Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001856.1 Kokia drynarioides strain JFW-HI SEQ_113613, 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, 1000
Length: 1801
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Found at i:337 original size:85 final size:85
Alignment explanation
Indices: 189--345 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
179 CAAACCCCAT
* * *
189 CTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGGTCATATTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCATATTCCAGATGAGATACA
254 GAGAAGTGGAGCAAATTTGC
66 GAGAAGTGGAGCAAATTTGC
** * * * * *
274 CTTCCTGATGAGATACAGAGAAGTGGATTGAATCTATGAAGCGGTCATCCTT-CAGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCAT-ATTCCAGATGAGATAC
338 AGAGAAGT
65 AGAGAAGT
346 AAACTGAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 59 0.97
86 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGAGGTCATATTCCAGATGAGATACA
GAGAAGTGGAGCAAATTTGC
Found at i:381 original size:208 final size:208
Alignment explanation
Indices: 1--468 Score: 661
Period size: 208 Copynumber: 2.2 Consensus size: 208
* * ** *
1 AAGTGGGTCAAAGAAATAAAGTGACCATCTTCCTAATGAGATACAGAGAAGTGGATCAAATCTGC
1 AAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAAGTGGAGCAAATCTGC
*
66 CTTCCTGATGAGATACAGAGAAGTGAATTAAATTAATGAAGAGGTCATCTTCCTGATGAGATACA
66 CTTCCTGATGAGATACAGAGAAGTGAATTAAATTAATGAAGAGGTCATCTTCCAGATGAGATACA
* * * * * * *
131 TAGAAGTAGACCAAATCAATGAAGCAAAGCTCAATTCGAATGAGACTTCAAACCCCATCTTCTTG
131 GAGAAGTAAACCAAATAAATGAAACAAAGCTAAATACGAATGAGACTTCAAACCCCATCTTCCTG
*
196 ATGAGATACAGAG
196 ATGAGATAAAGAG
* * *
209 AAGTGGGTCAAAGCAATAAAGAGGTCATATTCCTGATGAGATACAGAGAAGTGGAGCAAATTTGC
1 AAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAAGTGGAGCAAATCTGC
* * *
274 CTTCCTGATGAGATACAGAGAAGTGGATTGAATCT-ATGAAGCGGTCATCCTT-CAGATGAGATA
66 CTTCCTGATGAGATACAGAGAAGTGAATTAAAT-TAATGAAGAGGTCAT-CTTCCAGATGAGATA
** ** * *
337 CAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGATTTTAAACCCCATCTTCC
129 CAGAGAAGTAAACCAAATAAATGAAACAAAGCTAAATACGAATGAGACTTCAAACCCCATCTTCC
402 TGATGAGATAAAGAG
194 TGATGAGATAAAGAG
*
417 AAGTGGGCCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAAGT
1 AAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAAGT
469 ACACAAAATC
Statistics
Matches: 229, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
208 225 0.98
209 4 0.02
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (208 bp):
AAGTGGGTCAAAGCAATAAAGAGGTCATCTTCCTAATGAGATACAGAGAAGTGGAGCAAATCTGC
CTTCCTGATGAGATACAGAGAAGTGAATTAAATTAATGAAGAGGTCATCTTCCAGATGAGATACA
GAGAAGTAAACCAAATAAATGAAACAAAGCTAAATACGAATGAGACTTCAAACCCCATCTTCCTG
ATGAGATAAAGAG
Found at i:498 original size:123 final size:124
Alignment explanation
Indices: 329--592 Score: 298
Period size: 124 Copynumber: 2.1 Consensus size: 124
319 CATCCTTCAG
** ** * * *
329 ATGAGATACAGAGAAGTAAACTGAATAAATGAAATGAAGCTAAATACGAATGAGATTTTAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
*
394 C-ATCTTCCTGATGAGATAAAGAGAAGTGGGCCA-AAGCAATAAAGAGGTCATCTTCCTA
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGG-CAGAAGCAATAAAGAGATCATCTTCCTA
* * * * * *
452 ATGAGATACAGAGAAGTACACAAAATCAATGAAGCAAAGTTCAATACGAGTGAAACTTCAAACCC
1 ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
* * * * * ** *
517 CTATTTTCTTGATGAGATACAGAGAAGTGGGTAGAAGTAATAAATTGATCATCTTCCTG
66 CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCATCTTCCTA
*
576 ATGAGATACAGGGAAGT
1 ATGAGATACAGAGAAGT
593 GGACCAAGAG
Statistics
Matches: 116, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
123 54 0.47
124 62 0.53
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (124 bp):
ATGAGATACAGAGAAGTAAACAAAATAAATGAAACAAAGCTAAATACGAATGAAACTTCAAACCC
CTATCTTCCTGATGAGATAAAGAGAAGTGGGCAGAAGCAATAAAGAGATCATCTTCCTA
Found at i:1107 original size:27 final size:27
Alignment explanation
Indices: 1076--1135 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1066 CCAAATTACA
* * *
1076 AAACCCAATACCACTAAGCC-AAACACT
1 AAACCCAAAACCACAAACCCTAAA-ACT
1103 AAACCCAAAACCACAAACCCTAAAACT
1 AAACCCAAAACCACAAACCCTAAAACT
1130 AAACCC
1 AAACCC
1136 TGACCCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.52, C:0.38, G:0.02, T:0.08
Consensus pattern (27 bp):
AAACCCAAAACCACAAACCCTAAAACT
Done.