Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014472.1 Kokia drynarioides strain JFW-HI SEQ_129511, 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: 33382
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:43 original size:16 final size:16
Alignment explanation
Indices: 1--45 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
*
1 TAATTACCAAAAT-A-
1 TAATTATCAAAATAAT
*
15 TAA-TATAAAAATAAT
1 TAATTATCAAAATAAT
30 TAATTATCAAAATAAT
1 TAATTATCAAAATAAT
46 ATCCCCATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 7 0.28
14 4 0.16
15 3 0.12
16 11 0.44
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTATCAAAATAAT
Found at i:1387 original size:43 final size:43
Alignment explanation
Indices: 1305--1389 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
1295 ATTAACCTGT
* *
1305 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* * *
1348 TAAATTATATTATTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
1390 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:2092 original size:45 final size:45
Alignment explanation
Indices: 1957--2093 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
1947 GCATAGCTCA
* *
1957 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATAT
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * *
2002 TCAAGCCAAGGATATCAACCTCAATTTGACGAGCCACCACAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
** * * * *
2047 TCAAGGGAAGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
2092 TC
1 TC
2094 TATTCCTCCC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:2114 original size:21 final size:21
Alignment explanation
Indices: 2088--2130 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2078 AGCCATCGCG
*
2088 ATACTCTATTCCTCCCGGGCA
1 ATACTCTACTCCTCCCGGGCA
*
2109 ATACTCTACTCCTCCGGGGCA
1 ATACTCTACTCCTCCCGGGCA
2130 A
1 A
2131 ATAGACCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (21 bp):
ATACTCTACTCCTCCCGGGCA
Found at i:2375 original size:14 final size:14
Alignment explanation
Indices: 2358--2403 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
2348 CATTAAACCC
*
2358 TAAAACCTAAATTA
1 TAAACCCTAAATTA
2372 TAAACCCTAAACTTA
1 TAAACCCTAAA-TTA
*
2387 -AAACCCTAAATCA
1 TAAACCCTAAATTA
2400 TAAA
1 TAAA
2404 GTTAGATGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 23 0.82
15 3 0.11
ACGTcount: A:0.54, C:0.22, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAATTA
Found at i:5551 original size:15 final size:15
Alignment explanation
Indices: 5529--5593 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
5519 AACACATTAC
*
5529 CTTTCTTTTCTTCTT
1 CTTTCTTTCCTTCTT
* *
5544 CATTCTTTCCTCCTT
1 CTTTCTTTCCTTCTT
5559 CTTTCTTTCC-TC-T
1 CTTTCTTTCCTTCTT
5572 CTTTCTTT-CTT-TT
1 CTTTCTTTCCTTCTT
5585 CTTTCTTTC
1 CTTTCTTTC
5594 TTCCCCGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 1 0.02
13 19 0.45
14 1 0.02
15 21 0.50
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCTTTCCTTCTT
Found at i:5566 original size:4 final size:4
Alignment explanation
Indices: 5557--5595 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
5547 TCTTTCCTCC
*
5557 TTCT TTCT TTCCT CTCT TTCT TTCTT TTCT TTCT TTCT T
1 TTCT TTCT TT-CT TTCT TTCT TTC-T TTCT TTCT TTCT T
5596 CCCCGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 24 0.77
5 7 0.23
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:5576 original size:13 final size:13
Alignment explanation
Indices: 5546--5593 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
5536 TTCTTCTTCA
5546 TTCTTTCCTCCTTCT
1 TTCTTTCCT-C-TCT
5561 TTCTTTCCTCTCT
1 TTCTTTCCTCTCT
* *
5574 TTCTTTCTTTTCT
1 TTCTTTCCTCTCT
5587 TTCTTTC
1 TTCTTTC
5594 TTCCCCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 21 0.68
14 1 0.03
15 9 0.29
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTTTCCTCTCT
Found at i:6038 original size:16 final size:17
Alignment explanation
Indices: 6007--6039 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5997 TCCACTTAAC
*
6007 TAAATATATCATTTTGG
1 TAAATATATAATTTTGG
6024 TAAATA-ATAATTTTGG
1 TAAATATATAATTTTGG
6040 GGTACCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.45
Consensus pattern (17 bp):
TAAATATATAATTTTGG
Found at i:18321 original size:21 final size:21
Alignment explanation
Indices: 18295--18338 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
18285 ATTAAAACAA
18295 AATAATTTTGCA-TTTTAACTT
1 AATAATTTTG-ATTTTTAACTT
18316 AATAATTTTGATTTTTAACTT
1 AATAATTTTGATTTTTAACTT
18337 AA
1 AA
18339 AAAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (21 bp):
AATAATTTTGATTTTTAACTT
Found at i:22188 original size:6 final size:6
Alignment explanation
Indices: 22177--22205 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22167 AATTTTTAAA
22177 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
22206 AATTACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:23291 original size:20 final size:20
Alignment explanation
Indices: 23254--23291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23244 TAAAAGATCG
23254 AAAGATAGTAAATTATAATA
1 AAAGATAGTAAATTATAATA
23274 AAAGA-AGTAAATTCATAA
1 AAAGATAGTAAATT-ATAA
23292 AAATTCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (20 bp):
AAAGATAGTAAATTATAATA
Found at i:29722 original size:29 final size:30
Alignment explanation
Indices: 29663--29729 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
29653 AACTCTTTTT
* *
29663 AAAAAG-TTGATGGTCAAATTCGACTTAAAAA
1 AAAAAGATTGAGGGTCAAATTCAAC-T-AAAA
29694 AAAAAGATTGAGGGTCAAATTCAAC-AAAA
1 AAAAAGATTGAGGGTCAAATTCAACTAAAA
*
29723 ATAAAGA
1 AAAAAGA
29730 ATAAGGACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.31
31 6 0.19
32 16 0.50
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (30 bp):
AAAAAGATTGAGGGTCAAATTCAACTAAAA
Found at i:33155 original size:11 final size:11
Alignment explanation
Indices: 33152--33199 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
33142 TTATTTTAAA
*
33152 TTTAAATTTGT
1 TTTAAATTTAT
*
33163 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
33175 TTTAAATTAAG
1 TTTAAATTTAT
33186 TTTAAATTTAT
1 TTTAAATTTAT
33197 TTT
1 TTT
33200 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:33157 original size:6 final size:6
Alignment explanation
Indices: 33118--33226 Score: 70
Period size: 6 Copynumber: 19.0 Consensus size: 6
33108 TAAATTCCTT
* **
33118 TTTAAA TTT--A TTATAAGA TTT-AA TTT-AT TTTAAA TTTAAA TTT-GT
1 TTTAAA TTTAAA TT-TAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
33163 TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA TTTATT TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
33210 ATT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
33227 AAGTCCCATT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 53 0.67
7 1 0.01
8 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:33176 original size:23 final size:23
Alignment explanation
Indices: 33146--33226 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
33136 TTTAATTTAT
*
33146 TTTAAATTTAAATT-TGTTTTAAA
1 TTTAAATTTAAATTAAG-TTTAAA
33169 TTTAAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAATTAAGTTTAAA
** ** *
33192 TTTATTTTTAAAATTAAAATT-AT
1 TTTAAATTT-AAATTAAGTTTAAA
33215 TTTAAATTTAAA
1 TTTAAATTTAAA
33227 AAGTCCCATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
22 3 0.06
23 35 0.73
24 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTAAATTTAAATTAAGTTTAAA
Found at i:33195 original size:29 final size:29
Alignment explanation
Indices: 33163--33226 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
33153 TTAAATTTGT
*
33163 TTTAAATTT-AAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAAATTAAAATT-AGTTTAAA
** *
33192 TTTATTTTTAAAATTAAAATTATTTTAAA
1 TTTAAATTTAAAATTAAAATTAGTTTAAA
33221 TTTAAA
1 TTTAAA
33227 AAGTCCCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTAAATTTAAAATTAAAATTAGTTTAAA
Found at i:33227 original size:17 final size:17
Alignment explanation
Indices: 33118--33226 Score: 130
Period size: 17 Copynumber: 6.4 Consensus size: 17
33108 TAAATTCCTT
*
33118 TTTAAATTTATTATAAGA
1 TTTAAATTTATTTTAA-A
33136 TTT-AATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
33152 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
33169 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
33186 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
33204 ATTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
33221 TTTAAA
1 TTTAAA
33227 AAGTCCCATT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
16 4 0.05
17 58 0.75
18 15 0.19
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.