CpG Islands

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Sequence Manipulation Suite:

CpG Islands

CpG Islands reports potential CpG island regions using the method described by Gardiner-Garden and Frommer (1987). The calculation is performed using a 200 bp window moving across the sequence at 1 bp intervals. CpG islands are defined as sequence ranges where the Obs/Exp value is greater than 0.6 and the GC content is greater than 50%. The expected number of CpG dimers in a window is calculated as the number of 'C's in the window multiplied by the number of 'G's in the window, divided by the window length. CpG islands are often found in the 5' regions of vertebrate genes, therefore this program can be used to highlight potential genes in genomic sequences.

Paste the raw sequence or one or more FASTA sequences into the text area below. Input limit is 100000 characters.

taacatacttattgtttttaactactcgttttccattcgactcatcacgctccccccccc
cccccccccccttatccgttccgttcgacgtatttcgttgtctaatttctgacgtaactt
gttccctgttaagtaccgtttatggcctatactccggtatttaaaacgacgacgattcca
ccgtaaagccgtcaaccagatgaacgacctcgctcgttatatttttccggcaaaatccct
atttccgattcgcttagtgctaccgacgctatatcgttccgcaattcctcgagatcatcg
atttcttctccggcgacgtctcaagtttttccgttacaacgcgatctatcctgtaaattc
gaccgcgctcattctcacgttttatacattgcgcagttgattacgctaaataatccgctg
actgttaccttccctgttagattcgcgcattataaactacttactttaacaaacgatttt
cacagtttaatttctgcgatgacgtctaactcttcagttttaaccgataacaaccttctc
gacacttcgtttcttataccatcctcgttatccatacccattcttaaatttctcactact
attctctttacaaccacattagctctaatcttacatctaatttctatacataaaatgctc
cttctgctgtatgtttctctttctcataattacatttttaattactaaatccctcatccc
tcccacccatctattccaccatcaaggttatacaccatgtattactgtaaaacccactaa
tattaattgtcaccgatattaaacgaaattcattcacacaaatttcattaattacctttt
cttattaattgcatatgtactctacatatactcaaccaactaaaaatcgatattttacat
ttgatttctaatgtaccccacaactttcttgctttatgattgaacttagctttataataa
tagttatttaccctaacgcatatactcttatccttatatgaaccttgcttatttgttaga
tttatccaatctaaaccacagataatatcccttctcttacttcattttattatcaccatt
ttcacttcttcctagatatatacaattatataactctattaccacattttcccttaactt
tctgttctgcactattatatttactctttttctaaaaccttcttaactttttcagatgca

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new window | home | citation Tue Jun 15 14:20:12 2010