Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011452.1 Kokia drynarioides strain JFW-HI SEQ_126436, 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: 19454
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:826 original size:24 final size:24
Alignment explanation
Indices: 772--849 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
762 CGAAATACTT
* *
772 AACATAAGCGCATAAGTGCTGAGGA
1 AACAGAAGCACATAAGTGCTG-GGA
797 AACAGAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
821 AACAGAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
845 AACAG
1 AACAG
850 TGGCTATAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 32 0.63
25 19 0.37
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.13
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:7865 original size:19 final size:19
Alignment explanation
Indices: 7841--7921 Score: 55
Period size: 19 Copynumber: 4.4 Consensus size: 19
7831 ATTATAAACA
7841 TATAAAAATATAAAAATTT
1 TATAAAAATATAAAAATTT
* *
7860 TAT-AAAAT-TAATGAATACT
1 TATAAAAATATAA-AAAT-TT
* * *
7879 TATAAGTATTATAAACA---
1 TATAA-AAATATAAAAATTT
7896 TATAAAAATATAAAAATTT
1 TATAAAAATATAAAAATTT
7915 TATAAAA
1 TATAAAA
7922 TTAATAAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 16
0.64 0.13 0.23
Matches are distributed among these distances:
16 8 0.18
17 8 0.18
18 8 0.18
19 14 0.31
20 1 0.02
21 3 0.07
22 3 0.07
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
TATAAAAATATAAAAATTT
Found at i:7868 original size:55 final size:55
Alignment explanation
Indices: 7807--7959 Score: 245
Period size: 55 Copynumber: 2.8 Consensus size: 55
7797 AGAAATGAGT
7807 TAAAATTAATGAATACTTATAAGTATTATAAACATATAAAAATATAAAAATTTTA
1 TAAAATTAATGAATACTTATAAGTATTATAAACATATAAAAATATAAAAATTTTA
7862 TAAAATTAATGAATACTTATAAGTATTATAAACATATAAAAATATAAAAATTTTA
1 TAAAATTAATGAATACTTATAAGTATTATAAACATATAAAAATATAAAAATTTTA
* * * *
7917 TAAAATTAATAAAATAGTTA-AATTTTTATAAAACATATAAAAA
1 TAAAATTAAT-GAATACTTATAAGTATTAT-AAACATATAAAAA
7960 ATCTTAAAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
55 72 0.78
56 20 0.22
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (55 bp):
TAAAATTAATGAATACTTATAAGTATTATAAACATATAAAAATATAAAAATTTTA
Found at i:7956 original size:28 final size:27
Alignment explanation
Indices: 7832--7958 Score: 86
Period size: 28 Copynumber: 4.6 Consensus size: 27
7822 CTTATAAGTA
7832 TTAT-AAACATATAAAAATATAAAAATT
1 TTATAAAACATAT-AAAATATAAAAATT
* * *
7859 TTAT-AAA-AT-TAATGAATACTTATAAGTA
1 TTATAAAACATATAA--AATA--TAAAAATT
7887 TTAT-AAACATATAAAAATATAAAAATT
1 TTATAAAACATAT-AAAATATAAAAATT
* * *
7914 TTATAAAA-TTAATAAAATAGTTAAATTT
1 TTATAAAACAT-ATAAAATA-TAAAAATT
7942 TTATAAAACATATAAAA
1 TTATAAAACATATAAAA
7959 AATCTTAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
24 2 0.03
25 1 0.01
26 6 0.08
27 23 0.29
28 37 0.47
29 7 0.09
30 1 0.01
31 2 0.03
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.36
Consensus pattern (27 bp):
TTATAAAACATATAAAATATAAAAATT
Found at i:8804 original size:19 final size:19
Alignment explanation
Indices: 8734--8814 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 19
8724 TTTATTAGAG
* *
8734 TTTTTTATAATATTTATAA
1 TTTTTAATAATATTTTTAA
* * *
8753 -ATTT-ATATTAATTTTAA
1 TTTTTAATAATATTTTTAA
*
8770 TTTTTATTTAAATATTTTTAA
1 TTTTTA-AT-AATATTTTTAA
*
8791 TTTTTAATAATATTTGTAA
1 TTTTTAATAATATTTTTAA
8810 TTTTT
1 TTTTT
8815 CTGATTTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.21
18 6 0.12
19 15 0.31
20 2 0.04
21 15 0.31
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTTAATAATATTTTTAA
Found at i:11841 original size:6 final size:6
Alignment explanation
Indices: 11830--11857 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11820 CGACGTGGGA
11830 ATGGAG ATGGAG ATGGAG ATGGAG ATGG
1 ATGGAG ATGGAG ATGGAG ATGGAG ATGG
11858 GCCCTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
ATGGAG
Found at i:17897 original size:4 final size:4
Alignment explanation
Indices: 17888--17949 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
17878 AAATAAACGG
* * *
17888 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
17938 G-AA GAAG GAAA G
1 GAAA GAAA GAAA G
17950 TGTAACACCC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 38 0.78
5 8 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:17908 original size:17 final size:17
Alignment explanation
Indices: 17888--17949 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
17878 AAATAAACGG
17888 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
17905 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* *
17921 GAAGGAGAGGAAA-GAAA
1 GAAAGA-AAGAAAGGAAA
*
17938 G-AAGAAGGAAAG
1 GAAAGAAAGAAAG
17950 TGTAACACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 6 0.15
16 11 0.28
17 22 0.56
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:17916 original size:25 final size:26
Alignment explanation
Indices: 17888--17949 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
17878 AAATAAACGG
17888 GAAAGAAAGAAAGGA-AAGAAAGAAA
1 GAAAGAAAGAAAGGAGAAGAAAGAAA
* *
17913 GAAAGGAAG-AAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGGAGAAGAAAGAAA
*
17938 G-AAGAAGGAAAG
1 GAAAGAAAGAAAG
17950 TGTAACACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 10 0.32
25 21 0.68
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (26 bp):
GAAAGAAAGAAAGGAGAAGAAAGAAA
Found at i:17932 original size:29 final size:27
Alignment explanation
Indices: 17890--17947 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
17880 ATAAACGGGA
17890 AAGAAAGAAAGGAAAGAAAGAAAGAAAGG
1 AAGAAAGAAAGGAAAGAAAG-AAG-AAGG
* *
17919 AAGAAGGAGAGGAAAGAAAGAAGAAGG
1 AAGAAAGAAAGGAAAGAAAGAAGAAGG
17946 AA
1 AA
17948 AGTGTAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 3 0.11
29 18 0.67
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (27 bp):
AAGAAAGAAAGGAAAGAAAGAAGAAGG
Found at i:18480 original size:23 final size:23
Alignment explanation
Indices: 18454--18626 Score: 186
Period size: 23 Copynumber: 7.4 Consensus size: 23
18444 AGTGCTGGGC
*
18454 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
18477 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
**
18500 GTCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
**
18523 GTCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
18546 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
18570 TAACAGAGAGCACGA-GATGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
* *
18594 AACAGAGAGTACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
18617 ATCAGAGAGC
1 AACAGAGAGC
18627 GCGCTAGTGT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
22 1 0.01
23 107 0.84
24 2 0.02
25 16 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:18580 original size:48 final size:46
Alignment explanation
Indices: 18456--18626 Score: 218
Period size: 46 Copynumber: 3.7 Consensus size: 46
18446 TGCTGGGCAA
* * * *
18456 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAGT
1 CAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
* *
18502 CAGAGAGCACACAAAGTGCTAGTCAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
* * *
18548 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GATGTGCTAAA
1 CAGAGAGCACACACAGTGCTAAT--CAGAGAGCAC-ACAAAGTGCTAAT
*
18596 CAGAGAGTACACACAGTGCTAATCAGAGAGC
1 CAGAGAGCACACACAGTGCTAATCAGAGAGC
18627 GCGCTAGTGT
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
46 69 0.63
48 40 0.36
49 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAATCAGAGAGCACACAAAGTGCTAAT
Found at i:19057 original size:23 final size:23
Alignment explanation
Indices: 18993--19120 Score: 150
Period size: 23 Copynumber: 5.5 Consensus size: 23
18983 NNNNNNNTAG
* * *
18993 TCAGAGAGCACACAAAGTACTAG
1 TCAGAGAGCACACACAGTGCTAA
*
19016 TCAGAGAGCACACAAAGTGCTAA
1 TCAGAGAGCACACACAGTGCTAA
19039 TCAGAGAGCACACACAGTGCTAA
1 TCAGAGAGCACACACAGTGCTAA
* * *
19062 TAACAGAGAGCATGAGAC-GTGATAA
1 T--CAGAGAGCA-CACACAGTGCTAA
*
19087 ACAGAGAGCACACACAGTGCTAA
1 TCAGAGAGCACACACAGTGCTAA
19110 TCAGAGAGCAC
1 TCAGAGAGCAC
19121 GCTAGTGTTC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.03
23 69 0.77
25 15 0.17
26 3 0.03
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (23 bp):
TCAGAGAGCACACACAGTGCTAA
Found at i:19072 original size:48 final size:45
Alignment explanation
Indices: 18993--19120 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 45
18983 NNNNNNNTAG
* * * *
18993 TCAGAGAGCACACAAAGTACTAGTCAGAGAGCACACAAAGTGCTAA
1 TCAGAGAGCACACACAGTGCTAATCAGAGAGCACA-AAAGTGATAA
* * *
19039 TCAGAGAGCACACACAGTGCTAATAACAGAGAGCATGAGACGTGATAA
1 TCAGAGAGCACACACAGTGCTAAT--CAGAGAGCA-CAAAAGTGATAA
*
19087 ACAGAGAGCACACACAGTGCTAATCAGAGAGCAC
1 TCAGAGAGCACACACAGTGCTAATCAGAGAGCAC
19121 GCTAGTGTTC
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
46 30 0.43
48 39 0.56
49 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (45 bp):
TCAGAGAGCACACACAGTGCTAATCAGAGAGCACAAAAGTGATAA
Done.