Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003440.1 Kokia drynarioides strain JFW-HI SEQ_116224, 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: 9941
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:261 original size:23 final size:23
Alignment explanation
Indices: 144--262 Score: 132
Period size: 23 Copynumber: 5.1 Consensus size: 23
134 TAGGGTGCTA
*
144 TTTAGCA-TGTCTCGTGCTCTCTG
1 TTTAGCACTGTGT-GTGCTCTCTG
*
167 TTATTAGCACTGTGTTTGCTCTCTG
1 -T-TTAGCACTGTGTGTGCTCTCTG
* *
192 ATTAGCACTTTGTGTGCTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
* * * *
215 CTTAGTACTTTGTGTACTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
238 TTTAGCACTGTGTGTGCTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
261 TT
1 TT
263 GCCTAGCACC
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
23 61 0.75
24 1 0.01
25 15 0.19
26 4 0.05
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTAGCACTGTGTGTGCTCTCTG
Found at i:303 original size:69 final size:69
Alignment explanation
Indices: 160--309 Score: 171
Period size: 69 Copynumber: 2.1 Consensus size: 69
150 ATGTCTCGTG
* * *
160 CTCTCTGTTATTAGCACTGTGTTTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGCTTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAGCACTCTATGTGCTCTCTGCTTAGTACTT
*
225 TGTGTA
64 TGTGCA
* *
231 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGTTGCCTAGCAC-CTATGTGCTCTTTG-TTAGTACT
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGAT---TAGCACTCTATGTGCTCTCTGCTTAGTACT
294 TTG-GCA
63 TTGTGCA
*
300 CTCTTTGTTT
1 CTCTCTGTTT
310 GTTCCGTATA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
69 33 0.48
70 12 0.17
71 18 0.26
72 6 0.09
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACTCTATGTGCTCTCTGCTTAGTACTTTG
TGCA
Found at i:3587 original size:13 final size:13
Alignment explanation
Indices: 3569--3594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3559 TTGAGCAGAA
3569 AGTCAATGACAGC
1 AGTCAATGACAGC
3582 AGTCAATGACAGC
1 AGTCAATGACAGC
3595 CTTAAAGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
AGTCAATGACAGC
Found at i:5437 original size:16 final size:16
Alignment explanation
Indices: 5416--5452 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
5406 AAATTTTACC
5416 ATTTTTATTAAGTGAG
1 ATTTTTATTAAGTGAG
5432 A-TTTT-TTAAGTGAG
1 ATTTTTATTAAGTGAG
5446 ATTTTTA
1 ATTTTTA
5453 GAGAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.53
15 8 0.42
16 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (16 bp):
ATTTTTATTAAGTGAG
Found at i:6894 original size:23 final size:23
Alignment explanation
Indices: 6770--6896 Score: 159
Period size: 23 Copynumber: 5.4 Consensus size: 23
6760 ACACTAGCGC
* *
6770 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
*
6793 GCTCTCTATTATTAGCACTTTGTGT
1 GCTCTCT-GT-TTAGCACTTTGTGT
6818 GCTCTCT-TATTAGCACTTTGTGT
1 GCTCTCTGT-TTAGCACTTTGTGT
*
6841 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
6864 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
6887 GCTCTCTGTT
1 GCTCTCTGTT
6897 GCCAGTACCT
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
23 75 0.80
24 3 0.03
25 16 0.17
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:8784 original size:22 final size:23
Alignment explanation
Indices: 8734--8790 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
8724 CTAGGGAAAT
*
8734 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAGTGCAATCC
8757 AGTAGGCACACACAGTGCAAT-C
1 AGTAGGCACACACAGTGCAATCC
*
8779 AGTAGGCGCACA
1 AGTAGGCACACA
8791 TAACGCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.37, C:0.28, G:0.23, T:0.12
Consensus pattern (23 bp):
AGTAGGCACACACAGTGCAATCC
Found at i:8798 original size:22 final size:22
Alignment explanation
Indices: 8734--8812 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
8724 CTAGGGAAAT
* **
8734 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACACAACGCAAT-C
**
8757 AGTAGGCACACACAGTGCAATC
1 AGTAGGCACACACAACGCAATC
* *
8779 AGTAGGCGCACATAACGCAATTC
1 AGTAGGCACACACAACGCAA-TC
*
8802 AGTAAGCACAC
1 AGTAGGCACAC
8813 GAGGTGCTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.35
23 31 0.65
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (22 bp):
AGTAGGCACACACAACGCAATC
Found at i:8827 original size:23 final size:23
Alignment explanation
Indices: 8801--8854 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
8791 TAACGCAATT
8801 CAGTAAGCACACGA-GGTGCTGAA
1 CAGTAAGCACAC-ACGGTGCTGAA
*
8824 CAGTAAGCACACACTGTGCTGAA
1 CAGTAAGCACACACGGTGCTGAA
8847 CAGTAAGC
1 CAGTAAGC
8855 GCGCTAGCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (23 bp):
CAGTAAGCACACACGGTGCTGAA
Done.