Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002640.1 Kokia drynarioides strain JFW-HI SEQ_114871, 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: 3941
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Found at i:145 original size:39 final size:38
Alignment explanation
Indices: 25--372 Score: 160
Period size: 39 Copynumber: 9.0 Consensus size: 38
15 ACTGATGATG
* * *
25 ATCTTCCCCAGGTTCGAGGCAAGAGATCGAATGGCTGTA
1 ATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTG-A
* * * *
64 ATCT-GCCCAGGCTCGGGGTAAGAGATTTGCTAAT-GATG-
1 ATCTACCCCAGGCTCGAGGTAAGAGA--T-CGAATGGCTGA
**
102 ATCTACCCCAAACTCGAGGTAAGAGATCGAATGGCTGCA
1 ATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTG-A
* * * *
141 ATCTACCCTAGGCTCGGGGTAAGAGATTTG-CTGG-TGA
1 ATCTACCCCAGGCTCGAGGTAAGAGA-TCGAATGGCTGA
* * *
178 TGATCTTCCCTAGGGTCG-GTGTAAGAGATCGAATGGCTGTA
1 --ATCTACCCCAGGCTCGAG-GTAAGAGATCGAATGGCTG-A
* * * * *
219 ATCTGCTCCAGGCTTGGGGTAAGAGATTTGCTG-AT-GATG-
1 ATCTACCCCAGGCTCGAGGTAAGAGA--T-C-GAATGGCTGA
* * *
258 ATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGCA
1 ATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTG-A
* * * * * * *
297 ATTTGCCCCCGGCTCGGGGTAAGAGATTTG-TTGGTTTTG-
1 ATCTACCCCAGGCTCGAGGTAAGAGA-TCGAATGG--CTGA
* *
336 ATCTACTCCACGCTCGAGGTAAGAGATCGAATGGCTG
1 ATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTG
373 CAATTTGCCC
Statistics
Matches: 236, Mismatches: 46, Indels: 56
0.70 0.14 0.17
Matches are distributed among these distances:
35 1 0.00
36 7 0.03
37 11 0.05
38 28 0.12
39 162 0.69
40 11 0.05
41 12 0.05
42 3 0.01
43 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.26
Consensus pattern (38 bp):
ATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGA
Found at i:202 original size:78 final size:77
Alignment explanation
Indices: 1--442 Score: 481
Period size: 78 Copynumber: 5.7 Consensus size: 77
* * * * *
1 GGGGTAAGAGATTTACTGATGATGATCTTCCCCAGGTTCGAGGCAAGAGATCGAATGGCTGTAAT
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGCAAT
66 CTGCCCAGGCTC
66 CTGCCCAGGCTC
* **
78 GGGGTAAGAGATTTGCTAATGATGATCTACCCCAAACTCGAGGTAAGAGATCGAATGGCTGCAAT
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGCAAT
*
143 CTACCCTAGGCTC
66 CTGCCC-AGGCTC
* * * * *
156 GGGGTAAGAGATTTGCTGGTGATGATCTTCCCTAGGGTCG-GTGTAAGAGATCGAATGGCTGTAA
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAG-GTAAGAGATCGAATGGCTGCAA
*
220 TCTGCTCCAGGCTT
65 TCTGC-CCAGGCTC
* * *
234 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGCAAT
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGCAAT
* *
299 TTGCCCCCGGCTC
66 CTG-CCCAGGCTC
* * ** * *
312 GGGGTAAGAGATTTGTTGGTTTTGATCTACTCCACGCTCGAGGTAAGAGATCGAATGGCTGCAAT
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGCAAT
* * *
377 TTGCCCTAAGCTT
66 CTGCCC-AGGCTC
* * * * * ** * * *
390 GGTGAAAGAGATTGGTTGATGATGATATGGCTCAAGCTCGGGGTAAGAGATCG
1 GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCG
443 GGATCTTCAA
Statistics
Matches: 305, Mismatches: 54, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
77 66 0.22
78 235 0.77
79 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (77 bp):
GGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGAGGTAAGAGATCGAATGGCTGCAAT
CTGCCCAGGCTC
Found at i:286 original size:156 final size:154
Alignment explanation
Indices: 1--442 Score: 535
Period size: 156 Copynumber: 2.8 Consensus size: 154
* * * *
1 GGGGTAAGAGATTTACTGATGATGATCTTCCCCAGGTTCGAGGCAAGAGATCGAATGGCTGTAAT
1 GGGGTAAGAGATTTGCTGGTGATGATCTT-CCCAGGCTCGAGGTAAGAGATCGAATGGCTGTAAT
* * * *
66 CTGCCCAGGCTCGGGGTAAGAGATTTGCTAATGATGATCTACCCCAAACTCGAGGTAAGAGATCG
65 CTGCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCGGGGTAAGAGATCG
*
131 AATGGCTGCAATCTACCCTAGGCTC
130 AATGGCTGCAATCTACCCCAGGCTC
*
156 GGGGTAAGAGATTTGCTGGTGATGATCTTCCCTAGGGTCG-GTGTAAGAGATCGAATGGCTGTAA
1 GGGGTAAGAGATTTGCTGGTGATGATCTTCCC-AGGCTCGAG-GTAAGAGATCGAATGGCTGTAA
*
220 TCTGCTCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGAT
64 TCTGC-CCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCGGGGTAAGAGAT
* * * * *
285 CGGATGGTTGCAATTTGCCCCCGGCTC
128 CGAATGGCTGCAATCTACCCCAGGCTC
* ** * * *
312 GGGGTAAGAGATTTGTTGGTTTTGATCTACTCCACGCTCGAGGTAAGAGATCGAATGGCTGCAAT
1 GGGGTAAGAGATTTGCTGGTGATGATCTTC-CCAGGCTCGAGGTAAGAGATCGAATGGCTGTAAT
* * * * * * * ** *
377 TTGCCCTAAGCTTGGTGAAAGAGATTGGTTGATGATGATATGGCTCAAGCTCGGGGTAAGAGATC
65 CTGCCC-AGGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCGGGGTAAGAGATC
442 G
129 G
443 GGATCTTCAA
Statistics
Matches: 248, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
154 4 0.02
155 61 0.25
156 180 0.73
157 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (154 bp):
GGGGTAAGAGATTTGCTGGTGATGATCTTCCCAGGCTCGAGGTAAGAGATCGAATGGCTGTAATC
TGCCCAGGCTTGGGGTAAGAGATTTGCTGATGATGATCTACCCCAAGCTCGGGGTAAGAGATCGA
ATGGCTGCAATCTACCCCAGGCTC
Done.