Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001836.1 Kokia drynarioides strain JFW-HI SEQ_113584, 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, 715
Length: 1192
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Found at i:411 original size:216 final size:216
Alignment explanation
Indices: 37--1188 Score: 1454
Period size: 216 Copynumber: 5.3 Consensus size: 216
27 AAATAAGTCG
* * * * * * *
37 AAGGAATGGATCGTATTAAATACTCTGAGGAA-CTGAAGTTATAAAAGAACTCGTAAATGTTTGA
1 AAGGAATGGATCATCTTGAATACTATCAGGAATC-GAAGTTATAAAAGAACTAGTAAATGTTTAA
* * *
101 CAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAAGAATTCTAACGTAAAAAAGCTTTTAATTC
65 CAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTC
* * * *
166 AAAGACCAAAAGCTATTTACAAAATGACAAACTATTTTGACCATATGATGTGATTTCCCGGTCAT
130 AAAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCAT
* *
231 GGAATCTTCAAAAAATTGGTCA
195 GGAATGTTTAAAAAATTGGTCA
* * * * *
253 AAGGAATGGATCGTCTTGAATACTCTCAAGAATTGAAGTTATAAAAGAACTCGTAAATGTTTAAC
1 AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
* * *
318 CAGTTC-AGAAGTTCGTCCAAGAACCAAGAGAGAAATAATTCTCTCGTAAAAAAGTTTTTAATTC
66 AAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTC
* *
382 ACAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCAT
130 AAAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCAT
* *
447 GGAATGTTTGAAAAATTGGTCG
195 GGAATGTTTAAAAAATTGGTCA
* * * *
469 AGGGAGTTGATCATCTTGACTACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
1 AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
* * * *
534 AAGTTCGAAATTTCATCCAAGAACCAAGAGAGAAAGAATTCTAACGTAAAAAAGTTTTTAATTCA
66 AAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCA
* * * * * * * *
599 AAAACCAAAAGCTATTTACAAAATGACAAATTATTTTGACAAAATGATGCGATTTCCCAATAATG
131 AAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCATG
* * *
664 GAATCTTCAGAAAATTGGTCA
196 GAATGTTTAAAAAATTGGTCA
* * *
685 AAGGAATGGATCATCTTGAATACTCTCAGGAATCGGAGTTATAAAAGAACTTGTAAATGTTTAAC
1 AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
* ** * *
750 AACTTCGAAAGTTCGTCCAAGAACCAATTGAGAAACAGTTCTCTCGTAAAAAAGTTTTTAATTCA
66 AAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCA
* * * *
815 TAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATCCCGATCATG
131 AAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCATG
* *
880 GAATGTTTGAAAAATTGGTCG
196 GAATGTTTAAAAAATTGGTCA
* * * * ** *
901 AAGAAATGGATCGTCTTGACTACTATCAGGAAACGAAGTTATAAAAGATTTAGTAAATGTTTGAC
1 AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
* *
966 AAGTTC-AGAACTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAA-TATTTTAATT
66 AAGTTCGA-AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGT-TTTTAATT
* * * *
1029 CATAGACCTAAAACTT-TTTACAAAATGACTAAAGT-TTTAGACCAAATGAT-TCGATTTCTCGA
129 CAAAGACC-AAAAGTTATTTACAAAATGAC-AAACTATTTAGACCAAATGATGT-GATTTCCCGA
* *
1091 GCATGGAATGTTTAAAATATTGGTCA
191 TCATGGAATGTTTAAAAAATTGGTCA
* * * * * *
1117 AAGGAATGGATCATCTCGACTACTATCTGGAACCGAAGTTATAAAAGAACTAGGAAATGTTTGAC
1 AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
1182 AAGTTCG
66 AAGTTCG
1189 GCAC
Statistics
Matches: 811, Mismatches: 116, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
215 3 0.00
216 797 0.98
217 11 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (216 bp):
AAGGAATGGATCATCTTGAATACTATCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAAC
AAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCA
AAGACCAAAAGTTATTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCATG
GAATGTTTAAAAAATTGGTCA
Found at i:827 original size:432 final size:432
Alignment explanation
Indices: 71--1188 Score: 1636
Period size: 432 Copynumber: 2.6 Consensus size: 432
61 CTGAGGAACT
* * *
71 GAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAA
1 GAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGAA
*
136 AGAATTCTAACGTAAAAAAGCTTTTAATTCAAAGACCAAAAGCTATTTACAAAATGACAAACTAT
66 AGAATTCTAACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGCTATTTACAAAATGACAAACTAT
* * * *
201 TTTGACCATATGATGTGATTTCCCGGTCATGGAATCTTCAAAAAATTGGTCAAAGGAATGGATCG
131 TTTGACCAAATGATGCGATTTCCCGATCATGGAATCTTC-AAAAATTGGTCAAAGGAATGGATCA
* * * *
266 TCTTGAATACTCTCAAGAATTGAAGTTATAAAAGAACTCGTAAATGTTTAACCAGTTC-AGAAGT
195 TCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAACAAGTTCGAGAAGT
*
330 TCGTCCAAGAACCAAGAGAGAAATAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAGT
260 TCGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAGT
* *
395 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCGATCATGGAATGTTTGAAA
325 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTTGAAA
* * * * *
460 AATTGGTCGAGGGAGTTGATCATCTTGACTACTATCAGGAATC
390 AATTGGTCGAAGAAATGGATCATCTTGACTACTATCAGGAAAC
* *
503 GAAGTTATAAAAGAACTAGTAAATGTTTAACAAGTTCGAAATTTCATCCAAGAACCAAGAGAGAA
1 GAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGAA
* *
568 AGAATTCTAACGTAAAAAAGTTTTTAATTCAAAAACCAAAAGCTATTTACAAAATGACAAATTAT
66 AGAATTCTAACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGCTATTTACAAAATGACAAACTAT
* * *
633 TTTGACAAAATGATGCGATTTCCCAATAATGGAATCTTCAGAAAATTGGTCAAAGGAATGGATCA
131 TTTGACCAAATGATGCGATTTCCCGATCATGGAATCTTCA-AAAATTGGTCAAAGGAATGGATCA
* * *
698 TCTTGAATACTCTCAGGAATCGGAGTTATAAAAGAACTTGTAAATGTTTAACAACTTCGA-AAGT
195 TCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAACAAGTTCGAGAAGT
** * *
762 TCGTCCAAGAACCAATTGAGAAACAGTTCTCTCGTAAAAAAGTTTTTAATTCATAGACCAAAAGT
260 TCGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAGT
827 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTTGAAA
325 TGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTTGAAA
*
892 AATTGGTCGAAGAAATGGATCGTCTTGACTACTATCAGGAAAC
390 AATTGGTCGAAGAAATGGATCATCTTGACTACTATCAGGAAAC
**
935 GAAGTTATAAAAGATTTAGTAAATGTTTGACAAGTTC-AGAACTTCATCCAAGAACCAAGAGAGA
1 GAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGA-AACTTCATCCAAGAACCAAGAGAGA
* * * *
999 AACAATTCTCACGTAAAAAA-TATTTTAATTCATAGACCTAAAA-CTTTTTACAAAATGACTAAA
65 AAGAATTCTAACGTAAAAAAGT-TTTTAATTCAAAGACC-AAAAGCTATTTACAAAATGAC-AAA
* * * * * * *
1062 GT-TTTAGACCAAATGATTCGATTTCTCGAGCATGGAATGTTTAAAATATTGGTCAAAGGAATGG
127 CTATTTTGACCAAATGATGCGATTTCCCGATCATGGAATCTTCAAAA-ATTGGTCAAAGGAATGG
* * * * * * *
1126 ATCATCTCGACTACTATCTGGAACCGAAGTTATAAAAGAACTAGGAAATGTTTGACAAGTTCG
191 ATCATCTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAACAAGTTCG
1189 GCAC
Statistics
Matches: 617, Mismatches: 62, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
431 6 0.01
432 602 0.98
433 9 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (432 bp):
GAAGTTATAAAAGAACTAGTAAATGTTTGACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGAA
AGAATTCTAACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGCTATTTACAAAATGACAAACTAT
TTTGACCAAATGATGCGATTTCCCGATCATGGAATCTTCAAAAATTGGTCAAAGGAATGGATCAT
CTTGAATACTCTCAGGAATCGAAGTTATAAAAGAACTAGTAAATGTTTAACAAGTTCGAGAAGTT
CGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAGTT
GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATATCCCGATCATGGAATGTTTGAAAA
ATTGGTCGAAGAAATGGATCATCTTGACTACTATCAGGAAAC
Done.