Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003743.1 Kokia drynarioides strain JFW-HI SEQ_116704, 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: 2608
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Found at i:396 original size:215 final size:216
Alignment explanation
Indices: 1--1931 Score: 1622
Period size: 215 Copynumber: 8.9 Consensus size: 216
* ** *
1 CAATTCTCTCGT-AAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTTTT
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * *
65 TAGTCCAAATGATGCGATTTAC-CGAGCATGGAATGTTC-AGAAAATTG-GCTGAAGGAATGGAT
66 TAGACCAAATGATGTGATTT-CTCGAGCATGGAATGTTCGA-AAAATTGATC-GAAGGAATGGAT
* * **
127 CATCTTGAATACTCTCAGGAACCGAAGTTATAAAAGTACTCGTAAAAATTTGACAAGTTTGAAAG
128 CATCTTGAATACTCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGAAAG
* *
192 TTCGTCTAAGAA-CAAGGGAGAAA
193 TTCGTCCAAGAACCAAGAGAGAAA
* * *
215 CAATTCACACGTAAAAAAAATTTTAATTCAAACACCAAAAGTTGTTTCCAAAATGACAAACTATT
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * *
280 AAGACCAAATGATGTGATTTCTCGATCATGGAAT-TTACGATAAATTGATTGAAGGAATAGATCA
66 TAGACCAAATGATGTGATTTCTCGAGCATGGAATGTT-CGAAAAATTGATCGAAGGAATGGATCA
* * * *
344 TCTTGAATACTCACAGGAACCGATGTTATAGAGGAACTCGTAAATGTTTGACAAGTTT-AGAATT
130 TCTTGAATACTCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGA-AAGT
* **
408 TCATCCAAGAAGAAAGAGAGAAA
194 TCGTCCAAGAACCAAGAGAGAAA
** * ** * * * *
431 CAGCTCTCACGTAAACAAGTTTTTAATTTAAAGACCAAAAGTTCTTTACGAAATGACAAACTTTT
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * * * * * *
496 TAAACCAAATGATGTGA-TACCCAAAGCATGGAATGTTCGAAAGAA-TGCTTGAAGGAAGGGGTT
66 TAGACCAAATGATGTGATTTCTC-GAGCATGGAATGTTCGAAA-AATTGATCGAAGGAATGGATC
* * * * * * * * * * *
559 GTCTTGAATACTTTAAAGGAATCAAAGTTATAAAAGAACTCATAAAAGTTTGATAGGTTCGAAAT
129 ATCTTGAATAC-TCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGAAAG
* * * *
624 TTCATCAAAGAGCCAAGAGACAAA
193 TTCGTCCAAGAACCAAGAGAGAAA
* * * ** * *
648 AAATTCTTATGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTAGTTTACAAAATGACAAAATATT
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * *
713 TTGACCAAATGATGCGATTTC-CTGATCATGGAATGTTCGAAAAATTGGTCGAAGAAATGGATCA
66 TAGACCAAATGATGTGATTTCTC-GAGCATGGAATGTTCGAAAAATTGATCGAAGGAATGGATCA
*** * * ** * * * *
777 --AAAAATAAGTCAAAGGAATGGATCGTCTTAAATACTCTCAAGAAC-CGAAGTTATAAAAGGAC
130 TCTTGAAT-ACTCACAGGAACCGA-AG--TT--ATA----AAAGAACTC---G---T-AAATG-T
* * **
839 TTGTAAAAGTTTGACTAGTTCGTATGTTCATCTAAGAACCAAGAGAGCTA
177 TTG-ACAAGTTTGA-AAGTTC----G-TC--C-AAGAACCAAGAGAGAAA
** * *
889 CAATTCTCACGTAAATAAGCA--TTAATTCAAAGACTAAAAGTTGTTTACAAAATGATAAACTAT
1 CAATTCTCACGTAAA-AAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
* ** * * * * * * *
952 TTAGATCAAAT-ATGCAATTTTTTGAGCATAGAATGTTCGAAAAGTT-TTTGAAGGAATGGACCA
65 TTAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGATCGAAGGAATGGATCA
* * * * *
1015 TCTTTAATACTCTCAGGAATCGAAGTTATAAAAGAACTCGTAAATGTTTGACGAGTTCGAAAGTT
130 TCTTGAATACTCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGAAAGTT
** * *
1080 ATTCTAAGAACCAATAGAGAAA
195 CGTCCAAGAACCAAGAGAGAAA
* *
1102 CAATTCTCACGT-AAAAAAGTTTCTAATTCAAAGACCAAAAGTTGTTTACAAAATGAAAAACTAT
1 CAATTCTCACGTAAAAAAAATTT-TAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
* * * * *
1166 TTAGACCAAATGATGTGATTTCTC-AGCATAGAATGTTCGAAAAATTGCTCAAAGGATTGGATCG
65 TTAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGATCGAAGGAATGGATCA
* * * * * *
1230 TCTTGAATACTTTA-AGGAACCGAAGTTATAAAAGAACTTGTAAAAT-TTTTACTAGTTTGTATG
130 TCTTGAATAC-TCACAGGAACCGAAGTTATAAAAGAACTCGT-AAATGTTTGACAAGTTTGAAAG
* * *
1293 TTTGTCCAAGAACCAAAAGGGAAA
193 TTCGTCCAAGAACCAAGAGAGAAA
* *
1317 CAATTCTCTCGT-AAAAAAGTGTTTAATTCAAAG-CACAAAAGTTGTTTACAAAATGACAAACTA
1 CAATTCTCACGTAAAAAAAAT-TTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGACAAACTA
* * *
1380 TTTTGACCAAATGATGCGATTTCTCGATCATGGAATGTTCGAAAAATT-AGTCGAAGGAATGGAT
64 TTTAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGA-TCGAAGGAATGGAT
* * * * * *
1444 CATCTTGACTACT-ATTAGGAACCAAAGTTATCAAAGAACTAGTAAATGTTTGA-AA-TTTAGGA
128 CATCTTGAATACTCA-CAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTT-GAA
** * **
1506 ACCTCATCCAAGAACTGAGAGAGAAA
191 AGTTCGTCCAAGAACCAAGAGAGAAA
* *
1532 CAATTCTCACGT-AAAAAAATTTTAATTCAAAGATCAAAAGTTGTTTACAAAATGGCAAACGT-T
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC-TAT
* * * *
1595 TTAGACCAAATGATGTGATTTCCCGAGCATGGAATGTTCAAAAAATCGATCGAAGGAGTGGATCA
65 TTAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGATCGAAGGAATGGATCA
* * * * * * * *
1660 TCTTTACTACT-ATCAGGAACTGAAGTTATAAAAGAACTAGTATATGTTTGACAAGTTCGACACT
130 TCTTGAATACTCA-CAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGAAAGT
* *
1724 TCGTCCAAGAACCGAGAGATAAA
194 TCGTCCAAGAACCAAGAGAGAAA
* ** * *
1747 CAATTCTCACATAAAAAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAATTTT
1 CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * *
1812 TAGACCTAATGACGTGA-TTCCCGAGCATGGAATGTTCAAAAAATTTG-TCGAAAGAATGGATCA
66 TAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAA-TTGATCGAAGGAATGGATCA
* * * * * *
1875 TCTTGAATACTCTCAGAAACCAAAGTGATAAAAGAACTCGAAAATGTTCGACAAGTT
130 TCTTGAATACTCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTT
1932 CTGATATGAG
Statistics
Matches: 1381, Mismatches: 265, Indels: 141
0.77 0.15 0.08
Matches are distributed among these distances:
211 2 0.00
212 2 0.00
213 27 0.02
214 228 0.17
215 504 0.36
216 261 0.19
217 159 0.12
218 5 0.00
220 3 0.00
221 4 0.00
222 7 0.01
223 4 0.00
224 10 0.01
225 1 0.00
228 1 0.00
229 1 0.00
230 10 0.01
231 4 0.00
232 7 0.01
233 4 0.00
234 3 0.00
236 2 0.00
238 16 0.01
239 39 0.03
240 50 0.04
241 25 0.02
242 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
CAATTCTCACGTAAAAAAAATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGATCGAAGGAATGGATCAT
CTTGAATACTCACAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTTGAAAGTTC
GTCCAAGAACCAAGAGAGAAA
Done.