Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009162.1 Kokia drynarioides strain JFW-HI SEQ_123867, 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: 6921
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:463 original size:22 final size:22
Alignment explanation
Indices: 440--481 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
430 CCCTCTTAAT
440 TTTCTATTA-TTTATTTATTTA
1 TTTCTATTATTTTATTTATTTA
*
461 TTTGTATTATTTTATTTATTT
1 TTTCTATTATTTTATTTATTT
482 TGGGTATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTCTATTATTTTATTTATTTA
Found at i:472 original size:9 final size:9
Alignment explanation
Indices: 446--543 Score: 58
Period size: 9 Copynumber: 10.7 Consensus size: 9
436 TAATTTTCTA
446 TTATTTA-T
1 TTATTTATT
454 TTATTTATT
1 TTATTTATT
463 TGTA-TTATT
1 T-TATTTATT
472 TTATTTATT
1 TTATTTATT
***
481 TTGGGTATT
1 TTATTTATT
* *
490 TAATTTGTAT
1 TTATTTAT-T
*
500 TTATTTATGGG
1 TTATTTAT--T
511 TT-TTTATT
1 TTATTTATT
*
519 TCATTTCATT
1 TTATTT-ATT
*
529 TCATTTATT
1 TTATTTATT
538 TTATTT
1 TTATTT
544 TCTTTTAGTT
Statistics
Matches: 68, Mismatches: 15, Indels: 13
0.71 0.16 0.14
Matches are distributed among these distances:
8 10 0.15
9 33 0.49
10 23 0.34
11 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTTATT
Found at i:505 original size:24 final size:24
Alignment explanation
Indices: 449--529 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
439 TTTTCTATTA
**
449 TTTATTTATTTATTTGTA-TT-AT
1 TTTATTTATTTATGGGTATTTAAT
471 TTTATTTATTT-TGGGTATTTAAT
1 TTTATTTATTTATGGGTATTTAAT
*
494 TTGTATTTATTTATGGGT-TTTTAT
1 TT-TATTTATTTATGGGTATTTAAT
*
518 TTCATTTCATTT
1 TTTATTT-ATTT
530 CATTTATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.08
22 13 0.26
23 8 0.16
24 20 0.40
25 5 0.10
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.68
Consensus pattern (24 bp):
TTTATTTATTTATGGGTATTTAAT
Found at i:4656 original size:26 final size:26
Alignment explanation
Indices: 4618--4668 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
4608 ATCGCCCCAA
*
4618 AAAAAAGGGAAAAGGAAAA-GAAAAG
1 AAAAAAGGAAAAAGGAAAAGGAAAAG
4643 AAAAAAGAGAAAAAGGAAAAGGAAAA
1 AAAAAAG-GAAAAAGGAAAAGGAAAA
4669 AGAGAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (26 bp):
AAAAAAGGAAAAAGGAAAAGGAAAAG
Found at i:4661 original size:21 final size:20
Alignment explanation
Indices: 4633--4673 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
4623 AGGGAAAAGG
4633 AAAAGAAAAGAAAAAAGAGA
1 AAAAGAAAAGAAAAAAGAGA
*
4653 AAAAGGAAAAGGAAAAAGAGA
1 AAAA-GAAAAGAAAAAAGAGA
4674 GGTTGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAGAAAAAAGAGA
Found at i:5778 original size:199 final size:199
Alignment explanation
Indices: 5435--5920 Score: 661
Period size: 199 Copynumber: 2.4 Consensus size: 199
5425 GACCAGTGAA
* *
5435 ACACCAAATCCTACCTTCCCGAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCAAATCTCAATCT
1 ACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCAAATCTCAATCT
* * *
5500 CTATTGAAGTTGCAGTGGAATGGAGTAAAGCCACAACCTCAAATCCTATATCCCTGAAGTTACAG
66 CTACTGAAGTTGCAGTGGAATGCAGTAAAGCCACAACCTCAAATCCTATATCCCTGAACTTACAG
* *
5565 TAAATCGAATTAAAACAAGTAACGGACCTCGATCTCGC-TGAAGTTACAATAGAATAGAGCGAAG
131 TAAATCGAATTAAAACAAGTAACGAACCTCAATCTC-CTTGAAGTTACAATAGAATAGAGCGAAG
5629 TTACC
195 TTACC
* * * * *
5634 ACACCAAATCCTATCTTCCTAAAGTTGAAGTGAAGTGGAGTAAAACAAGTAGCAAATCTCAATAT
1 ACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCAAATCTCAATCT
* * * *
5699 CTACTAAAGTTGCAGTGGAATGCATTGAAGCCACAACCTCAAATCCTATATCCTTGAACTTACAG
66 CTACTGAAGTTGCAGTGGAATGCAGTAAAGCCACAACCTCAAATCCTATATCCCTGAACTTACAG
** * * * * * *
5764 TGGATCGGATTAAAACAAGTAACGAACTTCAATCTCCTTGAAGTTACAGTGGAATGGAGTGAAGT
131 TAAATCGAATTAAAACAAGTAACGAACCTCAATCTCCTTGAAGTTACAATAGAATAGAGCGAAGT
5829 TACC
196 TACC
* * * **
5833 ACACCAAATCCTATCTTCTTGAAGTTGCAGTGAAGCCGATTAAAAATATAGTAGCGGATCTCAAT
1 ACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATT-AAAACA-AGTAGCAAATCTCAAT
*
5898 CTC-CCTGAAGTTGCAGTGGAATG
64 CTCTACTGAAGTTGCAGTGGAATG
5921 GAGTGAATTT
Statistics
Matches: 248, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
198 1 0.00
199 208 0.84
200 23 0.09
201 16 0.06
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (199 bp):
ACACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGGATTAAAACAAGTAGCAAATCTCAATCT
CTACTGAAGTTGCAGTGGAATGCAGTAAAGCCACAACCTCAAATCCTATATCCCTGAACTTACAG
TAAATCGAATTAAAACAAGTAACGAACCTCAATCTCCTTGAAGTTACAATAGAATAGAGCGAAGT
TACC
Found at i:5842 original size:99 final size:100
Alignment explanation
Indices: 5455--5932 Score: 386
Period size: 99 Copynumber: 4.8 Consensus size: 100
5445 CTACCTTCCC
* * *
5455 GAAGTTGCAGTGAAGCGGATTAAAACAAGTAGC-AAATCTCAATCTCTATTGAAGTTGCAGTGGA
1 GAAGTTACAGTGAATCGGATTAAAACAAGTAGCGAAATCTCAATCTC-CTTGAAGTTGCAGTGGA
* ** *
5519 ATGGAGTAAAGCCACAACCTCAAATCCTATATCCCT
65 ATGGAGTGAAGTTACAACCTCAAATCCTATATCCTT
* * * * * * * * *
5555 GAAGTTACAGTAAATCGAATTAAAACAAGTAACG-GACCTCGATCTCGC-TGAAGTTACAATAGA
1 GAAGTTACAGTGAATCGGATTAAAACAAGTAGCGAAATCTCAATCTC-CTTGAAGTTGCAGTGGA
* * * *
5618 ATAGAGCGAAGTTACCACAC-CAAATCCTATCTTCC-T
65 ATGGAGTGAAGTTACAAC-CTCAAATCCTAT-ATCCTT
* * * *
5654 AAAGTTGA-AGTGAAGT-GGAGTAAAACAAGTAGC-AAATCTCAATAT-CTACTAAAGTTGCAGT
1 GAAGTT-ACAGTGAA-TCGGATTAAAACAAGTAGCGAAATCTCAATCTCCT--TGAAGTTGCAGT
* * **
5715 GGAATGCATTGAAGCCACAACCTCAAATCCTATATCCTT
62 GGAATGGAGTGAAGTTACAACCTCAAATCCTATATCCTT
* * * * *
5754 GAACTTACAGTGGATCGGATTAAAACAAGTAACGAACT-TCAATCTCCTTGAAGTTACAGTGGAA
1 GAAGTTACAGTGAATCGGATTAAAACAAGTAGCGAAATCTCAATCTCCTTGAAGTTGCAGTGGAA
* * *
5818 TGGAGTGAAGTTACCACAC-CAAATCCTATCTTCTT
66 TGGAGTGAAGTTACAAC-CTCAAATCCTATATCCTT
* * * * * *
5853 GAAGTTGCAGTGAAGCCGATTAAAAATATAGTAGCG-GATCTCAATCTCCCTGAAGTTGCAGTGG
1 GAAGTTACAGTGAATCGGATT-AAAACA-AGTAGCGAAATCTCAATCTCCTTGAAGTTGCAGTGG
*
5917 AATGGAGTGAATTTAC
64 AATGGAGTGAAGTTAC
5933 GTAGCCACGA
Statistics
Matches: 290, Mismatches: 69, Indels: 37
0.73 0.17 0.09
Matches are distributed among these distances:
97 1 0.00
99 128 0.44
100 113 0.39
101 48 0.17
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (100 bp):
GAAGTTACAGTGAATCGGATTAAAACAAGTAGCGAAATCTCAATCTCCTTGAAGTTGCAGTGGAA
TGGAGTGAAGTTACAACCTCAAATCCTATATCCTT
Found at i:6242 original size:48 final size:47
Alignment explanation
Indices: 5942--6405 Score: 474
Period size: 46 Copynumber: 9.9 Consensus size: 47
5932 CGTAGCCACG
* *
5942 ATCCAATCTTATACCCCTAAATCCAGAGGGGTAGATTGAAGCCAC-C
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCACAC
* * * *
5988 AT-TAGTTCTTATACCCCTAAATCCAAAGAGGCAGATTGAAGTCAC-C
1 ATCCA-ATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCACAC
* ** * * *
6034 ATCCAATCTTATATCGATAAATCCAGAA-GGGAAAATTGAATCCA-AC
1 ATCCAATCTTATACCCCTAAATCCA-AAGGGGCAGATTGAAGCCACAC
* * * *
6080 ATCTAATCTTATACCCCTAAATCTAAAGGGGTAGATTGAAGCCGC-C
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCACAC
* * *
6126 ATCCAATCTTATACCCCTAAATCTAAAGGGGCAAATTGAAGTCAC-C
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCACAC
* * * *
6172 ATCGAATCTTATACCCCTAAATCTAGAGGGGCAGATTGGAGCCACCAC
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCA-CAC
* * * * * *
6220 ATCCAATCTTATACCCTTAAATCCAAAAGGACAGATTAAAGTCATCAT
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCA-CAC
* * * *
6268 ATCCAATCTTATACTCCTAAATCTAAAAGGGCAGATTGAAACCACCAC
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCA-CAC
* * *
6316 ATCCAATCTTATAACTCTAAATCCAAAGGGGCAGATTCAAGCCACTAC
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCAC-AC
* * *
6364 ATCCAATCTTATACCCCTAAATCTAGAGGGACAGATTGAAGC
1 ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGC
6406 TGCAGAAGCA
Statistics
Matches: 341, Mismatches: 68, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
45 3 0.01
46 181 0.53
47 5 0.01
48 152 0.45
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (47 bp):
ATCCAATCTTATACCCCTAAATCCAAAGGGGCAGATTGAAGCCACAC
Found at i:6495 original size:50 final size:50
Alignment explanation
Indices: 6368--6673 Score: 265
Period size: 50 Copynumber: 6.1 Consensus size: 50
6358 CACTACATCC
* * * * **
6368 AATCTTATACCCCTAAA-TC-TAGAGGGACAGATTGAAGCTGCAGAAGCAA
1 AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGC-A
* * ** * *
6417 AAACTTTTACCCCTAAAGTTGTAAAGGGGCAAATTAAAGCTATAGAAGAA
1 AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
* * * *
6467 AATCTTATACTCCTAAAGCCGTAGAGGGGCAGATTGAAGCTACAGAAGCA
1 AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
* * ** * * * *
6517 AATCTTATACCTCTACAGTTGTAGAGGGGCAAATTGAAGATGTAGAAGTA
1 AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
* * * * * * *
6567 AATCTTATGCCTCTAAAGCCATAGAGGGGCAAATTAAAGTTGTAAAATCA
1 AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
* * * *
6617 AATCTTATACCCCCTAAAACTGTAGAGGAGCAAATTAAAGCCATAGAAGCA
1 AATCTTATA-CCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
6668 AATCTT
1 AATCTT
6674 GATCTCCTTG
Statistics
Matches: 203, Mismatches: 51, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
49 15 0.07
50 130 0.64
51 58 0.29
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.24
Consensus pattern (50 bp):
AATCTTATACCCCTAAAGCCGTAGAGGGGCAAATTAAAGCTATAGAAGCA
Found at i:6514 original size:101 final size:99
Alignment explanation
Indices: 6368--6681 Score: 328
Period size: 100 Copynumber: 3.1 Consensus size: 99
6358 CACTACATCC
* * * * *
6368 AATCTTATACCCCTAAA-TCTAGAGGGACAGATTGAAGCTGCAGAAGCAAAAACTTTTACCCCTA
1 AATCTTATACTCCTAAAGCCTAGAGGGGCAGATTGAAGCTGCAGAAGC-AAATCTTATACCCCTA
*
6432 AAGTTGTAAAGGGGCAAATTAAAGCTATAGAAGAA
65 AAGTTGTAGAGGGGCAAATTAAAGCTATAGAAGAA
* *
6467 AATCTTATACTCCTAAAGCCGTAGAGGGGCAGATTGAAGCTACAGAAGCAAATCTTATACCTCTA
1 AATCTTATACTCCTAAAGCC-TAGAGGGGCAGATTGAAGCTGCAGAAGCAAATCTTATACCCCTA
* * * * *
6532 CAGTTGTAGAGGGGCAAATTGAAGATGTAGAAGTA
65 AAGTTGTAGAGGGGCAAATTAAAGCTATAGAAGAA
* * * * * * *
6567 AATCTTATGC-CTCTAAAGCCATAGAGGGGCAAATTAAAGTTGTAAAATCAAATCTTATACCCCC
1 AATCTTATACTC-CTAAAGCC-TAGAGGGGCAGATTGAAGCTGCAGAAGCAAATCTTATA-CCCC
** * * *
6631 TAAAACTGTAGAGGAGCAAATTAAAGCCATAGAAGCA
63 TAAAGTTGTAGAGGGGCAAATTAAAGCTATAGAAGAA
6668 AATCTTGAT-CTCCT
1 AATCTT-ATACTCCT
6682 TGAGGTTGCC
Statistics
Matches: 177, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
99 17 0.10
100 91 0.51
101 66 0.37
102 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (99 bp):
AATCTTATACTCCTAAAGCCTAGAGGGGCAGATTGAAGCTGCAGAAGCAAATCTTATACCCCTAA
AGTTGTAGAGGGGCAAATTAAAGCTATAGAAGAA
Done.