Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003359.1 Kokia drynarioides strain JFW-HI SEQ_116080, 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: 21668
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:3028 original size:289 final size:289
Alignment explanation
Indices: 2509--3091 Score: 1148
Period size: 289 Copynumber: 2.0 Consensus size: 289
2499 GGGAAAATCC
2509 TATTTAAAAAGCAAAAAGATTATGCTTCGACTCTTACAAAGAACGGACTATCAGAGTCAGCTGCC
1 TATTTAAAAAGCAAAAAGATTATGCTTCGACTCTTACAAAGAACGGACTATCAGAGTCAGCTGCC
*
2574 CAATCAATCCTCATCCTTACATACCGTTACTGTATAAGATAGATCTCGTTGTGAAAGATCAATTA
66 CAATCAATCCTCATCCTTACATACCATTACTGTATAAGATAGATCTCGTTGTGAAAGATCAATTA
2639 CTGGAAAATTTATGAGTAGAGCCGAAGAGTGTGAACTGTACAAGTTACCAATTACATGAAGGAAT
131 CTGGAAAATTTATGAGTAGAGCCGAAGAGTGTGAACTGTACAAGTTACCAATTACATGAAGGAAT
2704 GAGCTCCGGTGTACAGAGAAGACCTCACCGTTTATAAAGTAACCATAGAAACAATGGAACCCACT
196 GAGCTCCGGTGTACAGAGAAGACCTCACCGTTTATAAAGTAACCATAGAAACAATGGAACCCACT
2769 ATTTATTTATCCATTTCTATTTACTCCTT
261 ATTTATTTATCCATTTCTATTTACTCCTT
*
2798 TATTTAAAAAGCAAAAAGATTATGCTTCGACTCTTGCAAAGAACGGACTATCAGAGTCAGCTGCC
1 TATTTAAAAAGCAAAAAGATTATGCTTCGACTCTTACAAAGAACGGACTATCAGAGTCAGCTGCC
2863 CAATCAATCCTCATCCTTACATACCATTACTGTATAAGATAGATCTCGTTGTGAAAGATCAATTA
66 CAATCAATCCTCATCCTTACATACCATTACTGTATAAGATAGATCTCGTTGTGAAAGATCAATTA
2928 CTGGAAAATTTATGAGTAGAGCCGAAGAGTGTGAACTGTACAAGTTACCAATTACATGAAGGAAT
131 CTGGAAAATTTATGAGTAGAGCCGAAGAGTGTGAACTGTACAAGTTACCAATTACATGAAGGAAT
2993 GAGCTCCGGTGTACAGAGAAGACCTCACCGTTTATAAAGTAACCATAGAAACAATGGAACCCACT
196 GAGCTCCGGTGTACAGAGAAGACCTCACCGTTTATAAAGTAACCATAGAAACAATGGAACCCACT
3058 ATTTATTTATCCATTTCTATTTACTCCTT
261 ATTTATTTATCCATTTCTATTTACTCCTT
3087 TATTT
1 TATTT
3092 TAGTTAATAT
Statistics
Matches: 292, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
289 292 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (289 bp):
TATTTAAAAAGCAAAAAGATTATGCTTCGACTCTTACAAAGAACGGACTATCAGAGTCAGCTGCC
CAATCAATCCTCATCCTTACATACCATTACTGTATAAGATAGATCTCGTTGTGAAAGATCAATTA
CTGGAAAATTTATGAGTAGAGCCGAAGAGTGTGAACTGTACAAGTTACCAATTACATGAAGGAAT
GAGCTCCGGTGTACAGAGAAGACCTCACCGTTTATAAAGTAACCATAGAAACAATGGAACCCACT
ATTTATTTATCCATTTCTATTTACTCCTT
Found at i:9116 original size:16 final size:16
Alignment explanation
Indices: 9097--9176 Score: 56
Period size: 15 Copynumber: 4.9 Consensus size: 16
9087 ATAACATTGA
9097 ATTTTGAATTTTTTAT
1 ATTTTGAATTTTTTAT
*
9113 ATTTTAAAATCATTTTTAT
1 ATTTT-GAAT--TTTTTAT
* **
9132 TTTTTGAA-TTTAAAT
1 ATTTTGAATTTTTTAT
* *
9147 ATTTTTAATTTTTCAT
1 ATTTTGAATTTTTTAT
*
9163 ATTTT-TATTTTTTA
1 ATTTTGAATTTTTTA
9177 AAAATTTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
15 18 0.37
16 15 0.31
17 3 0.06
18 2 0.04
19 11 0.22
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
ATTTTGAATTTTTTAT
Found at i:18272 original size:18 final size:18
Alignment explanation
Indices: 18249--18289 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18239 TTTAAAAAGA
* *
18249 AAATTTATTTAGATTTTT
1 AAATTTATTTAAAATTTT
*
18267 AAATTTTTTTAAAATTTT
1 AAATTTATTTAAAATTTT
18285 AAATT
1 AAATT
18290 AATAAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
AAATTTATTTAAAATTTT
Found at i:18600 original size:17 final size:18
Alignment explanation
Indices: 18578--18611 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18568 ACCAATTTTT
*
18578 TATTTTTTAT-TTTTATC
1 TATTTTTAATATTTTATC
18595 TATTTTTAATATTTTAT
1 TATTTTTAATATTTTAT
18612 TTAATTGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTAATATTTTATC
Found at i:18862 original size:16 final size:16
Alignment explanation
Indices: 18841--18878 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18831 GCACTATACT
18841 TAAAAAAA-ATTAAAGA
1 TAAAAAAATATTAAA-A
*
18857 TAAAAAAATTTTAAAA
1 TAAAAAAATATTAAAA
18873 TAAAAA
1 TAAAAA
18879 TTTATCGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATATTAAAA
Found at i:19115 original size:32 final size:33
Alignment explanation
Indices: 19060--19157 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 33
19050 TATAATTTAT
19060 TATATTATTTATAAGTTTTTAAATATTT-TAAA
1 TATATTATTTATAAGTTTTTAAATATTTATAAA
19092 TATATT-TTTACTAA-TTTTATAAATATTTATAAA
1 TATATTATTTA-TAAGTTTT-TAAATATTTATAAA
*
19125 GTA-ATTTAATTTTATAAATTTTTATAATATTTA
1 -TATA-TT-A-TTTATAAGTTTTTA-AATATTTA
19158 CAATATTTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
31 8 0.14
32 18 0.32
33 5 0.09
34 4 0.07
36 5 0.09
37 16 0.29
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (33 bp):
TATATTATTTATAAGTTTTTAAATATTTATAAA
Found at i:19234 original size:10 final size:10
Alignment explanation
Indices: 19221--19327 Score: 57
Period size: 10 Copynumber: 11.0 Consensus size: 10
19211 TTTAGGATTT
19221 TTTTTATATA
1 TTTTTATATA
19231 TTTTTA-ATA
1 TTTTTATATA
* *
19240 ATTGTA-ATGA
1 TTTTTATAT-A
19250 TTTTTATA-A
1 TTTTTATATA
19259 CTTTTTA-ATA
1 -TTTTTATATA
*
19269 TTTTTATAGA
1 TTTTTATATA
* *
19279 ATTTTATAAA
1 TTTTTATATA
* *
19289 ATTTTAAATA
1 TTTTTATATA
*
19299 -TTTTAAATA
1 TTTTTATATA
19308 TGTTTTAT-TAA
1 T-TTTTATAT-A
19319 TTTTT-TATA
1 TTTTTATATA
19328 GATATTATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
9 28 0.36
10 42 0.54
11 8 0.10
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.60
Consensus pattern (10 bp):
TTTTTATATA
Found at i:19254 original size:31 final size:32
Alignment explanation
Indices: 19191--19254 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
19181 TTTTTATATG
*
19191 TTTATATCAATTTTAATAATTTTAGGATTTTT
1 TTTATATCAATTTTAATAATTTAAGGATTTTT
* *
19223 TTTATAT-ATTTTTAATAATTGTAATGATTTTT
1 TTTATATCAATTTTAATAATT-TAAGGATTTTT
19255 ATAACTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (32 bp):
TTTATATCAATTTTAATAATTTAAGGATTTTT
Found at i:19271 original size:19 final size:18
Alignment explanation
Indices: 19221--19323 Score: 68
Period size: 20 Copynumber: 5.3 Consensus size: 18
19211 TTTAGGATTT
19221 TTTTTATATATTTTTAATAA
1 TTTTTA-ATATTTTT-ATAA
*
19241 -TTGTAATGATTTTTATAA
1 TTTTTAAT-ATTTTTATAA
19259 CTTTTTAATATTTTTATAGAA
1 -TTTTTAATATTTTTAT--AA
*
19280 TTTTATAA-AATTTTA-AA
1 TTTT-TAATATTTTTATAA
19297 TATTTTAAATATGTTTTATTAA
1 T-TTTT-AATAT-TTTTA-TAA
19319 TTTTT
1 TTTTT
19324 TATAGATATT
Statistics
Matches: 67, Mismatches: 4, Indels: 23
0.71 0.04 0.24
Matches are distributed among these distances:
17 4 0.06
18 11 0.16
19 19 0.28
20 21 0.31
21 9 0.13
22 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTTAATATTTTTATAA
Found at i:20547 original size:9 final size:9
Alignment explanation
Indices: 20533--20561 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
20523 CCTTACACCT
20533 AATAAAATA
1 AATAAAATA
20542 AATAAAATA
1 AATAAAATA
20551 AAT-AAATA
1 AATAAAATA
20559 AAT
1 AAT
20562 CCATAACGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAAATA
Done.