Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014023.1 Kokia drynarioides strain JFW-HI SEQ_129054, 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: 82934
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:4636 original size:37 final size:37
Alignment explanation
Indices: 4576--4687 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 37
4566 TTTCGCTGCG
*
4576 TGAGCACTTCTAGATTGCGCCCAAAACTGTCGTTGCA
1 TGAGCACTTCTAGATTGCACCCAAAACTGTCGTTGCA
* *
4613 TGAGCACTTCTAGGTTGCACCCAAAACTGTCGCTGCA
1 TGAGCACTTCTAGATTGCACCCAAAACTGTCGTTGCA
** * * *
4650 TGAATATTTCTAGAATGCACCCAAGACTGTCGTTGCA
1 TGAGCACTTCTAGATTGCACCCAAAACTGTCGTTGCA
4687 T
1 T
4688 AAATATTCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (37 bp):
TGAGCACTTCTAGATTGCACCCAAAACTGTCGTTGCA
Found at i:4724 original size:38 final size:37
Alignment explanation
Indices: 4681--4752 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
4671 CAAGACTGTC
*
4681 GTTGCATAAATATTCTTCAAATTGCATCCAAAAATATT
1 GTTGCATAAATATTCTTC-AATTGCACCCAAAAATATT
* *
4719 GTTGCATAATTATTCTTCAATTGCACCCAGAAAT
1 GTTGCATAAATATTCTTCAATTGCACCCAAAAAT
4753 GTCACTGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (37 bp):
GTTGCATAAATATTCTTCAATTGCACCCAAAAATATT
Found at i:4762 original size:37 final size:38
Alignment explanation
Indices: 4683--4762 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
4673 AGACTGTCGT
* ***
4683 TGCATAAATATTCTTCAAATTGCATCCAAAAATATTGT
1 TGCATAAATATTCTTCAAATTGCACCCAAAAATATCAC
* * *
4721 TGCATAATTATTCTTC-AATTGCACCCAGAAATGTCAC
1 TGCATAAATATTCTTCAAATTGCACCCAAAAATATCAC
4758 TGCAT
1 TGCAT
4763 GAACATGTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
37 20 0.57
38 15 0.43
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (38 bp):
TGCATAAATATTCTTCAAATTGCACCCAAAAATATCAC
Found at i:10908 original size:25 final size:25
Alignment explanation
Indices: 10859--10922 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
10849 TTTAGTATAG
* * *
10859 CCAAAAAGAAAGAAATAGTGAAAAA
1 CCAAAAAGAAAAAAAAAGAGAAAAA
* *
10884 TCAAAAAGAAAAAAAAAGAGTAAAA
1 CCAAAAAGAAAAAAAAAGAGAAAAA
10909 CCAAAAGAGAAAAA
1 CCAAAA-AGAAAAA
10923 TCACGAGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.06
Consensus pattern (25 bp):
CCAAAAAGAAAAAAAAAGAGAAAAA
Found at i:28461 original size:21 final size:21
Alignment explanation
Indices: 28433--28479 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
28423 ATAAAGGAGC
28433 AAAA-GAAGAAGAGAAAGAAG
1 AAAAGGAAGAAGAGAAAGAAG
*
28453 AAAAGGAAGAAGAGAAGGAAG
1 AAAAGGAAGAAGAGAAAGAAG
28474 ACAAAG
1 A-AAAG
28480 AAAGCATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 16 0.67
22 4 0.17
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (21 bp):
AAAAGGAAGAAGAGAAAGAAG
Found at i:28470 original size:12 final size:12
Alignment explanation
Indices: 28435--28474 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28425 AAAGGAGCAA
* *
28435 AAGAAGAAGAGA
1 AAGAAGAAAAGG
28447 AAGAAGAAAAGG
1 AAGAAGAAAAGG
*
28459 AAGAAGAGAAGG
1 AAGAAGAAAAGG
28471 AAGA
1 AAGA
28475 CAAAGAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAGG
Found at i:28950 original size:17 final size:16
Alignment explanation
Indices: 28919--28952 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28909 TAGTTGCATG
28919 CATTTATTTTAATTGT
1 CATTTATTTTAATTGT
*
28935 CATTTCATTTTTATTGT
1 CATTT-ATTTTAATTGT
28952 C
1 C
28953 TCTGCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (16 bp):
CATTTATTTTAATTGT
Found at i:29571 original size:16 final size:17
Alignment explanation
Indices: 29550--29582 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29540 AATCGCATAA
29550 AGAAAA-GAAAAAAAAG
1 AGAAAAGGAAAAAAAAG
*
29566 AGAAAAGGAAAGAAAAG
1 AGAAAAGGAAAAAAAAG
29583 TTGATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAAGGAAAAAAAAG
Found at i:40104 original size:12 final size:12
Alignment explanation
Indices: 40087--40111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40077 TCATGTGGAG
40087 GAAGAAAAAGAT
1 GAAGAAAAAGAT
40099 GAAGAAAAAGAT
1 GAAGAAAAAGAT
40111 G
1 G
40112 TCGAGTCAAA
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAGAAAAAGAT
Found at i:42052 original size:26 final size:26
Alignment explanation
Indices: 42017--42074 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
42007 TTACACCCAG
*
42017 GAATT-TCGCTACATGAACATTTACA
1 GAATTGTCGCTACATGAACATGTACA
* * *
42042 GAATTGTCGCTGCATGAACGTGTCCA
1 GAATTGTCGCTACATGAACATGTACA
42068 GAATTGT
1 GAATTGT
42075 GCCCAGAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (26 bp):
GAATTGTCGCTACATGAACATGTACA
Found at i:44480 original size:12 final size:12
Alignment explanation
Indices: 44463--44487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44453 TCGTGTGAAG
44463 GAAGAAAAAGAT
1 GAAGAAAAAGAT
44475 GAAGAAAAAGAT
1 GAAGAAAAAGAT
44487 G
1 G
44488 TGGAGACAAA
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (12 bp):
GAAGAAAAAGAT
Found at i:45316 original size:17 final size:17
Alignment explanation
Indices: 45294--45359 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
45284 CTGTAGTATA
*
45294 ATTGTCCCTGCATTTTT
1 ATTGTCACTGCATTTTT
*
45311 ATTGTCACTGCGTTTTT
1 ATTGTCACTGCATTTTT
* * * **
45328 ATTGTCATTGTATCTAC
1 ATTGTCACTGCATTTTT
45345 ATTGTCACTGCATTT
1 ATTGTCACTGCATTT
45360 CCATATATAT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.50
Consensus pattern (17 bp):
ATTGTCACTGCATTTTT
Found at i:46578 original size:26 final size:26
Alignment explanation
Indices: 46543--46603 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
46533 AATTACAACA
*
46543 AGAA-TGTCGCTACATGAACATGTAT
1 AGAATTGTCGCTACATGAACATGTAC
* *
46568 AGAATTGTCGCTACATGAACGTGTCC
1 AGAATTGTCGCTACATGAACATGTAC
46594 AGAATTGTCG
1 AGAATTGTCG
46604 TCGCATCTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (26 bp):
AGAATTGTCGCTACATGAACATGTAC
Found at i:48814 original size:37 final size:37
Alignment explanation
Indices: 48764--48843 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
48754 TATTCCTGCG
* *
48764 GTGACAGTTTTGGGTGCAATCTAGAAGTGCTTATGCA
1 GTGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCA
48801 GTGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCA
1 GTGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCA
*
48838 GCGACA
1 GTGACA
48844 TTAGTAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (37 bp):
GTGACAGTTTTGGGCGCAATCTAGAAGTGCTCATGCA
Found at i:50480 original size:21 final size:21
Alignment explanation
Indices: 50454--50496 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
50444 ATTGTCGTTG
50454 AAGCGGATTAGAGAGGCGGTC
1 AAGCGGATTAGAGAGGCGGTC
50475 AAGCGGATTAGAGAGGCGGTC
1 AAGCGGATTAGAGAGGCGGTC
50496 A
1 A
50497 TTCTTAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.42, T:0.14
Consensus pattern (21 bp):
AAGCGGATTAGAGAGGCGGTC
Found at i:51282 original size:30 final size:28
Alignment explanation
Indices: 51228--51284 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
51218 CCGAATAAAC
* *
51228 ATTTTTAAATATATATTTATAATAATTA
1 ATTTTTAAATATATATGTAAAATAATTA
51256 ATTTTTAAATATATAAATGTAAAATAATT
1 ATTTTTAAATATAT--ATGTAAAATAATT
51285 TCAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.56
30 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
ATTTTTAAATATATATGTAAAATAATTA
Found at i:56852 original size:20 final size:21
Alignment explanation
Indices: 56814--56853 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56804 TAAATCGAGC
*
56814 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
56835 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
56854 TAAAAATGAT
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:72739 original size:36 final size:36
Alignment explanation
Indices: 72678--72779 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 36
72668 ATTGTTATTT
* *
72678 GTTTTACTCCCTATTGACCTC-AAGGTTATGATGCTC
1 GTTTTACTCCCTGTTGACC-CAAAGGTCATGATGCTC
* * *
72714 GTTTTACTCTCTGTTGACCCAAAGGTCATTATGTTC
1 GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
*
72750 ATGTTT-CTCCCTGTTGACCCAAAGGTCATG
1 GT-TTTACTCCCTGTTGACCCAAAGGTCATG
72780 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.02
36 52 0.93
37 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.38
Consensus pattern (36 bp):
GTTTTACTCCCTGTTGACCCAAAGGTCATGATGCTC
Found at i:76306 original size:6 final size:6
Alignment explanation
Indices: 76281--76319 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
76271 ACAATTCATA
* * *
76281 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
76320 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Done.