Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013567.1 Kokia drynarioides strain JFW-HI SEQ_128593, 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: 48427
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 132 characters in sequence are not A, C, G, or T
Found at i:325 original size:18 final size:18
Alignment explanation
Indices: 302--338 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
292 TTTGTGATCA
302 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
320 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
338 A
1 A
339 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:6997 original size:13 final size:13
Alignment explanation
Indices: 6967--6999 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6957 AGCTTAAACG
6967 AAAAAG-GAAGGA
1 AAAAAGAGAAGGA
6979 AGAAAAGAGAAGGA
1 A-AAAAGAGAAGGA
6993 AAAAAGA
1 AAAAAGA
7000 AAAAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 11 0.58
14 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAGGA
Found at i:7332 original size:17 final size:18
Alignment explanation
Indices: 7310--7345 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7300 TAAATAAGTT
7310 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
7327 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
7345 A
1 A
7346 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:7665 original size:6 final size:6
Alignment explanation
Indices: 7646--7701 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
7636 TTTGTGATCA
* * * *
7646 AAATTG AAAGTG AAATTG AAATTG GAATTG AAAGTG ATA-TG -AATTG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
7692 TAAATTG AAA
1 -AAATTG AAA
7702 ATCCCTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
4 1 0.03
5 4 0.10
6 30 0.75
7 5 0.12
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (6 bp):
AAATTG
Found at i:10746 original size:24 final size:24
Alignment explanation
Indices: 10701--10748 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10691 ATGGATGTTC
* *
10701 AACCTTTCATCTCCCTTGACTTTT
1 AACCTTCCATCTCCCTTAACTTTT
* *
10725 AACCTTCCATCTTCTTTAACTTTT
1 AACCTTCCATCTCCCTTAACTTTT
10749 TATGTTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.48
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACTTTT
Found at i:13152 original size:18 final size:18
Alignment explanation
Indices: 13129--13176 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
13119 GAAAAAAAAA
13129 AAAGGTTACAAGG-AGATG
1 AAAGGTTA-AAGGAAGATG
* *
13147 AAAGGTTTAAGGAATATG
1 AAAGGTTAAAGGAAGATG
13165 AAAGGTTAAAGG
1 AAAGGTTAAAGG
13177 TTAAAGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.46, C:0.02, G:0.31, T:0.21
Consensus pattern (18 bp):
AAAGGTTAAAGGAAGATG
Found at i:15572 original size:35 final size:35
Alignment explanation
Indices: 15533--15602 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
15523 TCATGTGATA
15533 GCTAAACATAACACTAATTGCGTTTGGGTTATGTT
1 GCTAAACATAACACTAATTGCGTTTGGGTTATGTT
* *
15568 GCTAAACGTAACACTAATTGTGTTTGGGTTATGTT
1 GCTAAACATAACACTAATTGCGTTTGGGTTATGTT
15603 CGTTTCAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (35 bp):
GCTAAACATAACACTAATTGCGTTTGGGTTATGTT
Found at i:17255 original size:2 final size:2
Alignment explanation
Indices: 17248--17283 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17238 TGGCTAGATA
*
17248 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17284 CATAACACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:19498 original size:18 final size:18
Alignment explanation
Indices: 19475--19520 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
19465 TAAGAAAAAT
19475 AGGTTTCAAGG-AGATGAA
1 AGGTTT-AAGGAAGATGAA
*
19493 AGGTTTAAGGAATATGAA
1 AGGTTTAAGGAAGATGAA
*
19511 AGGTTAAAGG
1 AGGTTTAAGG
19521 TTAAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.41, C:0.02, G:0.33, T:0.24
Consensus pattern (18 bp):
AGGTTTAAGGAAGATGAA
Found at i:19533 original size:24 final size:25
Alignment explanation
Indices: 19491--19538 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
19481 CAAGGAGATG
* *
19491 AAAGGTTTAAGGAATATGAAAGGTT
1 AAAGGTTTAAAGAAGATGAAAGGTT
19516 AAAGG-TTAAAGAAGATGAAAGGT
1 AAAGGTTTAAAGAAGATGAAAGGT
19539 GGAAGGTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (25 bp):
AAAGGTTTAAAGAAGATGAAAGGTT
Found at i:19544 original size:24 final size:24
Alignment explanation
Indices: 19489--19545 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
19479 TTCAAGGAGA
* *
19489 TGAAAGGTTTAAGGAATATGAAAGG
1 TGAAAGG-TTAAAGAAGATGAAAGG
*
19514 TTAAAGGTTAAAGAAGATGAAAGG
1 TGAAAGGTTAAAGAAGATGAAAGG
*
19538 TGGAAGGT
1 TGAAAGGT
19546 GGAAGGTCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (24 bp):
TGAAAGGTTAAAGAAGATGAAAGG
Found at i:19552 original size:31 final size:31
Alignment explanation
Indices: 19507--19576 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
19497 TTAAGGAATA
** *
19507 TGAAAGGTTAAAGGTTAAAGAAGATGAAAGG
1 TGAAAGGTGGAAGGTCAAAGAAGATGAAAGG
* * *
19538 TGGAAGGTGGAAGGTCAAGGGAGATGAAAGG
1 TGAAAGGTGGAAGGTCAAAGAAGATGAAAGG
19569 TGAAAGGT
1 TGAAAGGT
19577 TGAACATCCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.01, G:0.40, T:0.17
Consensus pattern (31 bp):
TGAAAGGTGGAAGGTCAAAGAAGATGAAAGG
Found at i:30816 original size:15 final size:15
Alignment explanation
Indices: 30798--30827 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30788 CTAAAGTATT
30798 CTAAGCTAAATTAAA
1 CTAAGCTAAATTAAA
*
30813 CTAAGTTAAATTAAA
1 CTAAGCTAAATTAAA
30828 ACTGAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
CTAAGCTAAATTAAA
Found at i:30837 original size:16 final size:15
Alignment explanation
Indices: 30798--30840 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
30788 CTAAAGTATT
*
30798 CTAAGCTAAATTAAA
1 CTAAGTTAAATTAAA
30813 CTAAGTTAAATTAAAA
1 CTAAGTTAAATT-AAA
30829 CTGAA-TTAAATT
1 CT-AAGTTAAATT
30841 CCTATGCACG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 11 0.44
16 12 0.48
17 2 0.08
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (15 bp):
CTAAGTTAAATTAAA
Found at i:31457 original size:17 final size:18
Alignment explanation
Indices: 31435--31471 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
31425 GGCCTATAAC
*
31435 AATATAAACATG-AATTA
1 AATATAAACAAGCAATTA
31452 AATATAAACAAGCAATTA
1 AATATAAACAAGCAATTA
31470 AA
1 AA
31472 CACAATCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (18 bp):
AATATAAACAAGCAATTA
Found at i:32829 original size:45 final size:45
Alignment explanation
Indices: 32780--32869 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
32770 TTATAACAAA
* * **
32780 TTGCTACCTCGGGTTGCTTGGCAACAATAGCTCACTTA-TGTCGAT
1 TTGCTACCCCGAGTTGCCCGGCAACAATAGCTCAC-TAGTGTCGAT
*
32825 TTGCTACCCCGAGTTGCCCGGCAACGATAGCTCACTAGTGTCGAT
1 TTGCTACCCCGAGTTGCCCGGCAACAATAGCTCACTAGTGTCGAT
32870 ATGCAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 2 0.05
45 37 0.95
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (45 bp):
TTGCTACCCCGAGTTGCCCGGCAACAATAGCTCACTAGTGTCGAT
Found at i:34196 original size:20 final size:21
Alignment explanation
Indices: 34173--34217 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
34163 GTTGTTCTGA
34173 TAGAAAC-ATACTTGTATCAG
1 TAGAAACTATACTTGTATCAG
*
34193 TAG-AACTATATTTGTATCAG
1 TAGAAACTATACTTGTATCAG
34213 TAGAA
1 TAGAA
34218 GAGGAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 18 0.82
21 1 0.05
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (21 bp):
TAGAAACTATACTTGTATCAG
Found at i:34439 original size:20 final size:20
Alignment explanation
Indices: 34414--34454 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
34404 AAGTCTTCAA
34414 TGTATCGGTAGAAGTGGAGT
1 TGTATCGGTAGAAGTGGAGT
*
34434 TGTATCGGTAGACGTGGAGT
1 TGTATCGGTAGAAGTGGAGT
34454 T
1 T
34455 CTACCGGTCT
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:0.22, C:0.07, G:0.39, T:0.32
Consensus pattern (20 bp):
TGTATCGGTAGAAGTGGAGT
Found at i:34462 original size:20 final size:20
Alignment explanation
Indices: 34419--34462 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34409 TTCAATGTAT
* *
34419 CGGTAGAAGTGGAGTTGTAT
1 CGGTAGAAGTGGAGTTCTAC
*
34439 CGGTAGACGTGGAGTTCTAC
1 CGGTAGAAGTGGAGTTCTAC
34459 CGGT
1 CGGT
34463 CTCACTAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (20 bp):
CGGTAGAAGTGGAGTTCTAC
Found at i:36407 original size:25 final size:25
Alignment explanation
Indices: 36363--36417 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
36353 TATTAAGGAA
36363 ATAA-TTTATGTTTAATTATTAAAT
1 ATAATTTTATGTTTAATTATTAAAT
*
36387 ATAATTTTATGTCTTAA-TATTTAAT
1 ATAATTTTATGT-TTAATTATTAAAT
36412 -TAATTT
1 ATAATTT
36418 ATGCATGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 10 0.36
25 14 0.50
26 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
ATAATTTTATGTTTAATTATTAAAT
Found at i:39854 original size:25 final size:25
Alignment explanation
Indices: 39810--39860 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
39800 GACCCCCTTT
*
39810 ATTAAACATAACAAATAAAATTAAA
1 ATTAAACATAACAAATAAAATGAAA
39835 ATTAAA-ATTAAC-AATAAAAATGAAA
1 ATTAAACA-TAACAAAT-AAAATGAAA
39860 A
1 A
39861 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.24
Consensus pattern (25 bp):
ATTAAACATAACAAATAAAATGAAA
Found at i:45467 original size:20 final size:21
Alignment explanation
Indices: 45429--45468 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
45419 TAAACCGAGC
*
45429 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
45450 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
45469 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:46951 original size:12 final size:12
Alignment explanation
Indices: 46901--46952 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
46891 CGACAGTAGG
46901 TTCTTCCTTCTTT
1 TTCTT-CTTCTTT
* *
46914 TCCTTCATCTTCT
1 TTCTTCTTCTT-T
46927 CGTTCTTCTTCTTT
1 --TTCTTCTTCTTT
46941 TTCTTCTTCTTT
1 TTCTTCTTCTTT
46953 CTCCTCATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
12 17 0.53
13 5 0.16
14 1 0.03
15 9 0.28
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (12 bp):
TTCTTCTTCTTT
Done.