DoriC database

DoriC accession number ORI10010023
Organism Dehalococcoides ethenogenes 195
RefSeq NC_002936.1
Topology Circular
Lineage Bacteria, Chloroflexi, Dehalococcoidetes, Dehalococcoides.
Chromosome size 1469720 nt
Chromosome GC content 0.4885
OriC length 325 nt
OriC AT content 0.6862
The number of DnaA box 5
The location of oriC region 1599..1923 nt
The location of dnaA gene 261..1598 nt
The extremes of GC disparity 1737 nt (minimum), 752702 nt (maximum)
Note Note that the DnaA box motif (ttatcgaaa) was looked for with no more than one mismatch instead of E. coli perfect DnaA box (ttatccaca).
OriC Sequence

tattagcccttttcgccgcaccgcttttccttatccttatatttttctttattttcattctgccagcagggtgcttttgccggtttttctattctttttagacagtcTTTCTATAActttattatattTTTCGATAAccgggctgaatTTTCGATAActttgcagatactttgctttaaaaataagaccggaggacaggaatagagtttttactcgtaaagccttattattagtatttctgatatacttaaaaataaaccagttaaagttaatgggaTTTCGACAActtaagaattagataacttTTTAGATAAggtgtttttat

The information of repeat
The following lines contain repeats found, one line each.
[1] - repeat length of the first part
[2] - starting position of the first part
[4] - repeat length of the second part
[5] - starting position of the second part
[6] - distance of this repeat
[7] - calculated evalue of this repeat
[8] - repeat sequence

For more details, please refer to The Manual of REPuter.

11 36 F 11 121 0 7.08e-03 ttatatttttc
11 127 F 11 147 0 7.08e-03 ttttcgataac
13 107 F 13 148 -1 1.73e-02 tttc[tg]ataacttt
13 197 R 13 303 -1 1.73e-02 ggaataga[gt]tttt
10 7 R 10 20 0 2.83e-02 ccttttcgcc
10 175 F 10 247 0 2.83e-02 ttaaaaataa
12 50 C 12 176 -1 6.37e-02 atttt[ct]attctg
12 148 F 12 277 -1 6.37e-02 tttcga[tc]aactt
12 149 F 12 294 -1 6.37e-02 tt[ca]gataacttt
9 40 R 9 91 0 1.13e-01 atttttctt
9 93 F 9 302 0 1.13e-01 ctttttaga
9 191 R 9 191 0 1.13e-01 aggacagga
9 287 R 9 287 0 1.13e-01 ttaagaatt
11 23 F 11 29 -1 2.34e-01 ctt[ta]tccttat
11 24 R 11 88 -1 2.34e-01 tttt[ct]cttatc
11 35 R 11 83 -1 2.34e-01 cttat[ac]ttttt
11 125 R 11 298 -1 2.34e-01 atttttc[ga]ata
11 126 F 11 303 -1 2.34e-01 ttttt[ca]gataa
8 27 C 8 196 0 4.53e-01 tccttatc
8 47 P 8 250 0 4.53e-01 tttatttt
8 112 F 8 153 0 4.53e-01 ataacttt
8 112 F 8 298 0 4.53e-01 ataacttt
8 113 P 8 263 0 4.53e-01 taacttta
8 143 C 8 245 0 4.53e-01 tgaatttt
8 223 R 8 223 0 4.53e-01 ttattatt
8 294 F 8 306 0 4.53e-01 ttagataa
10 5 R 10 72 -1 8.50e-01 gcc[cg]ttttcg
10 24 F 10 42 -1 8.50e-01 ttttc[ct]ttat
10 36 R 10 118 -1 8.50e-01 ttatatt[ta]tt
10 37 R 10 302 -1 8.50e-01 ta[tg]atttttc
10 38 R 10 105 -1 8.50e-01 atat[tc]tttct
10 40 C 10 248 -1 8.50e-01 attttt[ca]ttt
10 82 F 10 104 -1 8.50e-01 gt[tc]tttctat
10 83 R 10 121 -1 8.50e-01 ttttt[ca]tatt
10 85 C 10 177 -1 8.50e-01 ttt[ct]tattct
10 107 F 10 128 -1 8.50e-01 tttc[tg]ataac
10 118 R 10 121 -1 8.50e-01 tt[at]ttatatt
10 128 F 10 277 -1 8.50e-01 tttcga[tc]aac
10 147 F 10 304 -1 8.50e-01 tttt[ca]gataa
10 176 P 10 222 -1 8.50e-01 taa[at]aataag
10 245 F 10 285 -1 8.50e-01 acttaa[ag]aat
7 27 F 7 33 0 1.81e+00 tccttat
7 28 P 7 309 0 1.81e+00 ccttatc
7 33 C 7 196 0 1.81e+00 tccttat
7 36 R 7 36 0 1.81e+00 ttatatt
7 39 R 7 318 0 1.81e+00 tattttt
7 39 P 7 177 0 1.81e+00 tattttt
7 39 P 7 249 0 1.81e+00 tattttt
7 41 F 7 83 0 1.81e+00 tttttct
7 43 R 7 43 0 1.81e+00 tttcttt

Refseq NC_002936.1
Legend Figure1 shows the Z-curves for the original sequence. Figure2 shows the Z-curves for the rotated sequence beginning and ending in dif site or the maximum of the GC disparity curve. Short vertical red line indicates the indicator gene (such as dnaA, dnaN, gidA, hemE etc) location, and short up vertical dark blue arrow indicates the identified oriC location, short down vertical brown arrow indicates dif site location. Purple peaks with the diamonds indicates the DnaA box clusters.
Figure 1
zcurve
Figure 2
zcurve

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