DoriC database

DoriC accession number ORI10010037
Organism Listeria monocytogenes str. 4b F2365
RefSeq NC_002973.1
Topology Circular
Lineage Bacteria, Firmicutes, Bacillales, Listeriaceae, Listeria.
Chromosome size 2905187 nt
Chromosome GC content 0.3804
OriC length 505 nt
OriC AT content 0.6891
The number of DnaA box 11
The location of oriC region 2905001..318 nt
The location of dnaA gene 319..1674 nt
The extremes of GC disparity 2905079 nt (minimum), 1423383 nt (maximum)
Note Dif-like sequence acttcctataatatatattatgtaaact (1 chain) was found between 1421892 and 1421919 nt, matches 27 sites compared with the 28-bp dif sequence acttcctagaatatatattatgtaaact of B. subtilis.
OriC Sequence

ttttcacaacctcatttatttgtcttttttcttattctggtaaatagtttaacacattgtcgtaatgaaatccttttccggaaagTGTGGATAActagttaataacacctttttatTGTGGATAAccttttcaattagtttaaacTTATACACAattagtggttaattacacacaatggctTGTGGATAAttaaatctaacaatttcgttacagatttctttacacacaagTTATACACAagttaactggcTGTGGACAAccgtttttcacatctggacagtttTGTGGATAGattttgtaagtccttgctatcagagtgattttctgatattataattcctgtcgaatagaaatatagctggggaaaactaaagTTATCCACAatacatttttacttTGTGGATAAttttttaacagtgTTTGGATAAccttatccatggctttttctatcTGTGGATAActttatagcatccatttacattacataaaaaagggggggtacta

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.

14 370 P 14 452 0 2.67e-04 taaagttatccaca
16 113 P 16 371 -1 8.02e-04 tattgtggataac[ct]tt
12 180 F 12 397 0 4.28e-03 ttgtggataatt
14 118 F 14 422 -1 1.12e-02 tggataacctt[ta]tc
14 220 F 14 231 -1 1.12e-02 tta[ct]acacaagtta
14 371 P 14 397 -1 1.12e-02 aaa[ga]ttatccacaa
11 85 F 11 452 0 1.71e-02 tgtggataact
11 85 P 11 373 0 1.71e-02 tgtggataact
13 100 C 13 112 -1 4.17e-02 aataacacct[ta]tt
13 116 F 13 452 -1 4.17e-02 tgtggataac[ct]tt
13 133 P 13 136 -1 4.17e-02 at[ta]agtttaaact
13 142 F 13 228 -1 4.17e-02 aa[cg]ttatacacaa
13 210 R 13 214 -1 4.17e-02 aca[gc]atttcttta
13 228 F 13 372 -1 4.17e-02 aagttat[ac]cacaa
13 398 F 13 452 -1 4.17e-02 tgtggataa[tc]ttt
13 402 R 13 405 -1 4.17e-02 ga[tc]aattttttaa
13 422 F 13 454 -1 4.17e-02 tggataac[ct]ttat
10 22 R 10 22 0 6.84e-02 tcttttttct
10 74 P 10 74 0 6.84e-02 tttccggaaa
10 85 F 10 116 0 6.84e-02 tgtggataac
10 91 P 10 91 0 6.84e-02 taactagtta
10 115 F 10 180 0 6.84e-02 ttgtggataa
10 115 F 10 397 0 6.84e-02 ttgtggataa
10 166 F 10 220 0 6.84e-02 ttacacacaa
10 180 P 10 375 0 6.84e-02 ttgtggataa
10 224 F 10 235 0 6.84e-02 acacaagtta
10 282 F 10 396 0 6.84e-02 tttgtggata
10 375 P 10 397 0 6.84e-02 ttatccacaa
10 477 R 10 477 0 6.84e-02 tacattacat
12 85 F 12 181 -1 1.54e-01 tgtggataa[ct]ta
12 101 R 12 375 -1 1.54e-01 ataacacct[ta]tt
12 228 P 12 452 -1 1.54e-01 aagttat[ac]caca
12 280 P 12 376 -1 1.54e-01 gt[ta]ttgtggata
12 370 P 12 422 -1 1.54e-01 taa[ag]gttatcca
12 487 F 12 488 -1 1.54e-01 aaaaa[ag]gggggg
9 29 R 9 29 0 2.74e-01 tcttattct
9 48 R 9 148 0 2.74e-01 ttaacacat
9 85 F 9 398 0 2.74e-01 tgtggataa
9 115 F 9 283 0 2.74e-01 ttgtggata
9 180 F 9 283 0 2.74e-01 ttgtggata
9 181 F 9 452 0 2.74e-01 tgtggataa
9 387 R 9 387 0 2.74e-01 catttttac
11 20 C 11 483 -1 5.64e-01 tgt[ca]ttttttc
11 41 F 11 132 -1 5.64e-01 aa[at]tagtttaa
11 61 P 11 213 -1 5.64e-01 gtaa[ta]gaaatc
11 84 F 11 419 -1 5.64e-01 gt[gt]tggataac
11 85 P 11 229 -1 5.64e-01 tgtg[gt]ataact
11 97 F 11 161 -1 5.64e-01 gttaat[at]acac
11 114 P 11 145 -1 5.64e-01 attgtg[gt]ataa
11 115 P 11 230 -1 5.64e-01 ttgtg[gt]ataac

Refseq NC_002973.1
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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