Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000929.1 Kokia drynarioides strain JFW-HI SEQ_112080, 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: 32300
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2666 original size:12 final size:12
Alignment explanation
Indices: 2639--2689 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2629 ATTTTTACTA
* *
2639 TTTTGGTATTGC
1 TTTTGCTATTGT
*
2651 TTTTGCTGTTGT
1 TTTTGCTATTGT
*
2663 TTTTGTTATTG-
1 TTTTGCTATTGT
*
2674 TTTTGCTATTAT
1 TTTTGCTATTGT
2686 TTTT
1 TTTT
2690 ATAGCTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
11 9 0.29
12 22 0.71
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (12 bp):
TTTTGCTATTGT
Found at i:2688 original size:23 final size:24
Alignment explanation
Indices: 2639--2689 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2629 ATTTTTACTA
* *
2639 TTTTGGTATTGCTTTTGCTGTTGT
1 TTTTGGTATTGCTTTTGCTATTAT
*
2663 TTTTGTTATTG-TTTTGCTATTAT
1 TTTTGGTATTGCTTTTGCTATTAT
2686 TTTT
1 TTTT
2690 ATAGCTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (24 bp):
TTTTGGTATTGCTTTTGCTATTAT
Found at i:2903 original size:21 final size:21
Alignment explanation
Indices: 2861--2904 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2851 ATTTGTTTAT
* *
2861 TTTTTAATGTTTATTTTAATA
1 TTTTTAATGTGTATTTGAATA
2882 TTTTTAA-GTGTATTTGACATA
1 TTTTTAATGTGTATTTGA-ATA
2903 TT
1 TT
2905 ATATATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTTTAATGTGTATTTGAATA
Found at i:10060 original size:21 final size:23
Alignment explanation
Indices: 10036--10089 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
10026 CTTGCAACTT
*
10036 CTACCGATATAAGTAT-TCA-AA
1 CTACCGATATAACTATATCAGAA
*
10057 CTACAGATATAACTATGATCAGAA
1 CTACCGATATAACTAT-ATCAGAA
10081 CTACCGATA
1 CTACCGATA
10090 CTTTAGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.52
23 3 0.11
24 10 0.37
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (23 bp):
CTACCGATATAACTATATCAGAA
Found at i:10711 original size:25 final size:26
Alignment explanation
Indices: 10674--10724 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
10664 TTCGGTCTTC
10674 CAGAATTTAGCTCATACGAGCCCAAA
1 CAGAATTTAGCTCATACGAGCCCAAA
* *
10700 CAGAA-TTAGCTCTTGCGAGCCCAAA
1 CAGAATTTAGCTCATACGAGCCCAAA
10725 AAGGTTAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (26 bp):
CAGAATTTAGCTCATACGAGCCCAAA
Found at i:14307 original size:18 final size:19
Alignment explanation
Indices: 14276--14313 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
14266 AAAAATATTT
**
14276 AATTATATTTATTT-TAAA
1 AATTATATAAATTTATAAA
14294 AATTATATAAATTTATAAA
1 AATTATATAAATTTATAAA
14313 A
1 A
14314 GAAAGAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTATATAAATTTATAAA
Found at i:14577 original size:26 final size:26
Alignment explanation
Indices: 14541--14599 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
14531 TCCTTCTCTG
14541 CTTCTTTCTTCTTCTGAATATTTTGC
1 CTTCTTTCTTCTTCTGAATATTTTGC
14567 CTTCTTTCTTCTTCTGAATATTTTGC
1 CTTCTTTCTTCTTCTGAATATTTTGC
14593 CTTCTTT
1 CTTCTTT
14600 TGATTGCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.10, C:0.24, G:0.07, T:0.59
Consensus pattern (26 bp):
CTTCTTTCTTCTTCTGAATATTTTGC
Found at i:32158 original size:25 final size:23
Alignment explanation
Indices: 32101--32253 Score: 146
Period size: 23 Copynumber: 6.5 Consensus size: 23
32091 TATACGGAAC
*
32101 AAACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
32123 GGGCAACAGAGAGCACACACGGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* * * *
32149 AAACAAAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* *
32172 AATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
32195 AATCAGAGAGCACACACAGTGTT
1 AAACAGAGAGCACACACAGTGCT
32218 AATAACAGAGAGCACACACAGTGCT
1 -A-AACAGAGAGCACACACAGTGCT
*
32243 AATCAGAGAGC
1 AAACAGAGAGC
32254 GCGCTAGTGT
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
23 66 0.62
24 2 0.02
25 34 0.32
26 5 0.05
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:32231 original size:48 final size:48
Alignment explanation
Indices: 32127--32253 Score: 168
Period size: 46 Copynumber: 2.7 Consensus size: 48
32117 AGTGCTGGGC
* * * *
32127 AACAGAGAGCACACACGGTGCTAAACAAAGAGTACACAAAGTACTAAT
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTACTAAT
* * **
32175 --CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAGTGTTAAT
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTACTAAT
32221 AACAGAGAGCACACACAGTGCTAATCAGAGAGC
1 AACAGAGAGCACACACAGTGCTAATCAGAGAGC
32254 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
46 38 0.56
48 30 0.44
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (48 bp):
AACAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTACTAAT
Done.