Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000774.1 Kokia drynarioides strain JFW-HI SEQ_111830, 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: 72724
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:4703 original size:2 final size:2
Alignment explanation
Indices: 4696--4733 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4686 TGTATCCAGG
4696 AT AT 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 AT AT
4734 GAACAGTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7073 original size:3 final size:3
Alignment explanation
Indices: 7065--7097 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
7055 ATGAATGGCC
7065 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
7098 GTTGCCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:17376 original size:19 final size:19
Alignment explanation
Indices: 17339--17376 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17329 ATCTTACCCA
*
17339 GAAAAATAAAGAAATAAAG
1 GAAAAATAAAGAAAGAAAG
*
17358 GAAAAATAAAGATAGAAAG
1 GAAAAATAAAGAAAGAAAG
17377 CGGACGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (19 bp):
GAAAAATAAAGAAAGAAAG
Found at i:19308 original size:20 final size:18
Alignment explanation
Indices: 19280--19334 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
19270 AAACAAGTAT
19280 AAATAATTTATTAATATATTA
1 AAAT-ATTTA-TAATA-ATTA
19301 AAATATTTATAATAATTTA
1 AAATATTTATAATAA-TTA
*
19320 AATATAATTATAATA
1 AA-ATATTTATAATA
19335 CAAAAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 1 0.03
19 10 0.32
20 16 0.52
21 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTTATAATAATTA
Found at i:26750 original size:197 final size:198
Alignment explanation
Indices: 26415--26811 Score: 778
Period size: 197 Copynumber: 2.0 Consensus size: 198
26405 GTAAAATCTG
*
26415 CATCATTATGGCGGATGCTTGAATAGGAAATATTGTACTAGGAAAAAAATCTAGAGCGAATATTT
1 CATCATTATGACGGATGCTTGAATAGGAAATATTGTACTAGGAAAAAAATCTAGAGCGAATATTT
26480 TGGGCAGTTATTTTATCTTTATCAACATTCTCTTCATTAAAAAATGGGGGCAACTAGATGCTGTA
66 TGGGCAGTTATTTTATCTTTATCAACATTCTCTTCATTAAAAAATGGGGGCAACTAGATGCTGTA
26545 AGTTAGCAAATCTCATTTTGTAG-GTTTATTCTAGATATTATATAAATTCTTAAAGGCATAACTG
131 AGTTAGCAAATCTCATTTTGTAGTGTTTATTCTAGATATTATATAAATTCTTAAAGGCATAACTG
26609 CTT
196 CTT
26612 CATCATTATGACGGATGCTTGAATAGGAAATATTGTACTAGGAAAAAAATCTAGAGCGAATATTT
1 CATCATTATGACGGATGCTTGAATAGGAAATATTGTACTAGGAAAAAAATCTAGAGCGAATATTT
26677 TGGGCAGTTATTTTATCTTTATCAACATTCTCTTCATTAAAAAATGGGGGCAACTAGATGCTGTA
66 TGGGCAGTTATTTTATCTTTATCAACATTCTCTTCATTAAAAAATGGGGGCAACTAGATGCTGTA
26742 AGTTAGCAAATCTCATTTTGTAGTGTTTATTCTAGATATTATATAAATTCTTAAAGGCATAACTG
131 AGTTAGCAAATCTCATTTTGTAGTGTTTATTCTAGATATTATATAAATTCTTAAAGGCATAACTG
26807 CTT
196 CTT
26810 CA
1 CA
26812 GCTTGCAATG
Statistics
Matches: 198, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
197 152 0.77
198 46 0.23
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (198 bp):
CATCATTATGACGGATGCTTGAATAGGAAATATTGTACTAGGAAAAAAATCTAGAGCGAATATTT
TGGGCAGTTATTTTATCTTTATCAACATTCTCTTCATTAAAAAATGGGGGCAACTAGATGCTGTA
AGTTAGCAAATCTCATTTTGTAGTGTTTATTCTAGATATTATATAAATTCTTAAAGGCATAACTG
CTT
Found at i:41215 original size:13 final size:13
Alignment explanation
Indices: 41197--41221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41187 TCAAGTTTTT
41197 TTTTTAATTAATG
1 TTTTTAATTAATG
41210 TTTTTAATTAAT
1 TTTTTAATTAAT
41222 AAATATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:42866 original size:22 final size:22
Alignment explanation
Indices: 42838--42896 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 22
42828 TTTTTATTAT
42838 TATTTTGATTGCTGTTTTCTAC
1 TATTTTGATTGCTGTTTTCTAC
* *
42860 TATTTTGATT--TTTTTTTTAC
1 TATTTTGATTGCTGTTTTCTAC
42880 TATTTTGATTGCTGTTT
1 TATTTTGATTGCTGTTT
42897 AAATATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.56
22 14 0.44
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (22 bp):
TATTTTGATTGCTGTTTTCTAC
Found at i:42880 original size:20 final size:21
Alignment explanation
Indices: 42828--42889 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
42818 TTTGGTGTTA
* *
42828 TTTTTATTATTATTTTGATTGC
1 TTTTTTTTACTATTTTGATT-C
* *
42850 TGTTTTCTACTATTTTGATT-
1 TTTTTTTTACTATTTTGATTC
42870 TTTTTTTTACTATTTTGATT
1 TTTTTTTTACTATTTTGATT
42890 GCTGTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 18 0.53
22 16 0.47
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.69
Consensus pattern (21 bp):
TTTTTTTTACTATTTTGATTC
Found at i:42961 original size:24 final size:24
Alignment explanation
Indices: 42934--42989 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
42924 TGTTTCAGTT
* * *
42934 TTGTTTTTGCTGTTATTTTTGTTG
1 TTGTTTTTACTGCTATTTGTGTTG
*
42958 TTGTTTTTATTGCTATTTGTGTTG
1 TTGTTTTTACTGCTATTTGTGTTG
*
42982 TTTTTTTT
1 TTGTTTTT
42990 TTTGTTTTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.05, C:0.04, G:0.18, T:0.73
Consensus pattern (24 bp):
TTGTTTTTACTGCTATTTGTGTTG
Found at i:43031 original size:56 final size:57
Alignment explanation
Indices: 42932--43040 Score: 130
Period size: 56 Copynumber: 1.9 Consensus size: 57
42922 ATTGTTTCAG
** ** * *
42932 TTTTGTTTTTGCTGTTATTTTTGTTGTTGTTTTTATTGCTATTTGTGTTGTTTTTTT
1 TTTTGTTTTTGCTGTTATTTTTACTACTGTTTTGATTGCTATTTGTGCTGTTTTTTT
* * *
42989 TTTTG-TTTTGCTGTTATTTTTACTACTGTTTTGGTTGTTATTTTTGCTGTTT
1 TTTTGTTTTTGCTGTTATTTTTACTACTGTTTTGATTGCTATTTGTGCTGTTT
43041 GGATGTTATT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
56 38 0.88
57 5 0.12
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.71
Consensus pattern (57 bp):
TTTTGTTTTTGCTGTTATTTTTACTACTGTTTTGATTGCTATTTGTGCTGTTTTTTT
Found at i:43054 original size:21 final size:22
Alignment explanation
Indices: 42992--43055 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
42982 TTTTTTTTTT
*
42992 TGTTTT-GCTGTTATTTTTACTAC
1 TGTTTTGGATGTTATTTTT--TAC
* *
43015 TGTTTTGGTTGTTA-TTTTTGC
1 TGTTTTGGATGTTATTTTTTAC
43036 TG-TTTGGATGTTATTTTTTA
1 TGTTTTGGATGTTATTTTTTA
43056 TGCGTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
23 10 0.29
24 6 0.17
ACGTcount: A:0.11, C:0.06, G:0.19, T:0.64
Consensus pattern (22 bp):
TGTTTTGGATGTTATTTTTTAC
Found at i:51780 original size:83 final size:83
Alignment explanation
Indices: 51662--51824 Score: 281
Period size: 83 Copynumber: 2.0 Consensus size: 83
51652 TCCAATATCT
*
51662 TTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAATCCATTAACCAAAAAATTCAATATCTT
1 TTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAACCAAAAAATTCAATATCTT
* *
51727 TGGTTCCAATATCTTTAA
66 CGGTTACAATATCTTTAA
*
51745 TTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAACCAAAAGATTCAATATCTT
1 TTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAACCAAAAAATTCAATATCTT
*
51810 CGGTTATAATATCTT
66 CGGTTACAATATCTT
51825 CTTCCCGTTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 75 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (83 bp):
TTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATTAACCAAAAAATTCAATATCTT
CGGTTACAATATCTTTAA
Found at i:57970 original size:46 final size:46
Alignment explanation
Indices: 57903--57995 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
57893 TATGGTAGGT
57903 CGCATTACATTCTCAAGGATAATTAGGTATGGCTTTGTATTTGAAG
1 CGCATTACATTCTCAAGGATAATTAGGTATGGCTTTGTATTTGAAG
*
57949 CGCATTACATTCTCAAGGATAATTAGGTATGGTTTTGTATTTGAAG
1 CGCATTACATTCTCAAGGATAATTAGGTATGGCTTTGTATTTGAAG
57995 C
1 C
57996 ACTGTTATGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (46 bp):
CGCATTACATTCTCAAGGATAATTAGGTATGGCTTTGTATTTGAAG
Found at i:59508 original size:2 final size:2
Alignment explanation
Indices: 59501--59529 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59491 TCTTGCGGTA
59501 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
59530 TCTGTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.