Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000823.1 Kokia drynarioides strain JFW-HI SEQ_111916, 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, 922
Length: 1538
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Found at i:753 original size:216 final size:215
Alignment explanation
Indices: 146--1537 Score: 1440
Period size: 216 Copynumber: 6.5 Consensus size: 215
136 TACAAAAAGA
* * *
146 AAAACAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGTAATCGGAA-TTAAAAAAGAAC
1 AAAA-AATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAA-C-GAAGCTAAAAAAGAAC
* * * *
210 TCGTAAAAGTTTGAGTAA-TTCGGAAGTTTGTCCAACAACCAAGAGAGAAACAATTCTCACATAA
63 TCGTAAAAGTTTGA-CAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAA
* * * * * * *
274 ATAAGTTTTTAATTCTAAGGCCAAAACTTATTTACAAAATGACAAAGTTTTTAGACCAAACGATA
127 ATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATG
*
339 CGACTTCCCGAGCATGTAACGTTC
192 CGACTTCCCTAGCATGTAACGTTC
* * * * * * * *
363 AGAAAATTGCTCGATGTACTGTATCGACTTG-ACTACTTTATGGAACCGAAGCTATAAAAGAACT
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAAC-ACTTTAAGGAA-CGAAGCTAAAAAAGAACT
* * * * * ** *
427 CATAAAAGTTCGAGAAGTTC-AGATGTACGTCCAGGAACCAAGAGAG-AA-AATTCTCATGTAAA
64 CGTAAAAGTTTGACAAGTTCGA-AAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAA
* * * * *
489 TAAGTTTATAATTCAAAAATCAAAACATGTTTACAAAATGAAAAACTTTTTAGACCAAATGATAC
128 TAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATGC
* * * *
554 GATTTCCCTCGCATGAAATGTTC
193 GACTTCCCTAGCATGTAACGTTC
** * * * * *
577 CGAATATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGGATCTAAAAAAAAACTC
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAA-CGAAGCTAAAAAAGAACTC
* * * *
642 GTAAAAGTTTGACAATTTTGTAAGTTCGTCCAACAACTAAGAGAGAAACAATTCTCACGTAAATA
65 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
707 AGTTTTTAATTCAAAGGCCAAAGCTTGTTTACAGAATGATAAACTTTTTAGACCAAATGATGCGA
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATGCGA
772 CTT-CCTGAGCATGTAACGTTC
195 CTTCCCT-AGCATGTAACGTTC
* * * * * *
793 AAAAAATTGCTCGAGGGATTGGATCGTCTTGTATACTTTAAGGAAACGAAGCTATAAAAGAACTG
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGG-AACGAAGCTAAAAAAGAACTC
* * * * * *
858 GTAAAAGTTCT-ACAAGTTCGAAAGTTCGTCCAA-GAGCAAGGGAGACACAATTCACACTTAAAT
65 GTAAAAGTT-TGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAAT
* * ** *
921 AAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATTTACCCCAAATGATGCA
129 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATGCG
* * * * *
986 ATTTTCCTCGCATGGAATGTTC
194 ACTTCCCTAGCATGTAACGTTC
* * * *
1008 GAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACTG-GGTTTAAAAAAGAACT
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAAC-GAAG-CTAAAAAAGAACT
* * * * * *
1072 AGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCACCAACCAAGAGAGAAATAATTGTCATGTAAAT
64 CGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAAT
* * * * * ** *
1137 AAGTTTTTAATTCAAAGGCAAAAACTTGTTTACAAAATGACAAACCTATTAGATGAAACGATGCG
129 AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATGCG
* * **
1202 AGTTCCCGAGCATGTAATATTC
194 ACTTCCCTAGCATGTAACGTTC
* * ** * * *
1224 AAAAAATTGCTCGAAGTATTTTATCGTCTTGCATACTTTAAGGAACTGAAGCTACAAAAGAACTC
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAAC-GAAGCTAAAAAAGAACTC
* * * * * **
1289 AT-AAAGTTCGGCAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTTGCGTAAATA
65 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
1353 AGTTTATAATTCAAAGATCAAAACATGTTTACAAAATCAAAAAACTTTTTAGACCAAATGATGCG
130 AGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-GAAAAACTTTTTAGACCAAATGATGCG
1418 ACTT-CCTAAGCATGTAACGTTC
194 ACTTCCCT-AGCATGTAACGTTC
* * * * *
1440 AAAAAATTGCTCGAGGGATTGGATCGTCTTGAATACTTTAAGGAAACGAAGCTATAAAAGAACTG
1 AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGG-AACGAAGCTAAAAAAGAACTC
*
1505 GTAAAAGTTCGACAAGTTCGAAAGTTCGTCCAA
65 GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAA
1538 G
Statistics
Matches: 951, Mismatches: 203, Indels: 42
0.80 0.17 0.04
Matches are distributed among these distances:
214 171 0.18
215 272 0.29
216 470 0.49
217 38 0.04
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (215 bp):
AAAAAATTGCTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACGAAGCTAAAAAAGAACTCG
TAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAA
GTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAACTTTTTAGACCAAATGATGCGAC
TTCCCTAGCATGTAACGTTC
Found at i:1100 original size:431 final size:430
Alignment explanation
Indices: 151--1537 Score: 1788
Period size: 431 Copynumber: 3.2 Consensus size: 430
141 AAAGAAAAAC
*
151 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGTAATCGGAAT-TAAAAAAGAACTCGTA
1 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGG-ATCTAAAAAAGAACTCGTA
* * *
215 AAAGTTTGAGTAA-TTCGGAAGTTTGTCCAACAACCAAGAGAGAAACAATTCTCACATAAATAAG
65 AAAGTTTGA-CAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* * * *
279 TTTTTAATTCTAAGGCCAAAACTTATTTACAAAATGACAAAGTTTTTAGACCAAACGATACGACT
129 TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACT
* * * * * *
344 TCCCGAGCATGTAACGTTCAGAAAATTGCTCGATGTACTGTATCGACTTGACTACTTTATGGAAC
194 TCCCGAGCATGTAACGTTCAAAAAATTGCTCGAAGTATTGTATCGTCTTGA-TACTTTAAGGAAA
* * * *
409 CGAAGCTATAAAAGAACTCATAAAAGTTCGAGAAGTTC-AGATGTACGTCCAGGAACCAAGAGAG
258 CGAAGCTATAAAAGAACTCATAAAAGTTCGACAAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAG
*
473 AA-AATTCTCA-TGTAAATAAGTTTATAATTCAAAAATCAAAACATGTTTACAAAATGAAAAACT
322 AACAATTCTCACT-TAAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATGAAAAACT
* *
536 TTTTAGACCAAATGATACGATTTCCCTCGCATGAAATGTTCCG-AA
386 TTTTAGACCAAATGATGCGATTTTCCTCGCATGAAATGTT-CGAAA
* *
581 TATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGGATCTAAAAAAAAACTCGTAA
1 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGGATCTAAAAAAGAACTCGTAA
* * * *
646 AAGTTTGACAATTTTGTAAGTTCGTCCAACAACTAAGAGAGAAACAATTCTCACGTAAATAAGTT
66 AAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * * *
711 TTTAATTCAAAGGCCAAAGCTTGTTTACAGAATGATAAACTTTTTAGACCAAATGATGCGACTTC
131 TTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTC
* * * *
776 CTGAGCATGTAACGTTCAAAAAATTGCTCGAGGGATTGGATCGTCTTGTATACTTTAAGGAAACG
196 CCGAGCATGTAACGTTCAAAAAATTGCTCGAAGTATTGTATCGTCTTG-ATACTTTAAGGAAACG
** * * *
841 AAGCTATAAAAGAACTGGTAAAAGTTCTACAAGTTCGAAAGTTCGTCCAAG-AGCAAGGGAGACA
260 AAGCTATAAAAGAACTCATAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA-A
* * * *
905 CAATTCACACTTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAAAAACTATT
324 CAATTCTCACTTAAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATGAAAAACTTTT
** * *
970 TACCCCAAATGATGCAATTTTCCTCGCATGGAATGTTCGAAA
389 TAGACCAAATGATGCGATTTTCCTCGCATGAAATGTTCGAAA
* * *
1012 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAA-CTGGGTTTAAAAAAGAACTAGTA
1 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATC-GGATCTAAAAAAGAACTCGTA
* * * *
1076 AAAGTTTGACAAGTTCGGAAGTTCGTCCACCAACCAAGAGAGAAATAATTGTCATGTAAATAAGT
65 AAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* * * ** *
1141 TTTTAATTCAAAGGCAAAAACTTGTTTACAAAATGACAAACCTATTAGATGAAACGATGCGAGTT
130 TTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTT
** *
1206 CCCGAGCATGTAATATTCAAAAAATTGCTCGAAGTATTTTATCGTCTTGCATACTTTAAGG-AAC
195 CCCGAGCATGTAACGTTCAAAAAATTGCTCGAAGTATTGTATCGTCTTG-ATACTTTAAGGAAAC
* * *
1270 TGAAGCTACAAAAGAACTCAT-AAAGTTCGGCAAGTTCGAAAGTTCATCCAAGAACCAAGAGAGA
259 -GAAGCTATAAAAGAACTCATAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAG-
** * *
1334 AACAATTCTTGCGTAAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATCAAAAAACT
322 AACAATTCTCACTTAAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAAT-GAAAAACT
* * * * *
1399 TTTTAGACCAAATGATGCGA-CTTCCTAAGCATGTAACGTTCAAAA
386 TTTTAGACCAAATGATGCGATTTTCCT-CGCATGAAATGTTCGAAA
* * * * * * * * *
1444 AATTGCTCGAGGGATTGGATCGTCTTGAATACTTTAAGGAAACGAAGCTATAAAAGAACTGGTAA
1 AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGGATCTAAAAAAGAACTCGTAA
* *
1509 AAGTTCGACAAGTTCGAAAGTTCGTCCAA
66 AAGTTTGACAAGTTCGGAAGTTCGTCCAA
1538 G
Statistics
Matches: 828, Mismatches: 114, Indels: 28
0.85 0.12 0.03
Matches are distributed among these distances:
429 13 0.02
430 303 0.37
431 393 0.47
432 118 0.14
433 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (430 bp):
AATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAATCGGATCTAAAAAAGAACTCGTAA
AAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
TTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACTTTTTAGACCAAACGATGCGACTTC
CCGAGCATGTAACGTTCAAAAAATTGCTCGAAGTATTGTATCGTCTTGATACTTTAAGGAAACGA
AGCTATAAAAGAACTCATAAAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAACA
ATTCTCACTTAAATAAGTTTATAATTCAAAGATCAAAACATGTTTACAAAATGAAAAACTTTTTA
GACCAAATGATGCGATTTTCCTCGCATGAAATGTTCGAAA
Done.