATTGC-TCAAAGGAATGGATC
194 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGAAA--AA-GGATC
* * * * * * *
1109 GACTAGAATACTTTATGGAACAAAAATTATAAAAGAACTCGTAAAATTTTTACAGGTTCAAAAGT
256 GTCT-GAATACTTTATGAAAC-AAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGGTTCGAAAGT
* * * *
1174 TCATCCAAGAACCAAAGGAGAAACAATTCTCACGTAAATAAATATTTAATTCAAAGACCAAAAGT
319 TCGTCCAAGAACC-AA-GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACT
*
1239 TGTTTACAAAATGACAAACTATTTAGACCAAGTGATGCGATTT
382 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * *
1282 CTCGAGCATGGAATGTTCAAAAAATTGCTC----GAA-GG----TCTTGAATACTCTAAGAAACC
1 C-CGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACC
* * * *
1338 GAAGTTATAAAAGAATTCGT-AGAGTTTGAAAAGTTCGAAAGTTCGTCAAAGAACCAAAAGAGAA
65 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAA
* * *
1402 ACGATTCTCACGT-AATAAGTGTTTAATCCAAAGACC
130 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
Statistics
Matches: 857, Mismatches: 127, Indels: 63
0.82 0.12 0.06
Matches are distributed among these distances:
418 3 0.00
419 88 0.10
420 123 0.14
421 60 0.07
422 37 0.04
424 4 0.00
425 2 0.00
426 3 0.00
427 10 0.01
428 150 0.18
429 231 0.27
430 34 0.04
431 106 0.12
432 6 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (424 bp):
CCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCG
AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAAAGAGAAA
CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAACTTGTTTACAAAATGACAAACTATTT
AGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTTGAAAAAGGATCGTCTG
AATACTTTATGAAACAAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGGTTCGAAAGTTCGTCCA
AGAACCAAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAA
AATGACAAACTATTTAGACCAAATGATGCGATTT
Done.