Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001171.1 Kokia drynarioides strain JFW-HI SEQ_112497, 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: 44834
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2558 original size:72 final size:72
Alignment explanation
Indices: 2254--2561 Score: 339
Period size: 72 Copynumber: 4.3 Consensus size: 72
2244 CAACTTGCAC
* * * * *
2254 CGTCAGCTTATATACGTTTACGCTCGTCAGCTTGCACATGTTTATGCTTGTCAGCTTATATACAT
1 CGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
*
2319 TTA-CCT
66 TTATGCT
** *
2325 CGTCAGCTTATATATATTTACACTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
1 CGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
2390 TTATGCT
66 TTATGCT
** * * * * * * * *
2397 CGTCAGCTTGCACACATTTACGCTCGTCAGCTTGCACATGTTTACCCTTGTCAGCTTATTTATGT
1 CGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
*
2462 TTACGCT
66 TTATGCT
* * ** * * * ** *
2469 CATCAACTTGCACACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCTGATTGCACACGT
1 CGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
2534 TTATGCT
66 TTATGCT
2541 CGTCAGCTTATATACGTTTAC
1 CGTCAGCTTATATACGTTTAC
2562 TTTACTTTGA
Statistics
Matches: 195, Mismatches: 41, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
71 60 0.31
72 135 0.69
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.37
Consensus pattern (72 bp):
CGTCAGCTTATATACGTTTACGCTCGTCAACTTGCACACGTTTACGCTCGTCAGCTTATATACGT
TTATGCT
Found at i:2560 original size:24 final size:24
Alignment explanation
Indices: 2267--2549 Score: 262
Period size: 24 Copynumber: 11.8 Consensus size: 24
2257 CAGCTTATAT
2267 ACGTTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* * * ** *
2291 ATGTTTATGCTTGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
* ** *
2315 ACATTTAC-CTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
** * *
2338 ATATTTACACTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
** *
2362 ACGTTTACGCTCGTCAGCTTATAT
1 ACGTTTACGCTCGTCAGCTTGCAC
*
2386 ACGTTTATGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
2410 ACATTTACGCTCGTCAGCTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* * * ****
2434 ATGTTTACCCTTGTCAGCTTATTT
1 ACGTTTACGCTCGTCAGCTTGCAC
* * *
2458 ATGTTTACGCTCATCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
2482 ACGTTTACGCTCGTCAACTTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
* *
2506 ACGTTTACGCTCGTCTGATTGCAC
1 ACGTTTACGCTCGTCAGCTTGCAC
*
2530 ACGTTTATGCTCGTCAGCTT
1 ACGTTTACGCTCGTCAGCTT
2550 ATATACGTTT
Statistics
Matches: 206, Mismatches: 52, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
23 21 0.10
24 185 0.90
ACGTcount: A:0.20, C:0.27, G:0.16, T:0.36
Consensus pattern (24 bp):
ACGTTTACGCTCGTCAGCTTGCAC
Found at i:10914 original size:52 final size:52
Alignment explanation
Indices: 10842--11221 Score: 571
Period size: 52 Copynumber: 7.5 Consensus size: 52
10832 TTCACATTTG
* * *
10842 ATACTCATGATGACACATAGTCACCTGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
10894 ATACTCACGATGACACATAGTCATCAGACTTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
10946 ATACTCACGATGAC-CATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
10997 ATACTCACGATGACACATAGTTATTGGACCT--T-A----T-AAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
11041 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCTTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * **
11093 ATACTCACAATGACACATAGTCTTCAGACCTCATAATCTATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
11145 ATACTCACGATGAAACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
11197 ATACTCACGATGACACATAGTCATC
1 ATACTCACGATGACACATAGTCATC
11222 AAACCCTTTT
Statistics
Matches: 297, Mismatches: 22, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
44 39 0.13
45 1 0.00
46 1 0.00
47 1 0.00
49 1 0.00
50 1 0.00
51 50 0.17
52 203 0.68
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:37608 original size:39 final size:39
Alignment explanation
Indices: 37554--37633 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
37544 TGCATGCAAG
37554 CATATATTTATGTTGGTACATTTACCCTTTTATTCTTTT
1 CATATATTTATGTTGGTACATTTACCCTTTTATTCTTTT
37593 CATATATTTATGTTGGTACATTTACCCTTTTATTCTTTT
1 CATATATTTATGTTGGTACATTTACCCTTTTATTCTTTT
37632 CA
1 CA
37634 GACCCATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.55
Consensus pattern (39 bp):
CATATATTTATGTTGGTACATTTACCCTTTTATTCTTTT
Found at i:37775 original size:4 final size:4
Alignment explanation
Indices: 37766--37798 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
37756 CGGCCAAAGC
*
37766 GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
37799 CATGCATACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:37783 original size:12 final size:12
Alignment explanation
Indices: 37766--37802 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
37756 CGGCCAAAGC
*
37766 GTATGTATGTAT
1 GTATGTATGCAT
37778 GTATGTATGCAT
1 GTATGTATGCAT
37790 GTATGTATGCAT
1 GTATGTATGCAT
37802 G
1 G
37803 CATACATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.43
Consensus pattern (12 bp):
GTATGTATGCAT
Found at i:38095 original size:4 final size:4
Alignment explanation
Indices: 38086--38117 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
38076 ATATTCGGTA
38086 TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
38118 CATATCGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:39265 original size:57 final size:57
Alignment explanation
Indices: 39174--39327 Score: 166
Period size: 57 Copynumber: 2.7 Consensus size: 57
39164 AAATTGAATA
* * * * *
39174 TTCATTTTTATTTTAGAGAAAATAACATTTATTTTCAAATG-ATTCAATTTTTTTATT
1 TTCATTTTTATTTTAGAGAAAATCATAATAATTTTCAAATGTATTC-ATTTCTTTATT
* * * * *
39231 TTCATTTTCATTTTAGAGAAAGTCATAATCATTTTTAAATGTTTTCATTTCTTTATT
1 TTCATTTTTATTTTAGAGAAAATCATAATAATTTTCAAATGTATTCATTTCTTTATT
* * * *
39288 TTTATTTTTATTTTGGAGAAAACCATAATAATTTCCAAAT
1 TTCATTTTTATTTTAGAGAAAATCATAATAATTTTCAAAT
39328 AATTTTTTAT
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
57 76 0.96
58 3 0.04
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (57 bp):
TTCATTTTTATTTTAGAGAAAATCATAATAATTTTCAAATGTATTCATTTCTTTATT
Found at i:41519 original size:27 final size:26
Alignment explanation
Indices: 41475--41549 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
41465 ATAACCTATA
* * *
41475 TAGTCCACTGGGATAGTAAACACAAGG
1 TAGTCCCCTAGGACAGTAAACAC-AGG
*
41502 TAGTCCCCTAGGACAGTAAACACGGG
1 TAGTCCCCTAGGACAGTAAACACAGG
* *
41528 AAGTCCGCC-AGGACATTAAACA
1 TAGTCC-CCTAGGACAGTAAACA
41550 TGAGACATGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 19 0.46
27 22 0.54
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
TAGTCCCCTAGGACAGTAAACACAGG
Found at i:41540 original size:26 final size:27
Alignment explanation
Indices: 41489--41549 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
41479 CCACTGGGAT
*
41489 AGTAAACACAAGGTAGTCCCCTAGGAC
1 AGTAAACACAAGGAAGTCCCCTAGGAC
*
41516 AGTAAACAC-GGGAAGTCCGCC-AGGAC
1 AGTAAACACAAGGAAGTCC-CCTAGGAC
*
41542 ATTAAACA
1 AGTAAACA
41550 TGAGACATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 19 0.63
27 11 0.37
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.13
Consensus pattern (27 bp):
AGTAAACACAAGGAAGTCCCCTAGGAC
Found at i:44631 original size:6 final size:6
Alignment explanation
Indices: 44620--44703 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
44610 CTGGGCCCAA
* *
44620 TAAATT TAAATT T-ATTT TAGAA-T TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT -TAAATT TAAATT
44666 T--ATT TAAAATT TAAATT T--ATT TAAAATT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT T-AAATT TAAATT TAAA
44704 ATCTATTTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
4 10 0.16
5 6 0.10
6 34 0.55
7 12 0.19
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:44650 original size:17 final size:17
Alignment explanation
Indices: 44620--44701 Score: 112
Period size: 17 Copynumber: 4.8 Consensus size: 17
44610 CTGGGCCCAA
44620 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
44637 TAGAA-TTAAGTTTATTC
1 TA-AATTTAAATTTATTT
44654 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
*
44671 AAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
*
44688 AAAATTTAAATTTA
1 TAAATTTAAATTTA
44702 AAATCTATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
16 2 0.03
17 54 0.93
18 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:44705 original size:24 final size:24
Alignment explanation
Indices: 44667--44714 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
44657 ATTTAAATTT
*
44667 ATTTAAAATTTAAATTTATTTAAA
1 ATTTAAAATTTAAATCTATTTAAA
44691 ATTT-AAATTTAAAATCTATTTAAA
1 ATTTAAAATTT-AAATCTATTTAAA
44715 TAATGTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTTAAAATTTAAATCTATTTAAA
Done.