Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003098.1 Kokia drynarioides strain JFW-HI SEQ_115663, 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: 25881
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Found at i:3834 original size:37 final size:37
Alignment explanation
Indices: 3784--3858 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3774 AAATATAAGA
3784 ATGCATATAAAAAAAATATCAAAATCCGATCCACAAG
1 ATGCATATAAAAAAAATATCAAAATCCGATCCACAAG
3821 ATGCATATAAAAAAAATATCAAAATCCGATCCACAAG
1 ATGCATATAAAAAAAATATCAAAATCCGATCCACAAG
3858 A
1 A
3859 CCTAGAGTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (37 bp):
ATGCATATAAAAAAAATATCAAAATCCGATCCACAAG
Found at i:5250 original size:25 final size:25
Alignment explanation
Indices: 5202--5308 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
5192 GCTAGCAAGT
5202 GTAAACGCATAAATAAGCTGACGAGC
1 GTAAACGCATAAA-AAGCTGACGAGC
*
5228 GTAAACGCATAAAAAGCTAACGAGC
1 GTAAACGCATAAAAAGCTGACGAGC
* * ** **
5253 ATAAATGTGT-GCAAGCTGACGAGC
1 GTAAACGCATAAAAAGCTGACGAGC
* *
5277 GTAAACGTATAAAAAGCTGGCGAGC
1 GTAAACGCATAAAAAGCTGACGAGC
5302 GTAAACG
1 GTAAACG
5309 TGTGCAAGCT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
24 18 0.27
25 35 0.53
26 13 0.20
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (25 bp):
GTAAACGCATAAAAAGCTGACGAGC
Found at i:5272 original size:49 final size:49
Alignment explanation
Indices: 5216--5331 Score: 178
Period size: 49 Copynumber: 2.4 Consensus size: 49
5206 ACGCATAAAT
*
5216 AAGCTGACGAGCGTAAACGCATAAAAAGCTAACGAGCATAAATGTGTGC
1 AAGCTGACGAGCGTAAACGCATAAAAAGCTAACGAGCATAAACGTGTGC
* ** *
5265 AAGCTGACGAGCGTAAACGTATAAAAAGCTGGCGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGCATAAAAAGCTAACGAGCATAAACGTGTGC
*
5314 AAGCTGGCGAGCGTAAAC
1 AAGCTGACGAGCGTAAAC
5332 ATGTGCAAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.37, C:0.19, G:0.28, T:0.16
Consensus pattern (49 bp):
AAGCTGACGAGCGTAAACGCATAAAAAGCTAACGAGCATAAACGTGTGC
Found at i:5274 original size:24 final size:24
Alignment explanation
Indices: 5216--5356 Score: 129
Period size: 24 Copynumber: 5.8 Consensus size: 24
5206 ACGCATAAAT
** **
5216 AAGCTGACGAGCGTAAACGCATAAA
1 AAGCTGACGAGCGTAAACGTGT-GC
* * *
5241 AAGCTAACGAGCATAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* **
5265 AAGCTGACGAGCGTAAACGTATAAA
1 AAGCTGACGAGCGTAAACGTGT-GC
*
5290 AAGCTGGCGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
5314 AAGCTGGCGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
5338 AAGCTGGCAAGCGTAAACG
1 AAGCTGACGAGCGTAAACG
5357 CATAAATAAG
Statistics
Matches: 95, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
24 58 0.61
25 37 0.39
ACGTcount: A:0.36, C:0.19, G:0.29, T:0.16
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:5402 original size:74 final size:74
Alignment explanation
Indices: 5186--5404 Score: 242
Period size: 74 Copynumber: 3.0 Consensus size: 74
5176 TATATATATA
* * ** * **
5186 GTGCAAGCTAGCAAGTGTAAACGCATAAATAAGCTGACGAGCGTAAACGCATAAAAAGCTAACGA
1 GTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGT-GAAAGCTGGCGA
* **
5251 GCATAAATGT
65 GCGTAAACAT
* * * * *
5261 GTGCAAGCTGACGAGCGTAAACGTATAAA-AAGCTGGCGAGCGTAAACGTGTGCAAGCTGGCGAG
1 GTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGAAAGCTGGCGAG
5325 CGTAAACAT
66 CGTAAACAT
* * * * *
5334 GTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTAACAAGCATAAACGTGTGGAAGTTGGCGAG
1 GTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGAAAGCTGGCGAG
5399 CGTAAA
66 CGTAAA
5405 TGCATATATA
Statistics
Matches: 119, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
73 41 0.34
74 54 0.45
75 24 0.20
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (74 bp):
GTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTGACGAGCGTAAACGTGTGAAAGCTGGCGAG
CGTAAACAT
Found at i:5433 original size:50 final size:50
Alignment explanation
Indices: 5321--5433 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 50
5311 TGCAAGCTGG
* *
5321 CGAGCGTAAACATGTGCAAGCTGGCAAGCGTAAACGCATAAATAAGCTAA
1 CGAGCGTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATAAATAAACTAA
* * * * * * * *
5371 CAAGCATAAACGTGTGGAAGTTGGCGAGCGTAAATGCATATATAAACTGA
1 CGAGCGTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATAAATAAACTAA
*
5421 CGAGCGTGAACGT
1 CGAGCGTAAACGT
5434 ATAAGTAAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (50 bp):
CGAGCGTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATAAATAAACTAA
Found at i:5940 original size:20 final size:21
Alignment explanation
Indices: 5906--5954 Score: 82
Period size: 20 Copynumber: 2.4 Consensus size: 21
5896 AGTGAAGTAA
5906 CATGTTTTGGTTGCTTATTGT
1 CATGTTTTGGTTGCTTATTGT
5927 CATGTTTT-GTTGCTTATTGT
1 CATGTTTTGGTTGCTTATTGT
*
5947 CGTGTTTT
1 CATGTTTT
5955 ACTCTCTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.59
Consensus pattern (21 bp):
CATGTTTTGGTTGCTTATTGT
Found at i:8221 original size:30 final size:29
Alignment explanation
Indices: 8174--8230 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
8164 TATATAATAT
8174 TTTTAAAATTAAAAAAATATTAAAAATCA
1 TTTTAAAATTAAAAAAATATTAAAAATCA
* *
8203 TTTTAAAATTCTAGAAAATATTAAAAAT
1 TTTTAAAATT-AAAAAAATATTAAAAAT
8231 TAAAAATTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (29 bp):
TTTTAAAATTAAAAAAATATTAAAAATCA
Found at i:8289 original size:18 final size:19
Alignment explanation
Indices: 8251--8290 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
8241 TTCCATGATG
*
8251 ATTTTAAAATATTATAAAA
1 ATTTTAAAATATTAAAAAA
*
8270 ATTTTGAAAT-TTAAAAAA
1 ATTTTAAAATATTAAAAAA
8288 ATT
1 ATT
8291 AATTAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTTTAAAATATTAAAAAA
Found at i:19841 original size:24 final size:24
Alignment explanation
Indices: 19797--19843 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19787 GGAATGGTTG
*
19797 AAGACTCTAAGAGATTGCAAGTTC
1 AAGACTCTAAGAGAGTGCAAGTTC
*
19821 AAGACTCTTAGAG-GTGACAAGTT
1 AAGACTCTAAGAGAGTG-CAAGTT
19844 GAAGTGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (24 bp):
AAGACTCTAAGAGAGTGCAAGTTC
Found at i:20075 original size:12 final size:11
Alignment explanation
Indices: 20058--20091 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
20048 CTTAAAATCC
20058 AAGAAAAACAGA
1 AAGAAAAA-AGA
20070 AAGAAAGAAAGA
1 AAGAAA-AAAGA
20082 AAGAAAAAAG
1 AAGAAAAAAG
20092 TTTCAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 15 0.71
13 2 0.10
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:20265 original size:29 final size:29
Alignment explanation
Indices: 20198--20265 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
20188 AATGTTGATT
*
20198 TTTAAGAAAAATTATCAGATTAGACTATA
1 TTTACGAAAAATTATCAGATTAGACTATA
***
20227 TTTTTTAAAAATTA-CGAGATTAGACTGATA
1 TTTACGAAAAATTATC-AGATTAGACT-ATA
20257 -TTACGAAAA
1 TTTACGAAAA
20266 CGCTTCCGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
28 1 0.03
29 27 0.87
30 3 0.10
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (29 bp):
TTTACGAAAAATTATCAGATTAGACTATA
Found at i:21233 original size:3 final size:3
Alignment explanation
Indices: 21225--21263 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
21215 CATTGAACCA
* * *
21225 ATC ATC ATC ATC ATC GTC GTC ATC ATC ACC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
21264 TCCATGATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.31
Consensus pattern (3 bp):
ATC
Done.