Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003644.1 Kokia drynarioides strain JFW-HI SEQ_116544, 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, 646
Length: 1078
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Found at i:502 original size:124 final size:124
Alignment explanation
Indices: 277--549 Score: 402
Period size: 124 Copynumber: 2.2 Consensus size: 124
267 GATGCAGTCA
*
277 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAGTGAAACT
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAGTGAAACC
* * * * * *
342 TCGAACCCCCATCTTCTTAATGATATACTAAGAAGTGCGTCAAAGTAATAAAACGGTCG
66 TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
* *
401 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGAAACC
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAGTGAAACC
* * * * * *
466 TCAAACCCCTATCTTCCTGATAAGATACTAATAAGTGGGTCAAAGCAATAAAGCGATTG
66 TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
*
525 TCTTCCTGATAAGATACAGAGAAGT
1 TCTTCCTGATGAGATACAGAGAAGT
550 GGATTAAATA
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
124 133 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (124 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATATGAGTGAAACC
TCAAACCCCCATCTTCCTAATAAGATACTAAGAAGTGCGTCAAAGCAATAAAACGATCG
Found at i:564 original size:37 final size:37
Alignment explanation
Indices: 523--594 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
513 ATAAAGCGAT
523 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
1 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
*
560 TGTCTTCCTGATGAGATACAGAGAAGTGGATTAAA
1 TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAA
595 ATAAGTGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (37 bp):
TGTCTTCCTGATAAGATACAGAGAAGTGGATTAAATA
Found at i:617 original size:210 final size:208
Alignment explanation
Indices: 395--1078 Score: 1008
Period size: 210 Copynumber: 3.3 Consensus size: 208
385 AGTAATAAAA
*
395 CGGTCGTCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * * * *
460 GAAACCTCAAACCCCTATCTTCCTGATAAGATACTAATAAGTGGGTCAAAGCAATAAAGCGATTG
66 GAAACTTCGAACCCC-ATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
* **
525 TCTTCCTGATAAGATACAGAGAAGTGGATTAAATATGTCTTCCTGATGAGATACAGAGAAGTGGA
130 TCTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TGTCTTCCTGATGAGATACAGAGAAGTGGA
* * *
590 TTAAAATAAGTGATG
194 TTAAAACAAATGAGG
*
605 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTGATGAAGCGAAGCTCAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * * *
670 GAAACTTCGAACACCCATCTTCTTGATGAGATACTAAGAAGTGGGTCAAAGCCATAAAACGATCA
66 GAAACTTCGAAC-CCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
*
735 TCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACGGAGAAGTGGA
130 TCTTCCTGATGAGATACAGAGAAGTGGACCAAATT-GTCTTCCTGATGAGATACAGAGAAGTGGA
800 TTAAAACAAATGAGG
194 TTAAAACAAATGAGG
* *
815 CGGTCATCTTCCTGATGAGATAGAGAGAAGTAGACCAAATCGATGAAGCGAAGCTAAATGTGAGT
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
* * * * *
880 GAAACTTTGAACCCCCATCTTTCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAGTGGTCG
66 GAAACTTCGAA-CCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCG
* * * * *
945 TCTTCCTGATGAGATATAAAGAAGTGGACCAAATCTGTCTTCCCGATGAGATACAAAAAAGTGGA
130 TCTTCCTGATGAGATACAGAGAAGTGGACCAAAT-TGTCTTCCTGATGAGATACAGAGAAGTGGA
*
1010 TTTTAAACAAATGAGG
194 -TTAAAACAAATGAGG
* *
1026 CGGTCATCTTCCTGATGAGATAGAAAGAAGTAGACCAAATCGATGAAGCGAAG
1 CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAG
Statistics
Matches: 431, Mismatches: 38, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
209 1 0.00
210 359 0.83
211 71 0.16
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (208 bp):
CGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGT
GAAACTTCGAACCCCATCTTCCTGATGAGATACTAAGAAGTGGGTCAAAGCAATAAAGCGATCGT
CTTCCTGATGAGATACAGAGAAGTGGACCAAATTGTCTTCCTGATGAGATACAGAGAAGTGGATT
AAAACAAATGAGG
Found at i:676 original size:334 final size:332
Alignment explanation
Indices: 65--768 Score: 1077
Period size: 334 Copynumber: 2.1 Consensus size: 332
55 AAATGAAGCA
* * * *
65 ATCATCTTCCTAATGAGATACAGAGAAGTAAACCAAATCAATTAAGCGAAACTCAATACGATGAG
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATACGATGAA
* *
130 ATTCCAAACCCCATCTTCCTGATCAGATACTAATAAGTGGATCAAAGCAATAAAGCGATCGTCTT
66 ACTCCAAACCCCATCTTCCTGATAAGATACTAATAAGTGGATCAAAGCAATAAAGCGATCGTCTT
* * *
195 CCTGATGAGATACAGAGAAGTGGACCAAATTTGTATTCCTGATGAGATATAGAGAAGCGGATTAA
131 CCTGATAAGATACAGAGAAGTGGACCAAATATGTATTCCTGATGAGATACAGAGAAGCGGATTAA
260 AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGC
196 AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGC
* * *
325 TCAATATGAGTGAAACTTCGAACCCCCATCTTCTTAATGATATACTAAGAAGTGCGTCAAAGTAA
261 TCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAGCAA
390 TAAAACG
326 TAAAACG
* * * * **
397 GTCGTCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTGA
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATACGA-TGA
* *
462 AAC-CTCAAACCCCTATCTTCCTGATAAGATACTAATAAGTGGGTCAAAGCAATAAAGCGATTGT
65 AACTC-CAAACCCC-ATCTTCCTGATAAGATACTAATAAGTGGATCAAAGCAATAAAGCGATCGT
** * *
526 CTTCCTGATAAGATACAGAGAAGTGGATTAAATATGTCTTCCTGATGAGATACAGAGAAGTGGAT
128 CTTCCTGATAAGATACAGAGAAGTGGACCAAATATGTATTCCTGATGAGATACAGAGAAGCGGAT
* * **
591 TAAAATAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATTGATGAAGCGA
193 TAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGA
* * *
656 AGCTCAATGTGAGTGAAACTTCGAACACCCATCTTCTTGATGAGATACTAAGAAGTGGGTCAAAG
258 AGCTCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAG
*
721 CCATAAAACG
323 CAATAAAACG
*
731 ATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAT
1 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAT
769 TCGTCTTCCT
Statistics
Matches: 334, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
332 53 0.16
333 12 0.04
334 269 0.81
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (332 bp):
ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATACGATGAA
ACTCCAAACCCCATCTTCCTGATAAGATACTAATAAGTGGATCAAAGCAATAAAGCGATCGTCTT
CCTGATAAGATACAGAGAAGTGGACCAAATATGTATTCCTGATGAGATACAGAGAAGCGGATTAA
AACAAGTGATGCAGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGC
TCAATATGAGTGAAACTTCGAACACCCATCTTCTTAATGAGATACTAAGAAGTGCGTCAAAGCAA
TAAAACG
Done.