Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001705.1 Kokia drynarioides strain JFW-HI SEQ_113394, 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, 736
Length: 1228
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Found at i:980 original size:426 final size:423
Alignment explanation
Indices: 65--1228 Score: 1406
Period size: 426 Copynumber: 2.7 Consensus size: 423
55 TCAAGAAGGC
65 AACAATTCTCACGTAAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AACAATTCTCACGT-AAAAAAGT-TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
* * ** * **
130 ATTTTGACCAAATAATGCGATTTCCCGATAATGGAATCTGCGGAAAATTGGTCAAAGGAATGGAT
64 ATTTTGACCAAATGATGTGATTTCCC-AGCATGGAATCTTCAAAAAATTGGTCAAAGGAATGGAT
** * * * * *
195 CGTCCCGAA-ACCTCTCAGGAACCGAAGTTATGAAAGATCTCGTAAATGTTTAACCAATTCGGAA
128 CGTCTTGAATA-CTCTCAGAAACCGAAGTTATAAAAGAACTC---AA-GTTTAA-TAGTTCGGAA
* * *
259 GTTTGTCCAAGAGCCAAGAGAGAAACAATTCTTTCGTAATAAAGTTTTTAATTCAAAGACCAAAA
187 GTTTGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCAAAGACCAAAA
* * * *
324 GTTGTTTACAAAATGACAAACGTTTTAGACCAAATGATGCGATTTCCCGAGCATGAAATGTTCAA
252 GTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGTGATTTCCCGAGAATGAAATGCTCAA
* * * * *
389 AAAATTGGCAAAGGAATGAATCATCTTGACTACTATCTGGGACCGAAGTTATAAAAGATCTACGA
317 AAAATAGGCAAAGGAATGAATCATATTAAATAC-ATCTGGGACCGAAGTTATAAAAGAACTACGA
* *
454 AATGTTTGACAAGTTCGACACTTCATCCAAGAACCGAGAGAGA
381 AATGTTTGACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGA
* * ** * *
497 AACAATTCTCACGTAATAAAGTTTTTAATTCAAAGACTAATTGTTGTTTATAAAATGACAGACT-
1 AACAATTCTCACGTAAAAAAG-TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
*
561 TTTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTTCAAAAAATTGGTCAAAGGAATGGAT
65 TTTT-GACCAAATGATGTGATTTCCC-AGCATGGAATCTTCAAAAAATTGGTCAAAGGAATGGAT
* * *
626 CGTATTGAATACTCTCAGAAACCAAAGTTATAAAAGAACTC-A-TTTGATGAGTTCGGAAGTTTG
128 CGTCTTGAATACTCTCAGAAACCGAAGTTATAAAAGAACTCAAGTTTAAT-AGTTCGGAAGTTTG
* * * * * * *
689 TTCGAGAACCAGGAGAGAACCAATTCTCACGTAAAAAAGTTTTTAAATCAAAGACCAAAAGTTTT
192 TCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGT
* * * * *
754 TTACAACATGCCAAACTTTTTAGACCAAGTGATGTGATTTCTCGAGAATGAAATGCTCGAAAAAT
257 TTACAAAATGACAAACTTTTTAGACCAAATGATGTGATTTCCCGAGAATGAAATGCTCAAAAAAT
* * * * *
819 AAGTCGAAGGAATGGATCGTATTAAATAC-TCTGAGGAACTGAAGTTATAAAAGAACT-CGTAAA
322 -AGGCAAAGGAATGAATCATATTAAATACATCTG-GG-ACCGAAGTTATAAAAGAACTACG-AAA
* *
882 TGTTTGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGA
383 TGTTTGACAAGTTCGAAACTTCATCCAAGAACCAAGAGAGA
* * * * *
923 AAGAATTCTAACGTAAAAAAGCTTTTAATTCAAAGGCCAAAAGCTATTTACAAAATGACAAACTA
1 AACAATTCTCACGTAAAAAAG-TTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
* *
988 TTTTGACCATATGATGTGATTTCCCGGTCATGGAATCTTCAAAAAATTGGTCAAAGGAATGGATC
65 TTTTGACCAAATGATGTGATTTCCCAG-CATGGAATCTTCAAAAAATTGGTCAAAGGAATGGATC
** *
1053 GTCTTGAATACTCTCA-AGAATTGAAGTTATAAAAGAACTCGTAAATGTTTAACTAGTTCAGAAG
129 GTCTTGAATACTCTCAGA-AACCGAAGTTATAAAAGAACTC---AA-GTTTAA-TAGTTCGGAAG
* * *
1117 TTCGTCCAAGAACCAAGAGAGAAATAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAG
188 TTTGTCCAAGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCAAAGACCAAAAG
*
1182 TTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCC
253 TTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGTGATTTCCC
Statistics
Matches: 620, Mismatches: 94, Indels: 36
0.83 0.13 0.05
Matches are distributed among these distances:
424 4 0.01
425 134 0.22
426 220 0.35
427 5 0.01
430 5 0.01
431 125 0.20
432 126 0.20
433 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (423 bp):
AACAATTCTCACGTAAAAAAGTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTAT
TTTGACCAAATGATGTGATTTCCCAGCATGGAATCTTCAAAAAATTGGTCAAAGGAATGGATCGT
CTTGAATACTCTCAGAAACCGAAGTTATAAAAGAACTCAAGTTTAATAGTTCGGAAGTTTGTCCA
AGAACCAAGAGAGAAACAATTCTCTCGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTAC
AAAATGACAAACTTTTTAGACCAAATGATGTGATTTCCCGAGAATGAAATGCTCAAAAAATAGGC
AAAGGAATGAATCATATTAAATACATCTGGGACCGAAGTTATAAAAGAACTACGAAATGTTTGAC
AAGTTCGAAACTTCATCCAAGAACCAAGAGAGA
Found at i:1005 original size:216 final size:215
Alignment explanation
Indices: 65--1228 Score: 1348
Period size: 216 Copynumber: 5.4 Consensus size: 215
55 TCAAGAAGGC
*
65 AACAATTCTCACGTAAAAAAAGTATTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
1 AACAATTCTCACGT-AAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT
* * ** **
130 ATTTTGACCAAATAATGCGATTTCCCGATAATGGAAT-CTGCGGAAAATTGGTCAAAGGAATGGA
65 -TTTTGACCAAATGATGTGATTTCCCGAGCATGGAATGCT-CAAAAAATTGGTCAAAGGAATGGA
** * * * *
194 TCGTCCCGAA-ACCTCTCAGGAACCGAAGTTATGAAAGATCTCGTAAATGTTTAACCAA-TTCGG
128 TCGTCTTGAATA-CTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGA-CAAGTTCGA
* *
257 AAGTTTGTCCAAGAGCCAAGAGAGA
191 AAGTTCGTCCAAGAACCAAGAGAGA
** *
282 AACAATTCTTTCGTAATAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACGT
1 AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC-T
* * * * *
347 TTTAGACCAAATGATGCGATTTCCCGAGCATGAAATGTTCAAAAAATTGG-CAAAGGAATGAATC
65 TTTTGACCAAATGATGTGATTTCCCGAGCATGGAATGCTCAAAAAATTGGTCAAAGGAATGGATC
* * * * * * * *
411 ATCTTGACTACTATCTGGGACCGAAGTTATAAAAGATCTACG-AAATGTTTGACAAGTTCGACAC
130 GTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACT-CGTAAATGTTTGACAAGTTCGAAAG
* *
475 TTCATCCAAGAACCGAGAGAGA
194 TTCGTCCAAGAACCAAGAGAGA
* * ** * *
497 AACAATTCTCACGTAATAAAGTTTTTAATTCAAAGACTAATTGTTGTTTATAAAATGACAGACTT
1 AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTT
* *
562 TTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTTCAAAAAATTGGTCAAAGGAATGGATC
66 TTT-GACCAAATGATGTGATTTCCCGAGCATGGAATGCTCAAAAAATTGGTCAAAGGAATGGATC
* * * ** *
627 GTATTGAATACTCTCAGAAACCAAAGTTATAAAAGAACTC----A--TTTGATGAGTTCGGAAGT
130 GTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAAGT
* * * *
686 TTGTTCGAGAACCAGGAGAGA
195 TCGTCCAAGAACCAAGAGAGA
* * * * *
707 ACCAATTCTCACGTAAAAAAGTTTTTAAATCAAAGACCAAAAGTTTTTTACAACATGCCAAACTT
1 AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTT
* * * * * ** *
772 TTTAGACCAAGTGATGTGATTTCTCGAGAATGAAATGCTCGAAAAATAAGTCGAAGGAATGGATC
66 TTT-GACCAAATGATGTGATTTCCCGAGCATGGAATGCTCAAAAAATTGGTCAAAGGAATGGATC
* * * *
837 GTATTAAATACTCTGAGGAACTGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAAGT
130 GTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAAGT
902 TCGTCCAAGAACCAAGAGAGA
195 TCGTCCAAGAACCAAGAGAGA
* * * * * *
923 AAGAATTCTAACGTAAAAAAGCTTTTAATTCAAAGGCCAAAAGCTATTTACAAAATGACAAACTA
1 AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT-
*
988 TTTTGACCATATGATGTGATTTCCCG-GTCATGGAAT-CTTCAAAAAATTGGTCAAAGGAATGGA
65 TTTTGACCAAATGATGTGATTTCCCGAG-CATGGAATGC-TCAAAAAATTGGTCAAAGGAATGGA
* ** * *
1051 TCGTCTTGAATACTCTCAAGAATTGAAGTTATAAAAGAACTCGTAAATGTTTAACTAGTTC-AGA
128 TCGTCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGA-A
1115 AGTTCGTCCAAGAACCAAGAGAGA
192 AGTTCGTCCAAGAACCAAGAGAGA
* * *
1139 AATAATTCTCTCGTAAAAAAGTTTTTAATTCACAGACCAAAAGTTGTTTACAAAATGACAAACTA
1 AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACT-
*
1204 TTTAGACCAAATGATGTGATTTCCC
65 TTTTGACCAAATGATGTGATTTCCC
Statistics
Matches: 800, Mismatches: 130, Indels: 35
0.83 0.13 0.04
Matches are distributed among these distances:
210 172 0.22
212 1 0.00
214 8 0.01
215 177 0.22
216 424 0.53
217 18 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (215 bp):
AACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTT
TTTGACCAAATGATGTGATTTCCCGAGCATGGAATGCTCAAAAAATTGGTCAAAGGAATGGATCG
TCTTGAATACTCTCAGGAACCGAAGTTATAAAAGAACTCGTAAATGTTTGACAAGTTCGAAAGTT
CGTCCAAGAACCAAGAGAGA
Done.