Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012282.1 Kokia drynarioides strain JFW-HI SEQ_127283, 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: 56414
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4722 original size:32 final size:32
Alignment explanation
Indices: 4681--4986 Score: 387
Period size: 32 Copynumber: 9.6 Consensus size: 32
4671 CAAAAAATTC
* * *
4681 TTCACAGATTGATAGCTCCTATGAGCATATTG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
*
4713 TTCACAGATTAATAGCTCTTATGAGCATGCTG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* * * *
4745 TTCACAAATTGATAGCTCTTATGACCATATTG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* *
4777 TTCATAGATTAATAACTCTTATGAGCATACTG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* *
4809 TTCACAGATTGATAGCTCTTATGAGCATACTA
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* *
4841 TTCACAGATTAATAGCTCTTATGAGCATATTA
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* *
4873 TGCACAAATTAATAGCTCTTATGAGCATACTG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* * *
4905 TTCACAGATTAATAACTATTATGAGCATAATG
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
* * * * *
4937 TTCACAGATTGATATCTCTTACGAGTATACTA
1 TTCACAGATTAATAGCTCTTATGAGCATACTG
*
4969 TTCATAGATTAATAGCTC
1 TTCACAGATTAATAGCTC
4987 ATACAAATAT
Statistics
Matches: 234, Mismatches: 40, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 234 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (32 bp):
TTCACAGATTAATAGCTCTTATGAGCATACTG
Found at i:5844 original size:21 final size:21
Alignment explanation
Indices: 5818--5870 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
5808 ATAGGCGTGT
*
5818 GGGACACAC-AAGCGTGTGGAG
1 GGGACACACGAA-CATGTGGAG
5839 GGGACACACGAACATGTGGAG
1 GGGACACACGAACATGTGGAG
* *
5860 GAGCCACACGA
1 GGGACACACGA
5871 CCGTGTAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.32, C:0.23, G:0.38, T:0.08
Consensus pattern (21 bp):
GGGACACACGAACATGTGGAG
Found at i:8838 original size:24 final size:24
Alignment explanation
Indices: 8781--8844 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
8771 TAACTCAGAA
* *
8781 GAGCCCAGATAGGTTAGCTCATAC
1 GAGCCTAGATAAGTTAGCTCATAC
* *
8805 AAG-CTCAGATAAGTTAGCTCATTC
1 GAGCCT-AGATAAGTTAGCTCATAC
8829 GAGCCTAGATAGAGTT
1 GAGCCTAGATA-AGTT
8845 TAACCAGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.03
24 25 0.78
25 6 0.19
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (24 bp):
GAGCCTAGATAAGTTAGCTCATAC
Found at i:13742 original size:24 final size:24
Alignment explanation
Indices: 13693--13743 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
13683 CAGGAACTTT
*
13693 CTCTTTCTCTTCTTCTCTTTCGTC
1 CTCTTTCTCTTCTTCTCTTTCCTC
* *
13717 CTCTTTTTCTTTTTC-CTTCTCCTC
1 CTCTTTCTCTTCTTCTCTT-TCCTC
13741 CTC
1 CTC
13744 GATACCTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.00, C:0.39, G:0.02, T:0.59
Consensus pattern (24 bp):
CTCTTTCTCTTCTTCTCTTTCCTC
Found at i:27444 original size:14 final size:14
Alignment explanation
Indices: 27407--27436 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27397 TAGGATATTA
*
27407 TTTATATTTATCTT
1 TTTAGATTTATCTT
27421 TTTAGATTTATCTT
1 TTTAGATTTATCTT
27435 TT
1 TT
27437 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAGATTTATCTT
Found at i:31208 original size:23 final size:23
Alignment explanation
Indices: 31173--31217 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31163 GTCTTTTTTC
*
31173 TTGCCCAAGATTTTACCCATGAA
1 TTGCCCAAGATTTCACCCATGAA
** *
31196 TTGCCCACTATTTCATCCATGA
1 TTGCCCAAGATTTCACCCATGA
31218 GTAGGCTTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.11, T:0.33
Consensus pattern (23 bp):
TTGCCCAAGATTTCACCCATGAA
Found at i:33333 original size:32 final size:32
Alignment explanation
Indices: 33289--33683 Score: 261
Period size: 32 Copynumber: 12.3 Consensus size: 32
33279 GGTGAATTTT
*
33289 ATTGATAGCTCCTACGAGCTTATTGTTCACAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * *
33321 ATTGATACCTCCTGCGAGCTTGCTGTTCACAA
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * *
33353 ATTGATAGCTCCTATGAGCATACTGTTCATAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * * *
33385 ATTAATAGCTCTTATGAGCTTAATGCTCATAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * *
33417 ATTGATAGCTCTTATGAGCATAC-GATTCACAA
1 ATTGATAGCTCCTACGAGCTTACTG-TTCACAG
* * * * * *
33449 ATTAATAGCTCTTATGAGCATAATGTTCATAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * *
33481 ATTGATAGCTCTTATGAGCATACTATTAACAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * * *
33513 ATTAATAGCTCTTATGAGCATATTGTTCATAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * **
33545 ATTAATAGCTCTTATGAGCATACCATTCACAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * *
33577 ATTAATAGCTCTTATGAGCGTACTGTTCACAT
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * *
33609 ATTAATAGCTCTTATGAGCATACTGTTAACAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
* * * * * *
33641 ATTAATAGCTCTTATGAGCATACTATTCATAG
1 ATTGATAGCTCCTACGAGCTTACTGTTCACAG
33673 ATTGATAGCTC
1 ATTGATAGCTC
33684 TTACAGTATA
Statistics
Matches: 309, Mismatches: 52, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
31 1 0.00
32 307 0.99
33 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (32 bp):
ATTGATAGCTCCTACGAGCTTACTGTTCACAG
Found at i:33404 original size:64 final size:64
Alignment explanation
Indices: 33289--33714 Score: 496
Period size: 64 Copynumber: 6.7 Consensus size: 64
33279 GGTGAATTTT
* * * * * * * ** * * * *
33289 ATTGATAGCTCCTACGAGCTTATTGTTCACAGATTGATACCTCCTGCGAGCTTGCTGTTCACAA
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* * * * *
33353 ATTGATAGCTCCTATGAGCATACTGTTCATAGATTAATAGCTCTTATGAGCTTAATGCTCATAG
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* *
33417 ATTGATAGCTCTTATGAGCATAC-GATTCACAAATTAATAGCTCTTATGAGCATAATGTTCATAG
1 ATTGATAGCTCTTATGAGCATACTG-TTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* * *
33481 ATTGATAGCTCTTATGAGCATACTATTAACAGATTAATAGCTCTTATGAGCATATTGTTCATAG
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* ** * * *
33545 ATTAATAGCTCTTATGAGCATACCATTCACAGATTAATAGCTCTTATGAGCGTACTGTTCACAT
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* * *
33609 ATTAATAGCTCTTATGAGCATACTGTTAACAGATTAATAGCTCTTATGAGCATACTATTCATAG
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
* * * * *
33673 ATTGATAGCTCTTA-CAGTATACTATTCATAGATTACTAGCTC
1 ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTC
33715 ATACAAATAT
Statistics
Matches: 316, Mismatches: 44, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
63 23 0.07
64 293 0.93
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (64 bp):
ATTGATAGCTCTTATGAGCATACTGTTCACAGATTAATAGCTCTTATGAGCATACTGTTCATAG
Found at i:33684 original size:32 final size:32
Alignment explanation
Indices: 33343--33714 Score: 451
Period size: 32 Copynumber: 11.7 Consensus size: 32
33333 TGCGAGCTTG
* * * *
33343 CTGTTCACAAATTGATAGCTCCTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
*
33375 CTGTTCATAGATTAATAGCTCTTATGAGCTTA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* * *
33407 ATGCTCATAGATTGATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* *
33439 C-GATTCACAAATTAATAGCTCTTATGAGCATA
1 CTG-TTCATAGATTAATAGCTCTTATGAGCATA
* *
33471 ATGTTCATAGATTGATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* * *
33503 CTATTAACAGATTAATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
*
33535 TTGTTCATAGATTAATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
** * *
33567 CCATTCACAGATTAATAGCTCTTATGAGCGTA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* *
33599 CTGTTCACATATTAATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* *
33631 CTGTTAACAGATTAATAGCTCTTATGAGCATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* * * *
33663 CTATTCATAGATTGATAGCTCTTA-CAGTATA
1 CTGTTCATAGATTAATAGCTCTTATGAGCATA
* *
33694 CTATTCATAGATTACTAGCTC
1 CTGTTCATAGATTAATAGCTC
33715 ATACAAATAT
Statistics
Matches: 292, Mismatches: 46, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
31 25 0.09
32 266 0.91
33 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (32 bp):
CTGTTCATAGATTAATAGCTCTTATGAGCATA
Found at i:35775 original size:26 final size:26
Alignment explanation
Indices: 35724--35789 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
35714 ACATTGCTCC
35724 CAGAATTGTCGTTGCAGGAACTTGTT
1 CAGAATTGTCGTTGCAGGAACTTGTT
*
35750 CAGAATTATCGTTGC-GTGAA-TATGTT
1 CAGAATTGTCGTTGCAG-GAACT-TGTT
* *
35776 TAGAGTTGTCGTTG
1 CAGAATTGTCGTTG
35790 TATGAGTAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.38
Consensus pattern (26 bp):
CAGAATTGTCGTTGCAGGAACTTGTT
Found at i:45810 original size:44 final size:44
Alignment explanation
Indices: 45747--45833 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
45737 TCACAATCCG
*
45747 TTGGCTATCGTGGTCTACACTGGACCACTCGAAGTGATCCATCT
1 TTGGCTATCGTGATCTACACTGGACCACTCGAAGTGATCCATCT
*
45791 TTGGCTATCGTGATTTACACTGGACCACTCGAAGTGATCCATC
1 TTGGCTATCGTGATCTACACTGGACCACTCGAAGTGATCCATC
45834 CGATAGAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (44 bp):
TTGGCTATCGTGATCTACACTGGACCACTCGAAGTGATCCATCT
Found at i:54010 original size:40 final size:41
Alignment explanation
Indices: 53884--54044 Score: 172
Period size: 41 Copynumber: 4.0 Consensus size: 41
53874 TTGTTATGAT
*
53884 GGTGTA-TTTATCGAGCTTTGTGCCTAGTAGG-TTTAGTGTA
1 GGTGTATTTTATCGAGCTTTGTGCCTAGCAGGCTTT-GTGTA
* * * * *
53924 GTTGTATTTTATCGAGCTTTGAGCCTAGCAGTCTTAGTATCA
1 GGTGTATTTTATCGAGCTTTGTGCCTAGCAGGCTTTGTGT-A
53966 -GTGTA-TTTATCGAGCTTTGTGCCTAGCAGGCTTTGTGCT-
1 GGTGTATTTTATCGAGCTTTGTGCCTAGCAGGCTTTGTG-TA
* *
54005 GGTGTATTTTATC-AGGTTTTGTGCCTAGCAGGCTTCGTGT
1 GGTGTATTTTATCGA-GCTTTGTGCCTAGCAGGCTTTGTGT
54045 CGATTTATTT
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
40 40 0.40
41 58 0.57
42 3 0.03
ACGTcount: A:0.16, C:0.15, G:0.27, T:0.42
Consensus pattern (41 bp):
GGTGTATTTTATCGAGCTTTGTGCCTAGCAGGCTTTGTGTA
Found at i:54031 original size:81 final size:81
Alignment explanation
Indices: 53885--54035 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 81
53875 TGTTATGATG
* *
53885 GTGTATTTATCGAGCTTTGTGCCTAGTAGGTTTAGTGTAGTTGTATTTTATCGAGCTTTGAGCCT
1 GTGTATTTATCGAGCTTTGTGCCTAGCAGGTTTAGTGTAGGTGTATTTTATCGAGCTTTGAGCCT
53950 AGCAGTCTTAGTATCA
66 AGCAGTCTTAGTATCA
* *
53966 GTGTATTTATCGAGCTTTGTGCCTAGCAGGCTTT-GTGCT-GGTGTATTTTATC-AGGTTTTGTG
1 GTGTATTTATCGAGCTTTGTGCCTAGCAGG-TTTAGTG-TAGGTGTATTTTATCGA-GCTTTGAG
54028 CCTAGCAG
63 CCTAGCAG
54036 GCTTCGTGTC
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
80 1 0.02
81 58 0.92
82 4 0.06
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (81 bp):
GTGTATTTATCGAGCTTTGTGCCTAGCAGGTTTAGTGTAGGTGTATTTTATCGAGCTTTGAGCCT
AGCAGTCTTAGTATCA
Found at i:54253 original size:14 final size:14
Alignment explanation
Indices: 54236--54268 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54226 ACGAAATGAT
54236 TATATGGAAATAGA
1 TATATGGAAATAGA
*
54250 TATAT-GAAATAGT
1 TATATGGAAATAGA
54263 TATATG
1 TATATG
54269 AAGTGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (14 bp):
TATATGGAAATAGA
Done.