Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001068.1 Kokia drynarioides strain JFW-HI SEQ_112319, 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: 41542
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Found at i:2149 original size:16 final size:16
Alignment explanation
Indices: 2128--2158 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2118 ATAATGTGAA
2128 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
2144 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
2159 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:5513 original size:30 final size:30
Alignment explanation
Indices: 5477--5537 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
5467 TTGTAAGAGC
*
5477 GATACTGGCTTGTAAGAGCGATACTGGCTT
1 GATACTGGCTCGTAAGAGCGATACTGGCTT
*
5507 GATACTGGCTCGTGAGAGCGATACTGGCTT
1 GATACTGGCTCGTAAGAGCGATACTGGCTT
5537 G
1 G
5538 TGAGAGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (30 bp):
GATACTGGCTCGTAAGAGCGATACTGGCTT
Found at i:5614 original size:19 final size:19
Alignment explanation
Indices: 5433--5645 Score: 127
Period size: 19 Copynumber: 11.6 Consensus size: 19
5423 TATTGGCTCA
*
5433 AAGAGCAATACTGGCTCGC
1 AAGAGCAATACTGGCTCGT
* * * * *
5452 AAGAGTAATATTAGATTGT
1 AAGAGCAATACTGGCTCGT
* *
5471 AAGAGCGATACTGGCTTGT
1 AAGAGCAATACTGGCTCGT
*
5490 AAGAGCGATACTGGCT--T
1 AAGAGCAATACTGGCTCGT
5507 ----G--ATACTGGCTCGT
1 AAGAGCAATACTGGCTCGT
* * *
5520 GAGAGCGATACTGGCTTGT
1 AAGAGCAATACTGGCTCGT
* ** *
5539 GAGAGTGATATTGGCTCGT
1 AAGAGCAATACTGGCTCGT
* * * *
5558 AGGAGCAATATTGGCTTGC
1 AAGAGCAATACTGGCTCGT
* *
5577 AAGAGCAGTATTGGCTCGT
1 AAGAGCAATACTGGCTCGT
*
5596 AAGAGCAATACTGGTTCGT
1 AAGAGCAATACTGGCTCGT
* **
5615 GAGAGCAATACTTACTCGT
1 AAGAGCAATACTGGCTCGT
*
5634 AAGAGAAATACT
1 AAGAGCAATACT
5646 ATACGGGCTC
Statistics
Matches: 152, Mismatches: 34, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
11 9 0.06
13 2 0.01
17 2 0.01
19 139 0.91
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (19 bp):
AAGAGCAATACTGGCTCGT
Found at i:7453 original size:52 final size:52
Alignment explanation
Indices: 7375--7478 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
7365 AGACGTCTAA
7375 GATAGAGCAGTAATGTAGACAGTAACTGGGGAGATTGCCAAAGAGGCACAAC
1 GATAGAGCAGTAATGTAGACAGTAACTGGGGAGATTGCCAAAGAGGCACAAC
7427 GATAGAGCAGTAATGTAGACAGTAACTGGGGAGATTGCCAAAGAGGCACAAC
1 GATAGAGCAGTAATGTAGACAGTAACTGGGGAGATTGCCAAAGAGGCACAAC
7479 TAGATCTAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (52 bp):
GATAGAGCAGTAATGTAGACAGTAACTGGGGAGATTGCCAAAGAGGCACAAC
Found at i:11961 original size:58 final size:56
Alignment explanation
Indices: 11870--11987 Score: 173
Period size: 58 Copynumber: 2.1 Consensus size: 56
11860 AAGGAATATA
*
11870 AATACTAGCTCGAAGAGCAATACTGGCTCGCAAGAGAAATACTGGCTCGTAAGAGC
1 AATACTAGCTCGAAGAACAATACTGGCTCGCAAGAGAAATACTGGCTCGTAAGAGC
* * * *
11926 AATACTAGCTCTTGAGGAACAATACTGGCTTGCAAGAGCAATACTGGCTCGTGAGAGC
1 AATACTAGCTC--GAAGAACAATACTGGCTCGCAAGAGAAATACTGGCTCGTAAGAGC
11984 AATA
1 AATA
11988 TTGACTTGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 11 0.20
58 44 0.80
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (56 bp):
AATACTAGCTCGAAGAACAATACTGGCTCGCAAGAGAAATACTGGCTCGTAAGAGC
Found at i:11982 original size:19 final size:19
Alignment explanation
Indices: 11870--12006 Score: 132
Period size: 19 Copynumber: 7.2 Consensus size: 19
11860 AAGGAATATA
*
11870 AATACTAGCTCG-AAGAGC
1 AATACTGGCTCGTAAGAGC
* *
11888 AATACTGGCTCGCAAGAGA
1 AATACTGGCTCGTAAGAGC
11907 AATACTGGCTCGTAAGAGC
1 AATACTGGCTCGTAAGAGC
* * * *
11926 AATACTAGCTCTTGAGGAAC
1 AATACTGGCTCGT-AAGAGC
* *
11946 AATACTGGCTTGCAAGAGC
1 AATACTGGCTCGTAAGAGC
*
11965 AATACTGGCTCGTGAGAGC
1 AATACTGGCTCGTAAGAGC
* * * *
11984 AATATTGACTTGTAAGAGA
1 AATACTGGCTCGTAAGAGC
12003 AATA
1 AATA
12007 TTGTACTGAC
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
18 11 0.12
19 71 0.75
20 13 0.14
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (19 bp):
AATACTGGCTCGTAAGAGC
Found at i:15180 original size:195 final size:194
Alignment explanation
Indices: 14865--15291 Score: 515
Period size: 195 Copynumber: 2.2 Consensus size: 194
14855 TATGGTGCCG
* * * *
14865 CATATGTT-CGAGTCCTCGACAGCTCGTGCGAGTAGCATCGTGAATCGAGAAGATGAGAAATGAA
1 CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAATCGAGAAGAAGAGAAATGAA
* **
14929 TCCAAGAATGGATTATAGGCCCTACGATGGTTGGGATTTATGCATAAGTGCATATTCTCGACAGC
66 TCCAAGAATGGATTACAGGCCCTACGATGGTTACGATTTATGCATAAGTGCATATTCTCGACAGC
* * *
14994 TCGTGTGAGCAACATCGTTAGGGGACAGTTATATGCACAGATACCGTATTGATGGCTAAGGTAAC
131 TCGTGTGAGCAACATCGTTAGGGGACAGTTACA-G-ACAGACACCGTATCGATGGCTAAGGTAAC
15059 A
194 A
* * * *
15060 CAT-TGGTTGTGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAGTTGA-AA-AAGAGATATGA
1 CATAT-GTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAATCGAGAAGAAGAGAAATG-
* *
15122 AATCCTAA-AATGGATTACAGGCCTTACGATGGTTACGATTTATGCTTGAA-TGCATATTCTCGA
64 AATCC-AAGAATGGATTACAGGCCCTACGATGGTTACGATTTATGCAT-AAGTGCATATTCTCGA
* * * * **
15185 CAGCTTGTGTGAGCAGCATCGTTAGGGGACTGTTACAGACAGACATCGTATCGATGGCTGGGGTA
127 CAGCTCGTGTGAGCAACATCGTTAGGGGACAGTTACAGACAGACACCGTATCGATGGCTAAGGTA
* *
15250 CCG
192 ACA
* * *
15253 CATATGTTGCGAGTCATTGATAGCTTGTGTGAGCAGCAT
1 CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCAT
15292 TCGGCATTGG
Statistics
Matches: 198, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
193 56 0.28
194 11 0.06
195 93 0.47
196 38 0.19
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (194 bp):
CATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCGTGAATCGAGAAGAAGAGAAATGAA
TCCAAGAATGGATTACAGGCCCTACGATGGTTACGATTTATGCATAAGTGCATATTCTCGACAGC
TCGTGTGAGCAACATCGTTAGGGGACAGTTACAGACAGACACCGTATCGATGGCTAAGGTAACA
Found at i:19265 original size:16 final size:16
Alignment explanation
Indices: 19244--19275 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19234 AGTAATTTTT
*
19244 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
19260 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
19276 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:21148 original size:17 final size:17
Alignment explanation
Indices: 21123--21156 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21113 GTTTGTGTTG
*
21123 ATCGCCCCGTCATTAAA
1 ATCGCCCCGTCAATAAA
*
21140 ATCGTCCCGTCAATAAA
1 ATCGCCCCGTCAATAAA
21157 CATGAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (17 bp):
ATCGCCCCGTCAATAAA
Found at i:22782 original size:18 final size:18
Alignment explanation
Indices: 22759--22796 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
22749 GTAGTAACAC
22759 CAGAGATTCAAACTTGAT
1 CAGAGATTCAAACTTGAT
22777 CAGAGATTCAAACTTGAT
1 CAGAGATTCAAACTTGAT
22795 CA
1 CA
22797 ATCGGGTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26
Consensus pattern (18 bp):
CAGAGATTCAAACTTGAT
Found at i:34354 original size:6 final size:6
Alignment explanation
Indices: 34343--34393 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
34333 TCAGTCACTT
* *
34343 GAAAAA GAAAAA -AAATGA GAAAAA GAAAGA GAAAAA G-AAAA GAAAAA
1 GAAAAA GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
34390 -AAAA
1 GAAAA
34394 TTGCTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 12 0.32
6 23 0.61
7 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:37801 original size:19 final size:20
Alignment explanation
Indices: 37774--37812 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
37764 CTACCTTTTA
37774 TGTCACGACA-CGACTCCTG
1 TGTCACGACATCGACTCCTG
*
37793 TGTCGCGACATCGACTCCTG
1 TGTCACGACATCGACTCCTG
37813 AATGCGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.18, C:0.36, G:0.23, T:0.23
Consensus pattern (20 bp):
TGTCACGACATCGACTCCTG
Done.