Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011226.1 Kokia drynarioides strain JFW-HI SEQ_126204, 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: 23219
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:4161 original size:66 final size:65
Alignment explanation
Indices: 4055--4218 Score: 256
Period size: 66 Copynumber: 2.5 Consensus size: 65
4045 TCAACATAAG
* * * *
4055 TGATTGGAACATCTATCAAGGCAGCTTCATCAATGATTGGAACATTTATCGCGGCAGCTTTATCA
1 TGATTGGAACATCTCT-AGGGCAGCTTCATCAATGATTGGAACATCTATCGCGGCAGCTTCATCA
4120 T
65 T
*
4121 TGATTGGAACATCTCTAGGGCCAGCTTCATCAATGATTGGAACATCTATCGCGGTAGCTTCATCA
1 TGATTGGAACATCTCTAGGG-CAGCTTCATCAATGATTGGAACATCTATCGCGGCAGCTTCATCA
4186 T
65 T
4187 TGATTGGAACATCTCTAGGGGCAGCTTCATCA
1 TGATTGGAACATCTCTA-GGGCAGCTTCATCA
4219 TTTTGTTCGA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
65 3 0.03
66 85 0.93
67 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (65 bp):
TGATTGGAACATCTCTAGGGCAGCTTCATCAATGATTGGAACATCTATCGCGGCAGCTTCATCAT
Found at i:4219 original size:33 final size:33
Alignment explanation
Indices: 4055--4220 Score: 201
Period size: 33 Copynumber: 5.0 Consensus size: 33
4045 TCAACATAAG
* *
4055 TGATTGGAACATCTATCA-AGGCAGCTTCATCAA
1 TGATTGGAACATCTAT-AGCGGCAGCTTCATCAT
* * *
4088 TGATTGGAACATTTATCGCGGCAGCTTTATCAT
1 TGATTGGAACATCTATAGCGGCAGCTTCATCAT
* *
4121 TGATTGGAACATCTCTAG-GGCCAGCTTCATCAA
1 TGATTGGAACATCTATAGCGG-CAGCTTCATCAT
* *
4154 TGATTGGAACATCTATCGCGGTAGCTTCATCAT
1 TGATTGGAACATCTATAGCGGCAGCTTCATCAT
* *
4187 TGATTGGAACATCTCTAGGGGCAGCTTCATCAT
1 TGATTGGAACATCTATAGCGGCAGCTTCATCAT
4220 T
1 T
4221 TTGTTCGACT
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
32 2 0.02
33 108 0.96
34 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (33 bp):
TGATTGGAACATCTATAGCGGCAGCTTCATCAT
Found at i:6972 original size:23 final size:23
Alignment explanation
Indices: 6937--6982 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6927 TGTTTTCATC
* *
6937 TTGGATGTTGATGTATCTTGATT
1 TTGGATATGGATGTATCTTGATT
* *
6960 TTGGATATGGATGTGTTTTGATT
1 TTGGATATGGATGTATCTTGATT
6983 GCCAAAGCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (23 bp):
TTGGATATGGATGTATCTTGATT
Found at i:12496 original size:39 final size:40
Alignment explanation
Indices: 12443--12522 Score: 101
Period size: 39 Copynumber: 2.0 Consensus size: 40
12433 AAGAGGTATG
* *
12443 TCCAATATGAAAAGGATTAG-GACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATT-GTGACTCTTCAAAACGTGTCCA
* *
12483 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAACGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAACGTGTCCA
12522 T
1 T
12523 TAAGTGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 1 0.03
39 26 0.74
40 8 0.23
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAACGTGTCCA
Found at i:17423 original size:39 final size:39
Alignment explanation
Indices: 17379--17462 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
17369 TGGGACAAGT
*
17379 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * * *
17418 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGGTTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
17457 CTCTTC
1 CTCTTC
17463 AAAAGGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:17463 original size:39 final size:40
Alignment explanation
Indices: 17396--17475 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
17386 AAGAGGTATG
*
17396 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* *
17436 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
17475 T
1 T
17476 TAAGTGCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Done.