Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000479.1 Kokia drynarioides strain JFW-HI SEQ_111354, 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, 844
Length: 1407
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Found at i:507 original size:211 final size:212
Alignment explanation
Indices: 1--1405 Score: 897
Period size: 215 Copynumber: 6.6 Consensus size: 212
* * *
1 CTTCGAGTAATTT-TCTGTACAGTCCATGCTTGGAAAATCACATCATTAGGTCTAAATAGTTGTC
1 CTTCGAGCAATTTAT-TGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTC
*
65 ATTTTGTAAACAACTTTTGGTTTTGAATT-AAAACTTATTTAGGTGAGAATTATTTCTCTCTTGG
65 ATTTTGTAAACAACTTTTGGTTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGG
* * * * * ** * * *
129 TTCTCGGTCGAACTTCCGAACTTGACTAATTTTTAAGAGTTCTTTTATAACTTCGGTTCCTTAAA
130 TTCTCAGCCAAACTTCCAAACTTGACAAAAATTTAAGAGTTCTTTTAAAAATT--GTTCATTAAA
194 GTAATCAAGACGATCCATTC
193 GTAATCAAGACGATCCATTC
* * * * * *
214 CTTCGAGCAATTTTTTGAACATTCCATGCTCGAGAAATCGCATCATTTGGTCTAAATAGTTGTCA
1 CTTCGAGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTCA
* * * *
279 TTTTGTAAACAACTTTTGGTCTTTGAATTAAAAAATTCTTTATGTGAGAATTGTTTCTTTCTTGG
66 TTTTGTAAACAACTTTTGGT-TTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGG
* *
344 TTCTCAGCCAAACTT-TAAACTTGACAAAAATTTCA-AGTTCTTTTTTAAAAATT-TTCATTAAA
130 TTCTCAGCCAAACTTCCAAACTTGACAAAAATTTAAGAGTTC--TTTTAAAAATTGTTCATTAAA
*
406 GTATTCAAGACGATCCATTC
193 GTAATCAAGACGATCCATTC
* *
426 CTTC-AGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATTATTTGGTCTAAATTGTTGTCA
1 CTTCGAGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTCA
* * * * *
490 TTCTGTAAACTACTTTTGGTTTTTCAATTAAAAACTTATTAAGGTGAGAATTGTTTCTCTATTGG
66 TTTTGTAAACAACTTTTGG-TTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGG
* * * * ** * * **
555 TTCACAGTTGAACTTCCGAACATCCGAACTTGACAAACTTTTACGAGTTCTTTTTTAACTTCTGT
130 TTCTCA---G-----CCAAACTTCCAAACTTGACAAAAATTTAAGAGTTC-TTTTAAAAAT-TGT
* *
620 TCCTTATAG-AATTCAAGACGATCCATTC
185 TCATTAAAGTAA-TCAAGACGATCCATTC
* * * ** * ** * * * *
648 CTTCAACCAATTTTTTAAACATTCCATGCTCAGGAAATCGCATCACTTGTTCTTAATAGATTGTC
1 CTTCGAGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAG-TTGTC
* * *** * * * * * * *
713 AATTTGAAAACAAAAGTT-ATTTATG--TT-AGAA-TTGTTT--CT-----TTCTTTGT-TCTCG
65 ATTTTGTAAACAACTTTTGGTTT-TGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTG
** ** * * **
765 GTTGAACTTCCGAACTTGACAAAC-T---------TTAACGAGTTCTTTTATAACTTTTGTTCAT
129 GTT-CTCAGCCAAACTT-CCAAACTTGACAAAAATTTAA-GAGTTCTTTTA-AA-AATTGTTCAT
* *
820 TAAAGTATTCAGGACGATCCATTC
189 TAAAGTAATCAAGACGATCCATTC
* **** * * *
844 TTTCGAGCAATTTCCCATACAGTCCATGCTTGGGAGATCACATCATTAGATCTAAATAGTTGTCA
1 CTTCGAGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTCA
* * *
909 TTTTTTAAACTACTTTTGGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTTTTGG
66 TTTTGTAAACAACTTTTGGT-TTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGG
* * * ** ** *
974 TTCTCGGCCAAACTTCCGAACTTGA-AAAACTTTTACCAGTTCTTTTATAACTTTGATTCCTTAA
130 TTCTCAGCCAAACTTCCAAACTTGACAAAA-ATTTAAGAGTTCTTTTA-AAAATTG-TTCATTAA
* * * * *
1038 ACTATTTAAGATGATCCCTTC
192 AGTAATCAAGACGATCCATTC
* * * * ** ** *
1059 CTTCGAGCAATTT-TAAG-AGCATTCGATGCTCT-AGAAATTGCATCATTTTATCTGAATAGTTG
1 CTTCGAGCAATTTAT-TGTA-CAGTCCATGCT-TGGGAAATCACATCATTTGGTCTAAATAGTTG
* * * * * *
1121 CCATTATGTATACAACTTTTGGTCTTTGAATTAAATACTTATTTAGGTGAGAATAGTTTTTCTCT
63 TCATTTTGTAAACAACTTTTGGT-TTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCT
* * * * ** * * * * *
1186 TGGTTCT-AGGCCGAACATCCGAAGTTGACAAACTTTTACGAGTTCTTTTACAACTTCGGCTCCT
127 TGGTTCTCA-GCCAAACTTCCAAACTTGACAAAAATTTAAGAGTTCTTTTAAAAATT--GTTCAT
* *
1250 TAAAGT-ATCCAAGACAAACCATTC
189 TAAAGTAAT-CAAGACGATCCATTC
* * * * * *
1274 CTTCGAGCAATTT-TATGAACATTCCAAGCTTAGGAAATCTCATCATTTGGTGTAAATAGTTGTC
1 CTTCGAGCAATTTAT-TGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTC
* * * * *
1338 ATTTTGTAAACAACTTTTTGTCTTTAAATTAAATAA-TTCTTTATGTGAGAATTGTTTCTTTCTT
65 ATTTTGTAAACAACTTTTGGT-TTTGAATTAAA-AACTTATTTAGGTGAGAATTGTTTCTCTCTT
1402 GGTT
128 GGTT
1406 AT
Statistics
Matches: 920, Mismatches: 208, Indels: 126
0.73 0.17 0.10
Matches are distributed among these distances:
195 23 0.03
196 79 0.09
197 5 0.01
198 2 0.00
199 3 0.00
200 5 0.01
202 1 0.00
204 8 0.01
205 4 0.00
206 4 0.00
207 15 0.02
208 6 0.01
211 117 0.13
212 40 0.04
213 80 0.09
214 34 0.04
215 350 0.38
216 10 0.01
217 1 0.00
219 10 0.01
220 25 0.03
221 9 0.01
222 31 0.03
223 42 0.05
224 16 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (212 bp):
CTTCGAGCAATTTATTGTACAGTCCATGCTTGGGAAATCACATCATTTGGTCTAAATAGTTGTCA
TTTTGTAAACAACTTTTGGTTTTGAATTAAAAACTTATTTAGGTGAGAATTGTTTCTCTCTTGGT
TCTCAGCCAAACTTCCAAACTTGACAAAAATTTAAGAGTTCTTTTAAAAATTGTTCATTAAAGTA
ATCAAGACGATCCATTC
Done.