Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014503.1 Kokia drynarioides strain JFW-HI SEQ_129542, 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: 28276
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:6517 original size:2 final size:2
Alignment explanation
Indices: 6510--6534 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6500 TGAAGACACA
6510 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6535 ACAATGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11258 original size:23 final size:23
Alignment explanation
Indices: 11232--11282 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
11222 ATGAATTTTC
*
11232 AAATTTAAAAAATAAAAAAATTA
1 AAATTTAAAAAATAAAAAAATAA
* *
11255 AAATTTTAAAAATAAAAATATAA
1 AAATTTAAAAAATAAAAAAATAA
11278 AAATT
1 AAATT
11283 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATTTAAAAAATAAAAAAATAA
Found at i:11265 original size:15 final size:15
Alignment explanation
Indices: 11239--11285 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
11229 TTCAAATTTA
*
11239 AAAAATAAAAAAATT
1 AAAAATATAAAAATT
* *
11254 AAAATTTTAAAAA-T
1 AAAAATATAAAAATT
11268 AAAAATATAAAAATT
1 AAAAATATAAAAATT
11283 AAA
1 AAA
11286 TTCTAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATATAAAAATT
Found at i:11279 original size:29 final size:28
Alignment explanation
Indices: 11239--11293 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
11229 TTCAAATTTA
*
11239 AAAAATAAAAAAATTAAAATTTTAAAAAT
1 AAAAATAAAAAAATT-AAATTCTAAAAAT
*
11268 AAAAATATAAAAATTAAATTCTAAAA
1 AAAAATAAAAAAATTAAATTCTAAAA
11294 TTTCAAATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAATAAAAAAATTAAATTCTAAAAAT
Found at i:13714 original size:36 final size:36
Alignment explanation
Indices: 13667--13740 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
13657 CATTACCACA
13667 AGGAATGGTTTACCCTAATATCAAAGGCTTTGCATT
1 AGGAATGGTTTACCCTAATATCAAAGGCTTTGCATT
13703 AGGAATGGTTTACCCTAATATCAAAGGCTTTGCATT
1 AGGAATGGTTTACCCTAATATCAAAGGCTTTGCATT
13739 AG
1 AG
13741 TCGTCCTCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (36 bp):
AGGAATGGTTTACCCTAATATCAAAGGCTTTGCATT
Found at i:18204 original size:21 final size:21
Alignment explanation
Indices: 18180--18231 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
18170 TAGAGGTAAA
*
18180 ACTTGTATCGGTAGAA-GAGTC
1 ACTTGTATCAGTAGAACGA-TC
*
18201 ACTTGTATCAGTAGAACTATC
1 ACTTGTATCAGTAGAACGATC
18222 ACTTGTATCA
1 ACTTGTATCA
18232 ATACAAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACGATC
Found at i:22806 original size:46 final size:46
Alignment explanation
Indices: 22732--22823 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
22722 GATTCATACT
* *
22732 CATCGGTTAGTTCCTGCGGACTTCTGCTTGAAAGACAGTCCATGCG
1 CATCGGTTAGTTCCTGCAGACTTCTGCTTGAAAGACAATCCATGCG
** *
22778 CATCGGTTAGTTTTTGCAGAC-TCTTGCTTGAAAGATAATCCATGCG
1 CATCGGTTAGTTCCTGCAGACTTC-TGCTTGAAAGACAATCCATGCG
22824 GACTCTTGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 2 0.05
46 38 0.95
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (46 bp):
CATCGGTTAGTTCCTGCAGACTTCTGCTTGAAAGACAATCCATGCG
Found at i:22836 original size:28 final size:28
Alignment explanation
Indices: 22796--22851 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
22786 AGTTTTTGCA
22796 GACTCTTGCTTGAAAGATAATCCATGCG
1 GACTCTTGCTTGAAAGATAATCCATGCG
* * *
22824 GACTCTTGCTTGAAGGATAGTCTATGCG
1 GACTCTTGCTTGAAAGATAATCCATGCG
22852 TACACGAGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (28 bp):
GACTCTTGCTTGAAAGATAATCCATGCG
Found at i:23431 original size:17 final size:17
Alignment explanation
Indices: 23411--23444 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23401 TTTCATTTGC
*
23411 ATTTTATTTTTATTAAA
1 ATTTTATTTTAATTAAA
23428 ATTTTATTTTAATTAAA
1 ATTTTATTTTAATTAAA
23445 GTAAGATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTATTTTAATTAAA
Done.