Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013942.1 Kokia drynarioides strain JFW-HI SEQ_128972, 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: 17139
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:3624 original size:21 final size:21
Alignment explanation
Indices: 3598--3648 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3588 GGAGTTTTTG
**
3598 GTATCGGTAGTTA-CATGACTT
1 GTATCGGTAGAAATCAT-ACTT
3619 GTATCGGTAGAAATCATACTT
1 GTATCGGTAGAAATCATACTT
3640 GTATCGGTA
1 GTATCGGTA
3649 AAACTAGCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAATCATACTT
Found at i:6019 original size:20 final size:20
Alignment explanation
Indices: 5994--6045 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
5984 CTGTGTGCCT
*
5994 AGCCCGTGTGGCATGGGTGC
1 AGCCCGTGTGGCATGGGAGC
6014 AGCCCGTGTGGCATGGGAGC
1 AGCCCGTGTGGCATGGGAGC
*
6034 AGCCCATGTGGC
1 AGCCCGTGTGGC
6046 CCTGTACCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.27, G:0.42, T:0.17
Consensus pattern (20 bp):
AGCCCGTGTGGCATGGGAGC
Found at i:10257 original size:21 final size:21
Alignment explanation
Indices: 10233--10283 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
10223 ACAGTGCAGA
* * *
10233 CTTCTACTGATACAAGTGAAG
1 CTTCTACTGAAACAAATCAAG
*
10254 CTTCTACTGAAACAAATCATG
1 CTTCTACTGAAACAAATCAAG
10275 CTTCTACTG
1 CTTCTACTG
10284 GTACTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (21 bp):
CTTCTACTGAAACAAATCAAG
Found at i:11009 original size:35 final size:35
Alignment explanation
Indices: 10946--11039 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 35
10936 TCATGCTTAT
*
10946 TCCCTGTTGACCCAAAGGTCATGATGCTCATTCCAC
1 TCCCTGTTGA-CCAAAGATCATGATGCTCATTCCAC
* **
10982 TCCCTGTTGACTAAAGATCATGATGCTCATTTTAC
1 TCCCTGTTGACCAAAGATCATGATGCTCATTCCAC
*
11017 TCCCTGTTGACCCAAAGGTCATG
1 TCCCTGTTGA-CCAAAGATCATG
11040 CCTATTACCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 31 0.61
36 20 0.39
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (35 bp):
TCCCTGTTGACCAAAGATCATGATGCTCATTCCAC
Found at i:13659 original size:29 final size:29
Alignment explanation
Indices: 13626--13689 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
13616 TTAATAACAC
* *
13626 AATAAAAATATAATTATAGTATTAAAT-AA
1 AATAAAAATATAATCATAGTAAT-AATGAA
*
13655 AATAATAATATAATCATAGTAATAATGAA
1 AATAAAAATATAATCATAGTAATAATGAA
13684 AATAAA
1 AATAAA
13690 TATTAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (29 bp):
AATAAAAATATAATCATAGTAATAATGAA
Found at i:14322 original size:11 final size:11
Alignment explanation
Indices: 14306--14331 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14296 TGTTAGTTTC
14306 AAAAGAAGAAA
1 AAAAGAAGAAA
14317 AAAAGAAGAAA
1 AAAAGAAGAAA
14328 AAAA
1 AAAA
14332 ATACAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Done.