Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009172.1 Kokia drynarioides strain JFW-HI SEQ_123877, 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: 46353
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:163 original size:66 final size:66
Alignment explanation
Indices: 14--170 Score: 172
Period size: 66 Copynumber: 2.4 Consensus size: 66
4 GTGGTATTGG
* * * *
14 GGCTGGTGGAGGGGTAGGAGCTGGTGGAGGTGCAGGTGGAGGTGTTGCAACATGTGAAGGTGTTG
1 GGCTGGTGGAGGGGTAGGAGCTGGTGGAGGCGCAAGTAGAGGTGTTGCAACATGTGAAGGTGCTG
*
79 G
66 A
* * * * * *
80 GGCTAGTGGAGGAGTAGGAGCTGGTGGTGGCGCAAGTAGAGGTGTTGGAGC-TGGTGCAGGTGCT
1 GGCTGGTGGAGGGGTAGGAGCTGGTGGAGGCGCAAGTAGAGGTGTTGCAACAT-GTGAAGGTGCT
144 GA
65 GA
* * *
146 TGTTGGTGGTGGGGTAGGAGCTGGT
1 GGCTGGTGGAGGGGTAGGAGCTGGT
171 ACAGGAGGAA
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
65 1 0.01
66 73 0.99
ACGTcount: A:0.16, C:0.08, G:0.52, T:0.24
Consensus pattern (66 bp):
GGCTGGTGGAGGGGTAGGAGCTGGTGGAGGCGCAAGTAGAGGTGTTGCAACATGTGAAGGTGCTG
A
Found at i:6383 original size:15 final size:15
Alignment explanation
Indices: 6352--6385 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6342 TCCCCCAAAG
* *
6352 TTTAATTTTTTTTAA
1 TTTAATTTTTGTAAA
6367 TTTAATTTTTGTAAA
1 TTTAATTTTTGTAAA
6382 TTTA
1 TTTA
6386 CACTATGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTAATTTTTGTAAA
Found at i:7665 original size:4 final size:4
Alignment explanation
Indices: 7656--7680 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
7646 TATGTGAATA
7656 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
7681 GTATGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:8446 original size:57 final size:56
Alignment explanation
Indices: 8370--8479 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 56
8360 AGATTATCCA
* * *
8370 AAGGCAAAGTTGAGCAATTAATCCACCGAC-ATATAGATTCTTGGAGGACTAATTCCG
1 AAGGCAAAATTCAGCAATTAATCCACCGACAAT-TAGATT-TTGGAGGACCAATTCCG
*
8427 AAGGCAAAATTCAGGAATTAATCCACCGACAATTAGATTTTGGAGGACCAATT
1 AAGGCAAAATTCAGCAATTAATCCACCGACAATTAGATTTTGGAGGACCAATT
8480 TTAATTTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 13 0.27
57 33 0.69
58 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (56 bp):
AAGGCAAAATTCAGCAATTAATCCACCGACAATTAGATTTTGGAGGACCAATTCCG
Found at i:11217 original size:31 final size:31
Alignment explanation
Indices: 11182--11245 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
11172 AAATAATTAT
11182 TAAATTATT-CAAAAGTTTTCATTTAAGTCAC
1 TAAATTATTGCAAAA-TTTTCATTTAAGTCAC
* *
11213 TAAATTATTGGAAAATTTTTATTTAAGTCAC
1 TAAATTATTGCAAAATTTTCATTTAAGTCAC
11244 TA
1 TA
11246 GATTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (31 bp):
TAAATTATTGCAAAATTTTCATTTAAGTCAC
Found at i:11260 original size:28 final size:29
Alignment explanation
Indices: 11194--11267 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
11184 AATTATTCAA
*
11194 AAGTTTTCATTTAAGTCACTAAATTATTGG
1 AAGTTTTTATTTAAGTCACTAAATTATT-G
* * *
11224 AAAATTTTTATTTAAGTCACTAGATTGTT-
1 -AAGTTTTTATTTAAGTCACTAAATTATTG
*
11253 AAGTTTTTTTTTAAG
1 AAGTTTTTATTTAAG
11268 GCCATCTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 13 0.35
31 24 0.65
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (29 bp):
AAGTTTTTATTTAAGTCACTAAATTATTG
Found at i:20643 original size:20 final size:20
Alignment explanation
Indices: 20587--20643 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
20577 AATTTTTTAA
20587 ATTTAAAAAATTCA-AAAAATT
1 ATTT-AAAAATT-ATAAAAATT
*
20608 ATTTTTAAAATT-TAAAAATT
1 A-TTTAAAAATTATAAAAATT
20628 ATTTAAAAATTATAAA
1 ATTTAAAAATTATAAA
20644 CAAAATAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 9 0.29
20 12 0.39
21 7 0.23
22 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTAAAAATTATAAAAATT
Found at i:28957 original size:12 final size:11
Alignment explanation
Indices: 28930--28958 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
28920 ACAAAATATA
28930 TAAAAATGAAT
1 TAAAAATGAAT
28941 TAAAAATGAAT
1 TAAAAATGAAT
28952 TAAAAAT
1 TAAAAAT
28959 AATAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (11 bp):
TAAAAATGAAT
Found at i:31877 original size:31 final size:29
Alignment explanation
Indices: 31833--31894 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
31823 TGTCTTATTA
*
31833 TGGTACTTATACTTTCATAAAATGT-TCAATG
1 TGGTACATATACTTT-A-AAAATGTCT-AATG
*
31864 TGGTACATGTACTTTAAAAATGTCTAATG
1 TGGTACATATACTTTAAAAATGTCTAATG
31893 TG
1 TG
31895 ATATATGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 13 0.46
30 2 0.07
31 13 0.46
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (29 bp):
TGGTACATATACTTTAAAAATGTCTAATG
Found at i:31893 original size:29 final size:31
Alignment explanation
Indices: 31833--31894 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
31823 TGTCTTATTA
*
31833 TGGTACTTATACTTTCATAAAATGTTCAATG
1 TGGTACATATACTTTCATAAAATGTTCAATG
*
31864 TGGTACATGTACTTT-A-AAAATG-TCTAATG
1 TGGTACATATACTTTCATAAAATGTTC-AATG
31893 TG
1 TG
31895 ATATATGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 12 0.43
30 1 0.04
31 13 0.46
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (31 bp):
TGGTACATATACTTTCATAAAATGTTCAATG
Found at i:33892 original size:17 final size:18
Alignment explanation
Indices: 33872--33918 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
33862 TTTTAATTTT
33872 TATAAATTTTTTAAA-AA
1 TATAAATTTTTTAAATAA
* *
33889 TATAAATTTTATAAATAT
1 TATAAATTTTTTAAATAA
*
33907 TTTAAATTTTTT
1 TATAAATTTTTT
33919 TTGTAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAAATTTTTTAAATAA
Found at i:33918 original size:9 final size:9
Alignment explanation
Indices: 33859--33918 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
33849 TACGTGTTGG
33859 ATTTTTT-A
1 ATTTTTTAA
33867 ATTTTTATAA
1 ATTTTT-TAA
33877 ATTTTTTAA
1 ATTTTTTAA
** *
33886 A-AATATAA
1 ATTTTTTAA
*
33894 ATTTTATAA
1 ATTTTTTAA
*
33903 ATATTTTAA
1 ATTTTTTAA
33912 ATTTTTT
1 ATTTTTT
33919 TTGTAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 11 0.27
9 23 0.56
10 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:40370 original size:2 final size:2
Alignment explanation
Indices: 40365--40390 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40355 AGGAAGCGTG
40365 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40391 AAAACGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.