Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009964.1 Kokia drynarioides strain JFW-HI SEQ_124712, 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: 22362
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:45 original size:5 final size:5
Alignment explanation
Indices: 25--66 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
15 GACCCATGGA
* * *
25 CCGAT CCGAC ACGAC CTGAC CCGAC CCGAC CCGAC CCGAC CC
1 CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CCGAC CC
67 AGCCTCAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.21, C:0.55, G:0.19, T:0.05
Consensus pattern (5 bp):
CCGAC
Found at i:489 original size:29 final size:29
Alignment explanation
Indices: 441--606 Score: 158
Period size: 29 Copynumber: 5.7 Consensus size: 29
431 GCCCTAGAGG
* *
441 CCCCGAAACTTCCAAAAATTATATTTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTTA
*** *
470 CCCTTGAACTTCCAAAAATTTCATTTTTTA
1 CCCCAAAACTTCCAAAAATTACA-TTTTTA
500 CCCCAAAACTTCCAAAAATTACATTTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTTA
* * * *
529 CCCTAAAATTTTCAAAAATTCCA-TTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTTA
* *
557 CCCCTAAACTTCC-AAAATTCCATTTTTGA
1 CCCCAAAACTTCCAAAAATTACATTTTT-A
* *
586 -CCCAGAAATTTTCAAAAATTA
1 CCCCA-AAACTTCCAAAAATTA
607 TCCTTTTACC
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
27 9 0.08
28 21 0.19
29 50 0.45
30 31 0.28
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
CCCCAAAACTTCCAAAAATTACATTTTTA
Found at i:545 original size:59 final size:57
Alignment explanation
Indices: 441--618 Score: 200
Period size: 59 Copynumber: 3.1 Consensus size: 57
431 GCCCTAGAGG
* * ** * * *
441 CCCCGAAACTTCCAAAAATTATATTTTTACCCTTGAACTTCCAAAAATTTCATTTTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTTACCCTAAAATTTTCAAAAATTCCA--TTTTA
500 CCCCAAAACTTCCAAAAATTACATTTTTACCCTAAAATTTTCAAAAATTCCATTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTTACCCTAAAATTTTCAAAAATTCCATTTTA
* *
557 CCCCTAAACTTCC-AAAATTCCATTTTTGACCC-AGAAATTTTCAAAAATTATCC-TTTTA
1 CCCCAAAACTTCCAAAAATTACATTTTT-ACCCTA-AAATTTTCAAAAA-T-TCCATTTTA
615 CCCC
1 CCCC
619 CGGATGTCCA
Statistics
Matches: 106, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
56 14 0.13
57 34 0.32
58 10 0.09
59 48 0.45
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.36
Consensus pattern (57 bp):
CCCCAAAACTTCCAAAAATTACATTTTTACCCTAAAATTTTCAAAAATTCCATTTTA
Found at i:7069 original size:17 final size:17
Alignment explanation
Indices: 7047--7085 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
7037 CTCCACCTTG
* *
7047 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
7064 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
7081 ACAAG
1 ACAAG
7086 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:11892 original size:51 final size:51
Alignment explanation
Indices: 11822--12111 Score: 332
Period size: 51 Copynumber: 5.6 Consensus size: 51
11812 GCTATAAACA
11822 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
* * *
11874 AAAGGTCCGATGACTAAGTGTCATCGTCAGTAAATGGATCCCTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
* * * * * * **
11925 AAAGGTCTGATGACCAAGTGTCATCGTGCGTAAATAAATTCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
* * * * *
11976 AAAGGTCCGATGACTAAGTGTCATCATGGGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
* * * *
12027 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAATTCCTATACGAAA-C
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TAC-AAATT
*
12079 AAGGGGTCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
12112 TTAAATGAAA
Statistics
Matches: 202, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
51 165 0.82
52 8 0.04
53 28 0.14
54 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACAAATT
Found at i:14893 original size:23 final size:23
Alignment explanation
Indices: 14843--14940 Score: 90
Period size: 23 Copynumber: 4.2 Consensus size: 23
14833 ATCCATAATA
* **
14843 TGCATATATAGTGCTAGAATGAAA
1 TGCACATA-AGTGCTAGAATGATT
*
14867 TGCACATAAGTGCTAGAGTGATT
1 TGCACATAAGTGCTAGAATGATT
*
14890 TGCACCA-AAATGCCTAGAATGATT
1 TGCA-CATAAGTG-CTAGAATGATT
* * *
14914 TGCAAACAAGTGCCAGAATGATT
1 TGCACATAAGTGCTAGAATGATT
14937 TGCA
1 TGCA
14941 GTGAAGTGCC
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
23 35 0.56
24 27 0.44
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (23 bp):
TGCACATAAGTGCTAGAATGATT
Found at i:14947 original size:23 final size:23
Alignment explanation
Indices: 14874--14956 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
14864 AAATGCACAT
* *
14874 AAGTGCTAGAGTGATTTGCACCAA-
1 AAGTGCCAGAATGATTTGCA--AAC
14898 AA-TGCCTAGAATGATTTGCAAAC
1 AAGTGCC-AGAATGATTTGCAAAC
***
14921 AAGTGCCAGAATGATTTGCAGTG
1 AAGTGCCAGAATGATTTGCAAAC
14944 AAGTGCCAGAATG
1 AAGTGCCAGAATG
14957 TTTTCTCCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 2 0.04
23 31 0.61
24 18 0.35
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (23 bp):
AAGTGCCAGAATGATTTGCAAAC
Found at i:16207 original size:53 final size:53
Alignment explanation
Indices: 16122--16369 Score: 257
Period size: 53 Copynumber: 4.7 Consensus size: 53
16112 TGTGCCAAAG
* *
16122 ATTAAAGGTTCGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATCACGA
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
* * * *
16175 ATTAAAGGTCCGATGACTCTGTATCATCGTGAGTTATATGAATCCTACCATGG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
* * * *
16228 ATTAAAGGTCCGATGACTATGTGCCATCATGAGTTATATGAATCCTATTAC-A
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
* * * * ** * * * * * *
16280 GATTAAGGGTTCGATAACTTTGTGTCATCGTGAAATACACGAA-CCCATTATGG
1 -ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
* *
16333 ATTAAAGGTCCAATGACTCTGTGTCATCATGAGTTAT
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
16370 CAAATGCGAA
Statistics
Matches: 157, Mismatches: 36, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
52 34 0.22
53 123 0.78
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (53 bp):
ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGA
Found at i:16368 original size:105 final size:106
Alignment explanation
Indices: 16121--16369 Score: 304
Period size: 106 Copynumber: 2.4 Consensus size: 106
16111 TTGTGCCAAA
* **
16121 GATTAAAGGTTCGATGACTCTGTGTCATTGTGAGTTATATGAATCCTATCACGAATTAAAGGTCC
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCACGAATTAAAGGTCC
* ** * * *
16186 GATGACTCTGTATCATCGTGAGTTATATGAATCCTACCATG
66 GATAACTCTGTATCATCGTGAAATACACGAATCCCACCATG
* * * * *
16227 GATTAAAGGTCCGATGACTATGTGCCATCATGAGTTATATGAATCCTATTAC-AGATTAAGGGTT
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCACGA-ATTAAAGGTC
* * **
16291 CGATAACTTTGTGTCATCGTGAAATACACGAA-CCCATTATG
65 CGATAACTCTGTATCATCGTGAAATACACGAATCCCACCATG
*
16332 GATTAAAGGTCCAATGACTCTGTGTCATCATGAGTTAT
1 GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTAT
16370 CAAATGCGAA
Statistics
Matches: 121, Mismatches: 21, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
105 42 0.35
106 79 0.65
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (106 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCATGAGTTATATGAATCCTATCACGAATTAAAGGTCC
GATAACTCTGTATCATCGTGAAATACACGAATCCCACCATG
Found at i:17070 original size:21 final size:21
Alignment explanation
Indices: 17046--17102 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
17036 TAGAAATAAG
* *
17046 ACTTGTTTTAGTAGAAGAGTC
1 ACTTGTATTAGTAGAACAGTC
** *
17067 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATTAGTAGAACAGTC
17088 ACTTGTATTAGTAGA
1 ACTTGTATTAGTAGA
17103 GGTTTACACT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (21 bp):
ACTTGTATTAGTAGAACAGTC
Found at i:18607 original size:23 final size:23
Alignment explanation
Indices: 18566--18668 Score: 95
Period size: 23 Copynumber: 4.5 Consensus size: 23
18556 ATGCATGTAT
* **
18566 AGTGCTAGAATGAAATGCACATA
1 AGTGCCAGAATGATTTGCACATA
*
18589 AGTGCCAGAGTGATTTGCACCA-A
1 AGTGCCAGAATGATTTGCA-CATA
* * * *
18612 AATGCCTAGAATGATTTACAAACA
1 AGTGCC-AGAATGATTTGCACATA
18636 AGTGCCAGAATGATTTGCAC-T-
1 AGTGCCAGAATGATTTGCACATA
18657 AGTGCCAGAATG
1 AGTGCCAGAATG
18669 TTTCCTCCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
21 12 0.18
23 34 0.52
24 19 0.29
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (23 bp):
AGTGCCAGAATGATTTGCACATA
Found at i:21328 original size:24 final size:23
Alignment explanation
Indices: 21296--21371 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 23
21286 ATTATTAAAT
*
21296 ATAATTTAATATAAATGATAATAA
1 ATAATTTAATATAAATAATAAT-A
**
21320 ATAATTTAATCAT--ATTTTAAT-
1 ATAATTTAAT-ATAAATAATAATA
*
21341 ATAATTTAATAAAAATAATAATA
1 ATAATTTAATATAAATAATAATA
21364 TATAATTT
1 -ATAATTT
21372 GATAACATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 10 0.24
22 6 0.14
23 6 0.14
24 17 0.40
25 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (23 bp):
ATAATTTAATATAAATAATAATA
Found at i:21340 original size:11 final size:10
Alignment explanation
Indices: 21293--21351 Score: 55
Period size: 10 Copynumber: 5.4 Consensus size: 10
21283 ATTATTATTA
21293 AATATAATTT
1 AATATAATTT
*
21303 AATATAAATGAT
1 AATAT-AAT-TT
21315 AATAAATAATTT
1 AAT--ATAATTT
*
21327 AATCATATTTT
1 AAT-ATAATTT
21338 AATATAATTT
1 AATATAATTT
21348 AATA
1 AATA
21352 AAAATAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 15 0.38
11 12 0.30
12 8 0.20
13 3 0.08
14 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
AATATAATTT
Found at i:21342 original size:45 final size:46
Alignment explanation
Indices: 21293--21392 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 46
21283 ATTATTATTA
* * * *
21293 AATATAATTTAATATAAATGATAATAAATAATTTAATCATATT-TT
1 AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
* *
21338 AATATAATTTAATAAAAATAATAATATATAATTTGATAACATTCTT
1 AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
21384 AATATAATT
1 AATATAATT
21393 ATTTTTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 37 0.77
46 11 0.23
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (46 bp):
AATATAATTTAATAAAAATAATAATAAATAATTTAATAACATTCTT
Found at i:22277 original size:14 final size:16
Alignment explanation
Indices: 22258--22290 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
22248 ATTATTTATG
22258 AATATA-AATAA-ATT
1 AATATAGAATAATATT
22272 AATATAGAATAATATT
1 AATATAGAATAATATT
22288 AAT
1 AAT
22291 TTTGTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAGAATAATATT
Found at i:22326 original size:63 final size:61
Alignment explanation
Indices: 22242--22362 Score: 197
Period size: 63 Copynumber: 2.0 Consensus size: 61
22232 AATTCCATTT
* *
22242 TTTATTATTATTTATGAATATAAATAAATTAATATAGAATAATATTAATTTTGTTTTATTA
1 TTTATTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTTTATTA
*
22303 TTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTGTTTTA
1 TTTA-TTATTATT-TATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 4 0.07
62 8 0.15
63 43 0.78
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (61 bp):
TTTATTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTTTATTA
Done.