Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013495.1 Kokia drynarioides strain JFW-HI SEQ_128521, 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: 52698
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:252 original size:23 final size:23
Alignment explanation
Indices: 226--279 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
216 CGTTCATCCT
226 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAGAAGC
*
249 TGCTGAAC-AGATCTTCTAGAAGC
1 TGCTG-ACTAGACCTTCTAGAAGC
272 TGCTGACT
1 TGCTGACT
280 GGATGCCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 24 0.86
24 2 0.07
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAGAAGC
Found at i:4031 original size:21 final size:22
Alignment explanation
Indices: 3980--4042 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
3970 TTCTAGTTTG
*
3980 AAATAAAAATAAAAATAATATTAAT
1 AAATAAAAAT--AAA-AATATCAAT
* *
4005 AAATAAAACTTAAAATATCAA-
1 AAATAAAAATAAAAATATCAAT
4026 AAATAAAAATAAAAATA
1 AAATAAAAATAAAAATA
4043 AAATAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 15 0.45
22 7 0.21
23 2 0.06
25 9 0.27
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (22 bp):
AAATAAAAATAAAAATATCAAT
Found at i:4056 original size:6 final size:6
Alignment explanation
Indices: 3980--4045 Score: 69
Period size: 6 Copynumber: 10.3 Consensus size: 6
3970 TTCTAGTTTG
* * *
3980 AAATAA AAATAA AAATAA TATTAA TAAATAA AACTTAA AATATCAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA -AAATAA AA-ATAA AA-AT-AA AAATAA
4032 AAATAA AAATAA AA
1 AAATAA AAATAA AA
4046 TAATATAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
6 34 0.68
7 12 0.24
8 4 0.08
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (6 bp):
AAATAA
Found at i:17221 original size:20 final size:20
Alignment explanation
Indices: 17196--17236 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
17186 TGAAAAATAT
*
17196 TACCAAAAGTTTGTTTTTAC
1 TACCAAAAGTTTGTTTCTAC
17216 TACCAAAAGTTTGTTTCTAC
1 TACCAAAAGTTTGTTTCTAC
17236 T
1 T
17237 CTGAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (20 bp):
TACCAAAAGTTTGTTTCTAC
Found at i:29570 original size:21 final size:21
Alignment explanation
Indices: 29544--29588 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29534 TCTTTCCTTT
29544 CCTCAACTTCTCGGCCTCTAA
1 CCTCAACTTCTCGGCCTCTAA
29565 CCTCAACTTCTCGGCCTCTAA
1 CCTCAACTTCTCGGCCTCTAA
29586 CCT
1 CCT
29589 TTGTGTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.44, G:0.09, T:0.29
Consensus pattern (21 bp):
CCTCAACTTCTCGGCCTCTAA
Found at i:31520 original size:79 final size:79
Alignment explanation
Indices: 31389--31552 Score: 328
Period size: 79 Copynumber: 2.1 Consensus size: 79
31379 ATTTGGAATT
31389 CTAATGCACAAATTGTATTCACATGAGAGAATAATGCACCGACAATTTATGGGTATGAATAATTA
1 CTAATGCACAAATTGTATTCACATGAGAGAATAATGCACCGACAATTTATGGGTATGAATAATTA
31454 AAACTGCAACTTCA
66 AAACTGCAACTTCA
31468 CTAATGCACAAATTGTATTCACATGAGAGAATAATGCACCGACAATTTATGGGTATGAATAATTA
1 CTAATGCACAAATTGTATTCACATGAGAGAATAATGCACCGACAATTTATGGGTATGAATAATTA
31533 AAACTGCAACTTCA
66 AAACTGCAACTTCA
31547 CTAATG
1 CTAATG
31553 TTAGTAACAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (79 bp):
CTAATGCACAAATTGTATTCACATGAGAGAATAATGCACCGACAATTTATGGGTATGAATAATTA
AAACTGCAACTTCA
Found at i:32209 original size:18 final size:18
Alignment explanation
Indices: 32180--32223 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
32170 AAATGAACTA
32180 ACAAAT-AAAATGCAATG
1 ACAAATAAAAATGCAATG
*
32197 ACAAATAAAAATGTAATG
1 ACAAATAAAAATGCAATG
*
32215 ACAACTAAA
1 ACAAATAAA
32224 TGCTATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.18
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:32386 original size:12 final size:12
Alignment explanation
Indices: 32371--32395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32361 GTCTTTCCTC
32371 TTTCTCTTTTTA
1 TTTCTCTTTTTA
32383 TTTCTCTTTTTA
1 TTTCTCTTTTTA
32395 T
1 T
32396 CCTTGGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTCTTTTTA
Found at i:48477 original size:46 final size:46
Alignment explanation
Indices: 48405--48503 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
48395 TCAGTGAATC
*
48405 ATTTTCACCCTTTAAACTTGATCACTTTTATATTTCCTACATTTAA
1 ATTTCCACCCTTTAAACTTGATCACTTTTATATTTCCTACATTTAA
* * * *
48451 ATTTCCACCCTTTACACTTGATCACTTTTCTATTTTCTGCATTTAA
1 ATTTCCACCCTTTAAACTTGATCACTTTTATATTTCCTACATTTAA
48497 ATTTCCA
1 ATTTCCA
48504 TTACTCACAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.25, C:0.24, G:0.03, T:0.47
Consensus pattern (46 bp):
ATTTCCACCCTTTAAACTTGATCACTTTTATATTTCCTACATTTAA
Found at i:48883 original size:19 final size:19
Alignment explanation
Indices: 48857--48897 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
48847 GTTATTGCAA
48857 TTAATTTT-ACTTAATTT-T
1 TTAATTTTGA-TTAATTTGT
48875 TTAACTTTTGATTAATTTGT
1 TTAA-TTTTGATTAATTTGT
48895 TTA
1 TTA
48898 TCGTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TTAATTTTGATTAATTTGT
Done.