Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014792.1 Kokia drynarioides strain JFW-HI SEQ_129834, 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: 8943
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:4647 original size:13 final size:13
Alignment explanation
Indices: 4631--4684 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
4621 TATTTTTTGG
4631 AAGTGTTTTTAAA
1 AAGTGTTTTTAAA
*
4644 AAGTGCTTTGTAAA
1 AAGTG-TTTTTAAA
* *
4658 AA-TGATTTTGAA
1 AAGTGTTTTTAAA
*
4670 AAGTATTTTTAAA
1 AAGTGTTTTTAAA
4683 AA
1 AA
4685 ATGTGGTTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 7 0.22
13 16 0.50
14 9 0.28
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.41
Consensus pattern (13 bp):
AAGTGTTTTTAAA
Found at i:4887 original size:30 final size:32
Alignment explanation
Indices: 4831--4890 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
4821 TTTTATAAGA
*
4831 ATATAAAAAATAATTTATTGATAATATTTTAT
1 ATATAAAAAATAAATTATTGATAATATTTTAT
4863 ATATGAAAAAATAAATT-TT-A-AATATTTT
1 ATAT-AAAAAATAAATTATTGATAATATTTT
4891 TTAAGCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
31 1 0.04
32 6 0.23
33 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
ATATAAAAAATAAATTATTGATAATATTTTAT
Found at i:5085 original size:18 final size:19
Alignment explanation
Indices: 5062--5097 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5052 TTTAACATTC
5062 TTTTTTAAT-TCAAAAGTA
1 TTTTTTAATGTCAAAAGTA
*
5080 TTTTTTTATGTCAAAAGT
1 TTTTTTAATGTCAAAAGT
5098 GCTTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTTTAATGTCAAAAGTA
Found at i:5103 original size:19 final size:19
Alignment explanation
Indices: 5061--5103 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5051 ATTTAACATT
5061 CTTTTTTAATTCAAAAGTA
1 CTTTTTTAATTCAAAAGTA
* *
5080 -TTTTTTTATGTCAAAAGTG
1 CTTTTTTAAT-TCAAAAGTA
5099 CTTTT
1 CTTTT
5104 GAAAAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (19 bp):
CTTTTTTAATTCAAAAGTA
Found at i:5375 original size:15 final size:16
Alignment explanation
Indices: 5355--5389 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5345 AAGCTTTTTG
*
5355 TTATTTTT-TATATTT
1 TTATTTTTAAATATTT
5370 TTATTTTTAAATATTT
1 TTATTTTTAAATATTT
5386 TTAT
1 TTAT
5390 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTTAAATATTT
Found at i:6935 original size:2 final size:2
Alignment explanation
Indices: 6928--6952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6918 CATTTCTAGA
6928 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6953 AGGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7068 original size:24 final size:23
Alignment explanation
Indices: 7019--7069 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
7009 TTTTTAAAAA
* *
7019 TTTTCAATTTTTAAAATTAATAT
1 TTTTCAATTTCTAAAATTAAGAT
* *
7042 TTTTCAATTTCTAGACATTAAGGT
1 TTTTCAATTTCTA-AAATTAAGAT
7066 TTTT
1 TTTT
7070 TTAAGTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (23 bp):
TTTTCAATTTCTAAAATTAAGAT
Found at i:7326 original size:2 final size:2
Alignment explanation
Indices: 7319--7352 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7309 CTTTTATAGA
7319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7353 TTTTAACAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.