RedOxiBase: Cis_element analysis

Cis Elements Analysis

PLACE
Search for Plant Cis-acting Regulatory DNA Elements

MEME
MEME will analyze your sequences for similarities among them and produce a description (motif) for each pattern it discovers.

Please enter the nucleotide sequence as FASTA formats (Max 20 sequences) and press submit button.
>AtPrxII01 TATGATCTACATGGTAAACGAATCAATCAAGAGGAGGTGGCAAAAGGAGAAAGCGAGAGTTGGTTAGTTTCAATTGACAAAGTCTAGTTTATATGTCCTTTGTTTTCTTTTAGCAACATTAATTTGTTTCTTCTCATCTCTTATTCAATATGAACAAGATTTTAGGATTTTTTTTGTTTTTTTTTAATTGTTACGAAATGGAGGGTGATCAAAGATTTAAGTACAAATTATATACAACCTGTAGCATTCTCTTCATCATCTTCATCCTTCTGGTCAATTTCACAGTTGCATTTACATATTTTCCAACTATCATCTGAAGACCATATGGTGGTGGAGATTGCTCGTCTGTGGTGGATCAACTGGATTGCTAATGTGCGCTTTTTGCTTGTACTACGGGTATGCGTGGAACGACTAATCGGGGTAAATGCAAATCTTGTTCTTCTTTGGATACATGGTTTGCATTTCCTATGGTTTCTTACTCATGCTTGGAACCATTTGATTTGGTTCTTCTCTTCTCCATAAAATGTGAATAAGCAGTGATTATTATTTTTTAATTACCCTCCCACTACTCAATTTCTCAACAGATTTGATATGACTGATTTTTTTTTTTTCATTTATGTATGATTATTTTAAAATGTGTTTGTAAAGAAATGTTATGCTTATATATTATTATTACTATAGAAAGTTAGATGTTGCTTAATTTTGTGGTTTTTTGTCATGGTACCAAAACATTCTTGGTCCTCTAGCCTTGTTGTCTACTTTTTTGAACAAAGCATCAGAGAGTTTTCACGAAGAGAATTATCTTGAAAAAAAGAAAAAAGAGAGAATTATCTTTGATTATTGTTTGGGACTATATGTTGTAGTCAAAGTCTCATTTTGGTTAAGGCGACAGTTAGAGAAACCGATGGTGAAGCTACGGTTCAAAGAAACCGTAGTATACTATTTTTCCTTATTCTTGAGTTCACTAAACCTGAGGTATCAATTCCCAAAATTGACCATT

NOTE: Length of submitting sequence must be less than 4,356. Otherwise, you will get empty result.

If you use this data file in published research, please cite:
Higo, K., Y. Ugawa, M. Iwamoto and T. Korenaga (1999) Plant cis-acting
regulatory DNA elements (PLACE) database. Nucleic Acids Res. 27 (1): 297-300.

Use this form to submit DNA or protein sequences to MEME. MEME will analyze your sequences for similarities among them and produce a description (motif) for each pattern it discovers.

Data Submission Form 1685362754

Your e-mail address

How do you think the occurrences of a single motif are distributed among the sequences?

One per sequence

Zero or one per sequence

Any number of repetitions

MEME will find the optimum width of each motif within the limits you specify here:

Minimum width (>= 2)

Maximum width (<= 300)

Maximum number of motifs to find

Please enter the sequences which you believe share one or more motifs.
The sequences may contain no more than 60000 characters total total in any of a large number of formats.

Enter the name of a file containing the sequences here:

Clear

or the actual sequences here (Sample Protein Input Sequences):
You need at least two differents nucleotide sequences (name and sequence)!

>AtPrxII01
TATGATCTACATGGTAAACGAATCAATCAAGAGGAGGTGGCAAAAGGAGAAAGCGAGAGTTGGTTAGTTTCAATTGACAAAGTCTAGTTTATATGTCCTTTGTTTTCTTTTAGCAACATTAATTTGTTTCTTCTCATCTCTTATTCAATATGAACAAGATTTTAGGATTTTTTTTGTTTTTTTTTAATTGTTACGAAATGGAGGGTGATCAAAGATTTAAGTACAAATTATATACAACCTGTAGCATTCTCTTCATCATCTTCATCCTTCTGGTCAATTTCACAGTTGCATTTACATATTTTCCAACTATCATCTGAAGACCATATGGTGGTGGAGATTGCTCGTCTGTGGTGGATCAACTGGATTGCTAATGTGCGCTTTTTGCTTGTACTACGGGTATGCGTGGAACGACTAATCGGGGTAAATGCAAATCTTGTTCTTCTTTGGATACATGGTTTGCATTTCCTATGGTTTCTTACTCATGCTTGGAACCATTTGATTTGGTTCTTCTCTTCTCCATAAAATGTGAATAAGCAGTGATTATTATTTTTTAATTACCCTCCCACTACTCAATTTCTCAACAGATTTGATATGACTGATTTTTTTTTTTTCATTTATGTATGATTATTTTAAAATGTGTTTGTAAAGAAATGTTATGCTTATATATTATTATTACTATAGAAAGTTAGATGTTGCTTAATTTTGTGGTTTTTTGTCATGGTACCAAAACATTCTTGGTCCTCTAGCCTTGTTGTCTACTTTTTTGAACAAAGCATCAGAGAGTTTTCACGAAGAGAATTATCTTGAAAAAAAGAAAAAAGAGAGAATTATCTTTGATTATTGTTTGGGACTATATGTTGTAGTCAAAGTCTCATTTTGGTTAAGGCGACAGTTAGAGAAACCGATGGTGAAGCTACGGTTCAAAGAAACCGTAGTATACTATTTTTCCTTATTCTTGAGTTCACTAAACCTGAGGTATCAATTCCCAAAATTGACCATT

Use sequence name not sequence Id.

Options

Description of your sequences:

MEME will find the optimum number of sites for each motif within the limits you specify here:

Minimum sites (>= 2)

Maximum sites (<= 600)

Shuffle sequence letters

Perform discriminative motif discovery – Enter the name of a file containing negative sequences :

Clear

Select background Markov model Order:

Or enter the name of a file containing a background Markov model:

Clear

DNA-ONLY OPTIONS (Ignored for protein searches)

Search given strand only

Look for palindromes only

pid 1685362754 Path ./assets/users/temp/1685362754/Meme/ Type terminator
You need at least two differents nucleotide sequences (name and sequence)!

PATTERN GET
formatedseq from SQL name: AtPrxII01