Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002446.1 Kokia drynarioides strain JFW-HI SEQ_114559, 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: 21787
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:149 original size:12 final size:12
Alignment explanation
Indices: 134--217 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
124 TAGATGGAAG
134 TGATGATGATTT
1 TGATGATGATTT
*
146 TGATGATGAGTT
1 TGATGATGATTT
*
158 CGATGATGAATTT
1 TGATGATG-ATTT
* *
171 GATTATGATGAATT
1 --TGATGATGATTT
**
185 TGATGATGATGA
1 TGATGATGATTT
*
197 AGATGATGATTT
1 TGATGATGATTT
209 TGATGATGA
1 TGATGATGA
218 GGAATTTGGT
Statistics
Matches: 55, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
12 43 0.78
13 3 0.05
14 3 0.05
15 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.27, T:0.40
Consensus pattern (12 bp):
TGATGATGATTT
Found at i:225 original size:15 final size:15
Alignment explanation
Indices: 159--225 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 15
149 TGATGAGTTC
159 GATGATGAATTTGAT
1 GATGATGAATTTGAT
*
174 TATGATGAATTTGAT
1 GATGATGAATTTGAT
189 GATGATGAA---GAT
1 GATGATGAATTTGAT
201 GATGAT---TTTGAT
1 GATGATGAATTTGAT
*
213 GATGAGGAATTTG
1 GATGATGAATTTG
226 GTCATGGACA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 17 0.40
15 26 0.60
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (15 bp):
GATGATGAATTTGAT
Found at i:885 original size:9 final size:9
Alignment explanation
Indices: 873--902 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
863 CCAAATGGGT
873 GGTCAGATG
1 GGTCAGATG
882 GGTCAGATG
1 GGTCAGATG
*
891 GGTCACATG
1 GGTCAGATG
900 GGT
1 GGT
903 GGTCAGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.43, T:0.23
Consensus pattern (9 bp):
GGTCAGATG
Found at i:889 original size:30 final size:30
Alignment explanation
Indices: 849--914 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
839 CGGTAAGAAT
*
849 ATGGGGCAGATGGGCCAAATGGGTGGTCAG
1 ATGGGTCAGATGGGCCAAATGGGTGGTCAG
* *
879 ATGGGTCAGATGGGTCACATGGGTGGTCAG
1 ATGGGTCAGATGGGCCAAATGGGTGGTCAG
909 ATGGGT
1 ATGGGT
915 TATAACATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.45, T:0.21
Consensus pattern (30 bp):
ATGGGTCAGATGGGCCAAATGGGTGGTCAG
Found at i:3694 original size:15 final size:15
Alignment explanation
Indices: 3671--3706 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3661 AAATTTAAAG
3671 AAAAATGAATCTTGT
1 AAAAATGAATCTTGT
* *
3686 AAAATTGAATGTTGT
1 AAAAATGAATCTTGT
3701 AAAAAT
1 AAAAAT
3707 CTTGGTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (15 bp):
AAAAATGAATCTTGT
Found at i:3770 original size:12 final size:13
Alignment explanation
Indices: 3755--3787 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
3745 TTTCTTTTTT
3755 TTTTTAAATTT-A
1 TTTTTAAATTTAA
*
3767 TTTTTAATTTTAA
1 TTTTTAAATTTAA
3780 TTTTTAAA
1 TTTTTAAA
3788 AGTCATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTAAATTTAA
Found at i:5764 original size:23 final size:24
Alignment explanation
Indices: 5738--5787 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
5728 TTACAATTTT
5738 AATAGACATT-TAATAATAA-TAAA
1 AATAGA-ATTATAATAATAATTAAA
* *
5761 AATATAATTATAATTATAATTAAA
1 AATAGAATTATAATAATAATTAAA
5785 AAT
1 AAT
5788 TGAAGAGCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 13 0.57
24 7 0.30
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AATAGAATTATAATAATAATTAAA
Found at i:6239 original size:16 final size:18
Alignment explanation
Indices: 6200--6233 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6190 TAAGTTTATA
6200 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
6217 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
6234 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:19175 original size:3 final size:3
Alignment explanation
Indices: 19167--19208 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
19157 AAGAGTGTAA
19167 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19209 TAAGAAGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19315 original size:30 final size:31
Alignment explanation
Indices: 19281--19353 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
19271 TCTTTGACTC
19281 AAGTGTAAATATTCA-AAATTT-AGAGGACCA
1 AAGTGTAAATATTCAGAAATTTGA-AGGACCA
* *
19311 AAGTGTAAA-AATGAGAAATTTGAAGGACCA
1 AAGTGTAAATATTCAGAAATTTGAAGGACCA
*
19341 AAGGTGAAAATAT
1 AA-GTGTAAATAT
19354 ACCAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 3 0.09
30 24 0.69
31 7 0.20
32 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (31 bp):
AAGTGTAAATATTCAGAAATTTGAAGGACCA
Found at i:19609 original size:13 final size:11
Alignment explanation
Indices: 19582--19624 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19572 AATTAAATAT
19582 TATTTTATTAA
1 TATTTTATTAA
19593 TATTTTACTTAA
1 TATTTTA-TTAA
*
19605 -ATATTTATTAT
1 TAT-TTTATTAA
19616 TATTTTATT
1 TATTTTATT
19625 TAGAAATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:21479 original size:4 final size:4
Alignment explanation
Indices: 21464--21508 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
21454 AACGAAAAAT
21464 GAAA GAAA -AAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
21509 GAAGGAGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 6 0.15
4 33 0.85
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21517 original size:16 final size:16
Alignment explanation
Indices: 21467--21520 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
21457 GAAAAATGAA
*
21467 AGAAAAAAGAAAGAA-
1 AGAAGAAAGAAAGAAG
21482 AGAAAGAAAGAAAGAA-
1 AG-AAGAAAGAAAGAAG
21498 AGAAGAAAG-AAGAAGG
1 AGAAGAAAGAAAGAA-G
21514 AGAAGAA
1 AGAAGAA
21521 GGGGAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
14 5 0.14
15 9 0.26
16 21 0.60
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAGAAAGAAAGAAG
Found at i:21519 original size:19 final size:19
Alignment explanation
Indices: 21464--21521 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
21454 AACGAAAAAT
21464 GAAAGAAA-AAAGAAAGAAA
1 GAAAGAAAGAAAGAAAG-AA
21483 GAAAGAAAGAAAGAAAGAA
1 GAAAGAAAGAAAGAAAGAA
*
21502 GAAAG-AAGAAGGAGAAGAA
1 GAAAGAAAGAAAGA-AAGAA
21521 G
1 G
21522 GGGAAAAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.19
19 21 0.58
20 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAAGAAAGAA
Done.