Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014568.1 Kokia drynarioides strain JFW-HI SEQ_129607, 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: 19424
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Found at i:1254 original size:37 final size:36
Alignment explanation
Indices: 1203--1278 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 36
1193 CTTTATCCTC
* *
1203 AAAATTTATTATGAATAAAAATTTGAAAAA-TATATTT
1 AAAATTTATCATGAATAAAAA-TT-AAAAAGTATATAT
1240 AAAATTTATCATGAATAAAAATTAAAAAGTATATAT
1 AAAATTTATCATGAATAAAAATTAAAAAGTATATAT
1276 AAA
1 AAA
1279 CTTGTAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 5 0.14
36 11 0.31
37 20 0.56
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (36 bp):
AAAATTTATCATGAATAAAAATTAAAAAGTATATAT
Found at i:10720 original size:15 final size:14
Alignment explanation
Indices: 10674--10721 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
10664 CAACTTCTCC
*
10674 GAAAATAAGATAAAA
1 GAAAAT-AGAAAAAA
**
10689 GAAAATCTAAAAAA
1 GAAAATAGAAAAAA
10703 GAAAATAGAAAGAAA
1 GAAAATAGAAA-AAA
10718 GAAA
1 GAAA
10722 CATGAATGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (14 bp):
GAAAATAGAAAAAA
Found at i:15248 original size:23 final size:23
Alignment explanation
Indices: 15222--15331 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 23
15212 TGCTAGGAAA
*
15222 CAGTAAGCACACACAGTGC-AAT
1 CAGTAGGCACACACAGTGCAAAT
15244 CCAGTAGGCACACACAGTGC-AAT
1 -CAGTAGGCACACACAGTGCAAAT
* * **
15267 CAGTAGGCGCACATAACGCAAAT
1 CAGTAGGCACACACAGTGCAAAT
15290 CAGTAGGCACACGA-AGTGCGAAA-
1 CAGTAGGCACAC-ACAGTGC-AAAT
*
15313 CAGTAAGCACACACAGTGC
1 CAGTAGGCACACACAGTGC
15332 TGAACAGTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
22 16 0.22
23 54 0.73
24 4 0.05
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.12
Consensus pattern (23 bp):
CAGTAGGCACACACAGTGCAAAT
Found at i:15337 original size:23 final size:22
Alignment explanation
Indices: 15195--15341 Score: 95
Period size: 23 Copynumber: 6.4 Consensus size: 22
15185 CGAAGCACTT
15195 AACAGTAAGCACACA-AGTGCTAGG
1 AACAGTAAGCACACACAGTGC---G
15219 AAACAGTAAGCACACACAGTGC-
1 -AACAGTAAGCACACACAGTGCG
*
15241 AATCCAGTAGGCACACACAGTGC-
1 AA--CAGTAAGCACACACAGTGCG
* * * ** *
15264 AATCAGTAGGCGCACATAACGCA
1 AA-CAGTAAGCACACACAGTGCG
*
15287 AATCAGTAGGCACACGA-AGTGCG
1 AA-CAGTAAGCACAC-ACAGTGCG
15310 AAACAGTAAGCACACACAGTGCTG
1 -AACAGTAAGCACACACAGTGC-G
15334 AACAGTAA
1 AACAGTAA
15342 ACGCGCTAGC
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.02
22 16 0.16
23 61 0.59
24 4 0.04
25 15 0.15
26 5 0.05
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.12
Consensus pattern (22 bp):
AACAGTAAGCACACACAGTGCG
Found at i:15444 original size:24 final size:26
Alignment explanation
Indices: 15406--15453 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
15396 TCTACATGGG
15406 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
15432 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
15454 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.