Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005345.1 Kokia drynarioides strain JFW-HI SEQ_119304, 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, 649
Length: 1083
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Found at i:292 original size:161 final size:161
Alignment explanation
Indices: 3--292 Score: 420
Period size: 161 Copynumber: 1.8 Consensus size: 161
1 TC
*** * *
3 AGCTTCCTGATGAGATATTGAGAAGTGGACCAAATCCGTTTTCCTGATGAGACACAGAAAAGTGG
1 AGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTGG
* * * *
68 ATCAAAACAAGTGATGCTGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAATGAAAT
66 ATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTAAGAAGAACACCAAATCAATGAAAT
133 CAGACTCAAAGTGAGCAAATCTTCGAACCTT
131 CAGACTCAAAGTGAGCAAATCTTCGAACCTT
* * *
164 AGCTTCCTGATGAGATACAAAGAAGTGAACCAGATTCGTCTTCCTGATGAGACACAGAGAAGTGG
1 AGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTGG
* * * *
229 ATCAAAAGAAGCGAGGCGGTCATCTTCCTGATGAGATA-TAGAGAAGTACACCAACTTAATGAAA
66 ATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTA-AGAAGAACACCAAATCAATGAAA
293 CAAAGCTTGA
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
160 2 0.02
161 110 0.98
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (161 bp):
AGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTGG
ATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTAAGAAGAACACCAAATCAATGAAAT
CAGACTCAAAGTGAGCAAATCTTCGAACCTT
Found at i:320 original size:161 final size:161
Alignment explanation
Indices: 2--342 Score: 418
Period size: 161 Copynumber: 2.1 Consensus size: 161
1 T
*** * *
2 CAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATCCGTTTTCCTGATGAGACACAGAAAAGTG
1 CAGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTG
* * * *
67 GATCAAAACAAGTGATGCTGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAATGAAA
66 GATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTAAGAAGAACACCAAATCAATGAAA
* *
132 TCAGACTCAAAGTGAGCAAATCTTCGAACCT
131 TCAAACTCAAAGTGAGCAAATCTTCGAACCC
* * * *
163 TAGCTTCCTGATGAGATACAAAGAAGTGAACCAGATTCGTCTTCCTGATGAGACACAGAGAAGTG
1 CAGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTG
* * * *
228 GATCAAAAGAAGCGAGGCGGTCATCTTCCTGATGAGATA-TAGAGAAGTACACCAACTTAATGAA
66 GATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTA-AGAAGAACACCAAATCAATGAA
** * *
292 A-CAAAGCTTGATGTGAGTGAAA-CTTCGAACCC
130 ATCAAA-CTCAAAGTGAG-CAAATCTTCGAACCC
*
324 CAGCTTCCTAATGAGATAC
1 CAGCTTCCTGATGAGATAC
343 TGAGAAGCAG
Statistics
Matches: 152, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
160 5 0.03
161 144 0.95
162 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (161 bp):
CAGCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAGACACAGAAAAGTG
GATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACTAAGAAGAACACCAAATCAATGAAA
TCAAACTCAAAGTGAGCAAATCTTCGAACCC
Found at i:440 original size:32 final size:33
Alignment explanation
Indices: 375--440 Score: 80
Period size: 37 Copynumber: 1.9 Consensus size: 33
365 AATCGGTTAC
*
375 CTTCCTGATGAGATACAGAGAAGTGAACCGGATCCGT
1 CTTCCTGATGAGATACAAAGAAGT--A--GGATCCGT
412 CTTCCTGATGAGATACAAAGAAGT-GGATC
1 CTTCCTGATGAGATACAAAGAAGTAGGATC
441 AAAATAGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 5 0.18
37 23 0.82
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (33 bp):
CTTCCTGATGAGATACAAAGAAGTAGGATCCGT
Found at i:533 original size:209 final size:208
Alignment explanation
Indices: 166--910 Score: 1001
Period size: 209 Copynumber: 3.6 Consensus size: 208
156 CGAACCTTAG
*
166 CTTCCTGATGAGATACAAAGAAGTGAACCAGATTCGTCTTCCTGATGAGACACAGAGAAGTGGAT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
* * * * * * *
231 CAAAAGAAGCGAGGCGGTCATCTTCCTGATGAGATA-TAGAGAAGTACACCAACTTAATGAAACA
66 CAAAACAAGAGATGCGGTCATCTTCCTGATGAGATACT-GAGAAGTAGACCAAATCAATGAAGCA
* * *
295 AAGCTTGATGTGAGTGAAACTTCGAACCCCAGCTTCCTAATGAGATACTGAGAAGCAGATCGAAG
130 AAGCTCGATGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACT-AGAAGCAGGTCGAAG
*
360 CAATAAATCGGTTAC
194 CAATAAAACGGTTAC
* * * *
375 CTTCCTGATGAGATACAGAGAAGTGAACCGGATCCGTCTTCCTGATGAGATACAAAGAAGTGGAT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
*
440 CAAAA-TAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCGA
66 CAAAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGC-A
* * ** * * *
504 AAGCTCGATGTGAGTGAATCTTTGAACCCCATCTTTTTTATGAGATACTAAGATGTAGGTCGAAG
130 AAGCTCGATGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACT-AGAAGCAGGTCGAAG
*
569 CAATAAAACTGTTAC
194 CAATAAAACGGTTAC
* ** *
584 CTTCCTGATTAGATACAAAGAAGTGAACTGGATCCGTCTTCCTGATGAGATACAGAGAAGTGGAT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
* * * *
649 CAAAACAA-AGATGCGGTTATCTTCCTGATGAGATACTAATAAGTAGACCAAATCAATTAAGCCA
66 CAAAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAG-CA
* * * *
713 AAGCTCAATGTGAGCGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAAAGCAGGTCAAAGC
130 AAGCTCGATGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAGAAGCAGGTCGAAGC
*
778 AATAAAGCGGTTAC
195 AATAAAACGGTTAC
* * * * *
792 CTTCCTGATGAGATACAGAGAAGTGAACTAGATCCTTCTTCTTGATGAGACACATAGAAGTGGAT
1 CTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
* * * *
857 CAAAACAAGTGATGCAGTCATCTTGCTGATGAGATATTGAGAAGTAGACCAAAT
66 CAAAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAAT
911 AAATAACACC
Statistics
Matches: 470, Mismatches: 61, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
208 138 0.29
209 330 0.70
210 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (208 bp):
CTTCCTGATGAGATACAAAGAAGTGAACCAGATCCGTCTTCCTGATGAGACACAGAGAAGTGGAT
CAAAACAAGAGATGCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAGCAA
AGCTCGATGTGAGTGAATCTTCGAACCCCAGCTTCCTAATGAGATACTAGAAGCAGGTCGAAGCA
ATAAAACGGTTAC
Done.