Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005730.1 Kokia drynarioides strain JFW-HI SEQ_119968, 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, 687
Length: 1146
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Found at i:791 original size:430 final size:426
Alignment explanation
Indices: 42--1146 Score: 1286
Period size: 430 Copynumber: 2.6 Consensus size: 426
32 GGAACCGAGT
* * * *
42 CGTAAAAGTTTAAAAAGTTCGGAAGTTCATCCAACAGCCAAGAGAAACAATTCTCACGTAAATAA
1 CGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAA
* * * * * *
107 GTTTTCGCTTTAAAGACCAAAACTTGTTTACAAAACGAAAAACTATTTAGACTAAATGATGCGAT
66 GTTTTTGATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
* * *
172 TACCCGAGAATGGAATGTTCG-AAATTGCTGAAAGGAATGGATGTTCTTGAATACTTCAAGGAAC
131 TTCCCAAGAATGGAATGTTCGAAAATTGCTGAAAGGAATGGAT-TTCTTGAATACTTTAAGGAAC
* * * * *
236 CGGAGTTATAAAAGAACTCGTAAAGGTTTGAAAAGTTTGGAAGTTCGTCCAAGAACAAAGAGAGA
195 CGAAGAT-TAAAAGAACTCGTAAAAGTTTG-ATAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGA
* *
301 GAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACAAAACTTGTTTACAAAATGACAAACA
258 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACAAAACTTGTTTACAAAATGACAAA-A
* *
366 -ATTTAGA-AAAATGATGCGATATTT-TGAGCATAGAACGTT-AAGAAAGTTGCTCGAAGGAATG
322 TATTTAGACAAAATGATGCGAT-TTTCCGAGAATAGAACGTTCAA-AAA-TTGCTCGAAGGAATG
* *
427 TATCGTCTTGAATACTGTAAGGAACTG-AAGTAATAAAAGAACG
384 GATCGTCTTGAATACTGTAAGGAACTGAAAAT-ATAAAAGAACG
* * *
470 CGTAAAAGTTTGACAAGTTCGGAAGTTTGTCCAAGAACCAAGCGAAACAATTCTCACGTAAATAA
1 CGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAA
** * * *
535 GTTTTTGATTCAAAGACCAAAACTTGTTTTTAAAATGACAAACTCTTTAGACCAAATGCTGCTAT
66 GTTTTTGATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
** * ** *
600 TTCTAAAGAATCGAGCGTTCAGAAAATTGTTCG-AAGGAATGGATTATCTTGAATACTTTAAGGA
131 TTCCCAAGAATGGAATGTTC-GAAAATTGCT-GAAAGGAATGGATT-TCTTGAATACTTTAAGGA
* * * *
664 ACCGAAGATGTGAAAGAACTCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCGAGAACTAAGAGA
193 ACCGAAGAT-TAAAAGAACTCGTAAAAGTTTGA-TAGTTCGGAAGTTCGTCCAAGAACAAAGAGA
729 GA-AAACAATTCTCACGTAAATAAGTTTTTAATTCAAACAACAAAACCTT-TTTACAAAATGACA
256 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA-AACAAAA-CTTGTTTACAAAATGACA
* * *
792 AAATATTTAGACCAAATGATGCGATTTTCCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAAT
319 AAATATTTAGACAAAATGATGCGATTTTCCGAGAATAGAACGTTC-AAAAATTGCTCGAAGGAAT
* * * *
857 GGATCGTCTTGAATGCTTTATGGAACTGAAAATATAAAAGAACT
383 GGATCGTCTTGAATACTGTAAGGAACTGAAAATATAAAAGAACG
* * * *
901 CGTAAAAGTTTGATAAG--C--CAGTTCGTCCAAGAACTATAAGAGAAACAATTCTCGCGTAAAT
1 CGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAAC--CAAGAGAAACAATTCTCACGTAAAT
* * * * * *
962 AAGTATTTAATTCAAACAACAAAACCTT-CTAACAAAATGACAAACTATTTAGACCAAATGATGC
64 AAGTTTTTGATTCAAAGACCAAAA-CTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGC
** * * *
1026 GATTTCCCAAGCTTGGAATGTTCGAAAAATTGCTAGAAAGGAATGGATCGTCTTGAATGCTTTAT
128 GATTTCCCAAGAATGGAATGTTCG-AAAATTGCT-GAAAGGAATGGAT-TTCTTGAATACTTTAA
* *
1091 GGAACTGAA-ATTATAGAAGAACTCATAAAAGTTTGATAAGTTCGGAAGTTCGTCCA
190 GGAACCGAAGATTA-A-AAGAACTCGTAAAAGTTTGAT-AGTTCGGAAGTTCGTCCA
Statistics
Matches: 571, Mismatches: 84, Indels: 42
0.82 0.12 0.06
Matches are distributed among these distances:
427 14 0.02
428 127 0.22
429 139 0.24
430 192 0.34
431 91 0.16
432 6 0.01
433 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (426 bp):
CGTAAAAGTTTGAAAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAAACAATTCTCACGTAAATAA
GTTTTTGATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGAT
TTCCCAAGAATGGAATGTTCGAAAATTGCTGAAAGGAATGGATTTCTTGAATACTTTAAGGAACC
GAAGATTAAAAGAACTCGTAAAAGTTTGATAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAAACAAAACTTGTTTACAAAATGACAAAATATT
TAGACAAAATGATGCGATTTTCCGAGAATAGAACGTTCAAAAATTGCTCGAAGGAATGGATCGTC
TTGAATACTGTAAGGAACTGAAAATATAAAAGAACG
Found at i:803 original size:217 final size:213
Alignment explanation
Indices: 41--1146 Score: 1116
Period size: 212 Copynumber: 5.2 Consensus size: 213
31 AGGAACCGAG
* * * * * *
41 TCGTAAAAGTTTAAAAAGTTCGGAAGTTCATCCAACAGC-CAAGAGAAACAATTCTCACGTAAAT
1 TCGTAAAAGTTT-GATAGTTCGGAAGTTCGTCCAAGAACTAAAGAGAAACAATTCTCACGTAAAT
*** * * * * *
105 AAGTTTTCGCTTTAAAGACCAAAACTTGTTTACAAAACGA-AAAACTATTTAGACTAAATGATGC
65 AAGTTTTTAATTCAAACAACAAAACTTGTTTACAAAATGACAAAA-TATTTAGACCAAATGATGC
* * *
169 GATTACCCGAGAATGGAATGTTCG-AAATTGCT-GAAAGGAATGGAT-GTTCTTGAATACTTCAA
129 GATTTCTCGAGAATGGAATGTTCGAAAATTGCTCG-AAGGAATGGATCG-TCTTGAATACTTTAA
* * *
231 GGAACCGGAGTTATAAAAGAAC
192 GGAACTGAAGATATAAAAGAAC
* * * *
253 TCGTAAAGGTTTGAAAAGTTTGGAAGTTCGTCCAAGAACAAAGAGAGAGAAACAATTCTCACGTA
1 TCGTAAAAGTTTG-ATAGTTCGGAAGTTCGTCCAAGAAC-TA-A-AGAGAAACAATTCTCACGTA
* * *
318 AATAAGTTTTTAATTTAAA-GACAAAACTTGTTTACAAAATGACAAACA-ATTTAGA-AAAATGA
62 AATAAGTTTTTAATTCAAACAACAAAACTTGTTTACAAAATGACAAA-ATATTTAGACCAAATGA
* * * * * * * *
380 TGCGATATT-TTGAGCATAGAACGTTAAGAAAGTTGCTCGAAGGAATGTATCGTCTTGAATACTG
126 TGCGAT-TTCTCGAGAATGGAATGTT-CGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTT
444 TAAGGAACTGAAG-TAATAAAAGAAC
189 TAAGGAACTGAAGAT-ATAAAAGAAC
* * * * *
469 GCGTAAAAGTTTGACAAGTTCGGAAGTTTGTCCAAGAAC-CAAGCGAAACAATTCTCACGTAAAT
1 TCGTAAAAGTTTGA-TAGTTCGGAAGTTCGTCCAAGAACTAAAGAGAAACAATTCTCACGTAAAT
* * * ** * * * *
533 AAGTTTTTGATTCAAAGACCAAAACTTGTTTTTAAAATGACAAACTCTTTAGACCAAATGCTGCT
65 AAGTTTTTAATTCAAACAACAAAACTTGTTTACAAAATGACAAAATATTTAGACCAAATGATGCG
** * ** * **
598 ATTTCTAAAGAATCGAGCGTTCAGAAAATTGTTCGAAGGAATGGATTATCTTGAATACTTTAAGG
130 ATTTCTCGAGAATGGAATGTTC-GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG
* * *
663 AACCGAAGATGTGAAAGAAC
194 AACTGAAGATATAAAAGAAC
* *
683 TCGTAAAAGTTTGACTAGTTCGAAAGTTCGTCCGAGAACTAAGAGAGAAAACAATTCTCACGTAA
1 TCGTAAAAGTTTGA-TAGTTCGGAAGTTCGTCCAAGAACTAA-AGAG-AAACAATTCTCACGTAA
748 ATAAGTTTTTAATTCAAACAACAAAACCTT-TTTACAAAATGACAAAATATTTAGACCAAATGAT
63 ATAAGTTTTTAATTCAAACAACAAAA-CTTGTTTACAAAATGACAAAATATTTAGACCAAATGAT
*
812 GCGATTT-TCCGAGAATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATGCTTT
127 GCGATTTCT-CGAGAATGGAATGTTCG-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTT
* *
876 ATGGAACTGAAAATATAAAAGAAC
190 AAGGAACTGAAGATATAAAAGAAC
* *
900 TCGTAAAAGTTTGATAAG--C--CAGTTCGTCCAAGAACTATAAGAGAAACAATTCTCGCGTAAA
1 TCGTAAAAGTTTGAT-AGTTCGGAAGTTCGTCCAAGAACTA-AAGAGAAACAATTCTCACGTAAA
* * * *
961 TAAGTATTTAATTCAAACAACAAAACCTT-CTAACAAAATGACAAACTATTTAGACCAAATGATG
64 TAAGTTTTTAATTCAAACAACAAAA-CTTGTTTACAAAATGACAAAATATTTAGACCAAATGATG
* * ** * *
1025 CGATTTCCCAAGCTTGGAATGTTCGAAAAATTGCTAGAAAGGAATGGATCGTCTTGAATGCTTTA
128 CGATTTCTCGAGAATGGAATGTTCG-AAAATTGCTCG-AAGGAATGGATCGTCTTGAATACTTTA
* *
1090 TGGAACTGAA-ATTATAGAAGAAC
191 AGGAACTGAAGA-TATAAAAGAAC
*
1113 TCATAAAAGTTTGATAAGTTCGGAAGTTCGTCCA
1 TCGTAAAAGTTTGAT-AGTTCGGAAGTTCGTCCA
Statistics
Matches: 755, Mismatches: 104, Indels: 65
0.82 0.11 0.07
Matches are distributed among these distances:
212 177 0.23
213 116 0.15
214 130 0.17
215 36 0.05
216 126 0.17
217 167 0.22
218 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (213 bp):
TCGTAAAAGTTTGATAGTTCGGAAGTTCGTCCAAGAACTAAAGAGAAACAATTCTCACGTAAATA
AGTTTTTAATTCAAACAACAAAACTTGTTTACAAAATGACAAAATATTTAGACCAAATGATGCGA
TTTCTCGAGAATGGAATGTTCGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
CTGAAGATATAAAAGAAC
Done.