Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003366.1 Kokia drynarioides strain JFW-HI SEQ_116089, 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, 847
Length: 1412
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.28
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:472 original size:214 final size:212
Alignment explanation
Indices: 36--1181 Score: 1061
Period size: 214 Copynumber: 5.4 Consensus size: 212
26 ATTTCTCAAT
* * * *
36 GGAATGGTTCGTCTTGAATACCTTAAGGAACCGAAGTTATAAAAGAACTTGTAAAAGTTTGTCAA
1 GGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAA
* * * * *
101 CTTCTG-AAGTTCGGCCTAGAAACAAGAGAGAAACTATTCTCACCTAAA-AAAGTTTTTAATTCA
65 GTTC-GAAAGTTCGGCCGAGAACCAAAAGAGAAAC-AATCTCACCTAAATAAA-TTTTTAATTCA
* * * * * *
164 AAGACCAAAAGTTGTTTGCATAATGGCAATTATTCAGA-CTAAATGATGTGATTTCTAGAGCATG
127 AAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCT-AATGATGCGATTTCTA-AGCATG
* * * ** * *
228 CAATTTTCTTAAAATTGCTTGAA
190 GAATGTACAAAAAATTACTCGAA
* * * *
251 GGAATGGATCGTCTTGAATAATTTAGGGAATCAAAGTTAT-AAAGTAACTCGTAAAAGTTTTTAA
1 GGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTATAAAAG-AACTCGTAAAAGTTTGTCA
* *
315 AGTTCGAAAGTTCGACCGAGAACCAAAAGAGAAACAATCTCACCTAAATAAAATTTTAATTCAAA
64 AGTTCGAAAGTTCGGCCGAGAACCAAAAGAGAAACAATCTCACCTAAATAAATTTTTAATTCAAA
* * * * * *
380 GACCAAAAGTAGTTTAAAAAATGACAACTATTTAAACCTAATGATGCAATTTCCCAAGCATGGAC
129 GACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCTAATGATGCGATTT-CTAAGCATGGAA
*
445 TGTACAAAAAATTACTCGAG
193 TGTACAAAAAATTACTCGAA
* * * * *
465 GGAATGGATCGTCTTGAATACTTTAATGAACAAAGGCTATAAATGTACTCGTAAAACTTTGTCAA
1 GGAATGGATCGTCTTGAATACTTTAAGGAACAAA-GTTATAAAAGAACTCGTAAAAGTTTGTCAA
* * * *
530 GTTCG---GTT-----GAGAACGAATAGAGAAACAATTCTCACCTAAATAAGTTTTTAATTGAAA
65 GTTCGAAAGTTCGGCCGAGAACCAAAAGAGAAACAA-TCTCACCTAAATAAATTTTTAATTCAAA
* * * * * * * *
587 AACCAAAAGTAGTTTACAAAATGACAGCTATTTAGACCTAAAGATGTGATTTCCCAGGCATGGAC
129 GACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCTAATGATGCGATTT-CTAAGCATGGAA
652 TGTACAAAAAATTACTCGAA
193 TGTACAAAAAATTACTCGAA
* * * * **
672 GGAATGTATCGTCTTGAATACTTTAATGAACAAAAGTTAAAAAAGAAGTTATAAAAGTTTGTCAA
1 GGAATGGATCGTCTTGAATACTTTAAGGAAC-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAA
* * * *
737 GTT-TAAAGTTCGGCCGAGAACCAAGAA-AGAAACAATTTTCACATAAA-GAATTTATTAATTCA
65 GTTCGAAAGTTCGGCCGAGAACCAA-AAGAGAAACAA-TCTCACCTAAATAAATTT-TTAATTCA
* * * *
799 AAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAAAT-ATGAGACTTACTAAGCTTG
127 AAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACC-TAATGATGCGA-TTTCTAAGCATG
* * *
863 TAATGTTA-AATAAATTTCTC-AA
190 GAATG-TACAAAAAATTACTCGAA
* * * * * *
885 CAGAATGGTTCGTCTTGAATACCTTATGGAACCGAAGTAATAAAAGAACTCGTAAAAGTTTGTCA
1 -GGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCA
* * * * * * *
950 ACTTCGAATGTTCGGCCTAGAACCAAGAGAGAAACTATTCTCACTTGAATAATAAGTTTTTAATT
64 AGTTCGAAAGTTCGGCCGAGAACCAAAAGAGAAAC-AATCTCACCT--A-AATAAATTTTTAATT
* * *
1015 CATAGACCAAAAGTTGTTTACATAATGAAAACTATTTAGA-CTAAATGATGCGATTTCTAGAGCA
125 CAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCT-AATGATGCGATTTCTA-AGCA
* * ** *
1079 TGTAATGTTCTTAAAATTGCTCGAA
188 TGGAATGTACAAAAAATTACTCGAA
* * *
1104 GGAATGGATCATCTTGAATAGTTTAAGGAATCAAAGTTATAAAAGAACTCGTAAAAGTTTTTCAA
1 GGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAA
*
1169 GTTCGGAAGTTCG
65 GTTCGAAAGTTCG
1182 ACNNNNNNNN
Statistics
Matches: 758, Mismatches: 137, Indels: 69
0.79 0.14 0.07
Matches are distributed among these distances:
206 18 0.02
207 156 0.21
208 3 0.00
209 3 0.00
211 3 0.00
213 10 0.01
214 288 0.38
215 126 0.17
216 1 0.00
217 11 0.01
218 133 0.18
219 6 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (212 bp):
GGAATGGATCGTCTTGAATACTTTAAGGAACAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAG
TTCGAAAGTTCGGCCGAGAACCAAAAGAGAAACAATCTCACCTAAATAAATTTTTAATTCAAAGA
CCAAAAGTTGTTTACAAAATGACAACTATTTAGACCTAATGATGCGATTTCTAAGCATGGAATGT
ACAAAAAATTACTCGAA
Found at i:900 original size:421 final size:422
Alignment explanation
Indices: 1--1183 Score: 1343
Period size: 421 Copynumber: 2.8 Consensus size: 422
* *
1 TTACTAAGCTTGTAATGTTAAATAAATTTCTCAATGGAATGGTTCGTCTTGAATACCTTAAGGAA
1 TTACTAAGCTTGTAATGTTAAATAAATTTCTCAACGGAATGGTTCGTCTTGAATACCTTAATGAA
*
66 CCGAAGTTATAAAAGAACTTGTAAAAGTTTGTCAACTTCTGAAGTTCGGCCTAGAAACAAGAGAG
66 CCGAAG-TATAAAAGAACTCGTAAAAGTTTGTCAACTTC-G-AGTTC-G-C-AG-AACAAGAGAG
* * * *
131 AAACTATTCTCACCTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTGCATAATGGCAATTA
124 AAACTATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGACAACTA
* * *
196 TTCAGACTAAATGATGTGATTTCTAGAGCATGCAATTTTCTTAAAATTGCTTGAAGGAATGGATC
189 TTTAGACTAAATGATGTGATTTCTAGAGCATGCAATGTTCTTAAAATTGCTCGAAGGAATGGATC
* * *
261 GTCTTGAATAATTTAGGGAATCAAAGTT-ATAAAGTAACTCGTAAAAGTTTTTAAAGTTCGAAAG
254 GTCTTGAATAATTTAAGGAATCAAAGTTAAAAAAG-AACTCGTAAAAGTTTTTCAAGTTCGAAAG
*
325 TTCGACCGAGAACCAAAAGAGAAACAATCTCACCTAAATAAAATTTTAATTCAAAGACCAAAAGT
318 TTCGACCGAGAACCAAAAGAGAAACAATCTCACATAAATAAAATTTTAATTCAAAGACCAAAAGT
* *
390 AGTTTAAAAAATGACAACTATTTAAACCTAATGATGCAAT
383 AGTTTAAAAAATGACAACTATTTAAACCAAATGATGCAAC
* * * * * * * * * * *
430 TTCCCAAGCATGGACTG-TACAAAAAATTACTCGAGGGAATGGATCGTCTTGAATACTTTAATGA
1 TTACTAAGCTTGTAATGTTA-AATAAATTTCTCAACGGAATGGTTCGTCTTGAATACCTTAATGA
* * * * * *
494 A-CAAAGGCTATAAATGTACTCGTAAAACTTTGTCAAGTTCG-GTT-G-AGAACGAATAGAGAAA
65 ACCGAA-G-TATAAAAGAACTCGTAAAAGTTTGTCAACTTCGAGTTCGCAGAAC-AAGAGAGAAA
* * * * * *
555 CAATTCTCACCTAAATAAGTTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATGACAGCTATTT
127 CTATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGACAACTATTT
* * * * ** * *
620 AGACCTAAA-GATGTGATTTCCCAG-GCATGGACTGTACAAAAAATTACTCGAAGGAATGTATCG
192 AGA-CTAAATGATGTGATTT-CTAGAGCATGCAATGTTCTTAAAATTGCTCGAAGGAATGGATCG
* * * ** * *
683 TCTTGAATACTTTAATGAA-CAAAAGTTAAAAAAGAAGTTATAAAAGTTTGTCAAGTT-TAAAGT
255 TCTTGAATAATTTAAGGAATC-AAAGTTAAAAAAGAACTCGTAAAAGTTTTTCAAGTTCGAAAGT
* * * *
746 TCGGCCGAGAACCAAGAA-AGAAACAATTTTCACATAAA-GAATTTATTAATTCAAAGACCAAAA
319 TCGACCGAGAACCAA-AAGAGAAACAA-TCTCACATAAATAAAATT-TTAATTCAAAGACCAAAA
* * *
809 GTTGTTTACAAAATGACAACTATTTAGACCAAAAT-ATG-AGAC
381 GTAGTTTAAAAAATGACAACTATTTAAACC-AAATGATGCA-AC
*
851 TTACTAAGCTTGTAATGTTAAATAAATTTCTCAACAGAATGGTTCGTCTTGAATACCTT-ATGGA
1 TTACTAAGCTTGTAATGTTAAATAAATTTCTCAACGGAATGGTTCGTCTTGAATACCTTAAT-GA
915 ACCGAAGTAATAAAAGAACTCGTAAAAGTTTGTCAACTTCGAATGTTCGGCCTAGAACCAAGAGA
65 ACCGAAGT-ATAAAAGAACTCGTAAAAGTTTGTCAACTTCG-A-GTTC-G-C-AGAA-CAAGAGA
* * *
980 GAAACTATTCTCACTTGAATAATAAGTTTTTAATTCATAGACCAAAAGTTGTTTACATAATGAAA
123 GAAACTATTCTCACCT--A-AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGACA
* *
1045 ACTATTTAGACTAAATGATGCGATTTCTAGAGCATGTAATGTTCTTAAAATTGCTCGAAGGAATG
185 ACTATTTAGACTAAATGATGTGATTTCTAGAGCATGCAATGTTCTTAAAATTGCTCGAAGGAATG
* * * *
1110 GATCATCTTGAATAGTTTAAGGAATCAAAGTTATAAAAGAACTCGTAAAAGTTTTTCAAGTTCGG
250 GATCGTCTTGAATAATTTAAGGAATCAAAGTTAAAAAAGAACTCGTAAAAGTTTTTCAAGTTCGA
1175 AAGTTCGAC
315 AAGTTCGAC
1184 NNNNNNNNNN
Statistics
Matches: 614, Mismatches: 108, Indels: 60
0.79 0.14 0.08
Matches are distributed among these distances:
420 39 0.06
421 284 0.46
422 21 0.03
424 4 0.01
426 4 0.01
428 6 0.01
429 101 0.16
430 1 0.00
431 9 0.01
432 136 0.22
433 9 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (422 bp):
TTACTAAGCTTGTAATGTTAAATAAATTTCTCAACGGAATGGTTCGTCTTGAATACCTTAATGAA
CCGAAGTATAAAAGAACTCGTAAAAGTTTGTCAACTTCGAGTTCGCAGAACAAGAGAGAAACTAT
TCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACATAATGACAACTATTTAGAC
TAAATGATGTGATTTCTAGAGCATGCAATGTTCTTAAAATTGCTCGAAGGAATGGATCGTCTTGA
ATAATTTAAGGAATCAAAGTTAAAAAAGAACTCGTAAAAGTTTTTCAAGTTCGAAAGTTCGACCG
AGAACCAAAAGAGAAACAATCTCACATAAATAAAATTTTAATTCAAAGACCAAAAGTAGTTTAAA
AAATGACAACTATTTAAACCAAATGATGCAAC
Done.