Sequence formatting tool

Input

Upload a file clear
or paste sequence(s) (FASTA or RAW)
clear

Pattern search ("[AB]" A or B, [^A] not A, "." any, "+" repeat) shortest longest matches
clear
"string1|string2" (separator — vertical bar) non-overlapping matches, no limit of string number
"string1:string2" (separator — colon) allows overlapping matches, up to 4 strings (2 strings when reverse complement is selected)
matches reverse complements as well (displayed with double-underlines) don't show match info ignore gaps in sequence

Output

• Aligned sequences ( additional spaces between blocks / sequences )
• Partial sequence from To positions on seq1 for a length of including gaps
  ... residue/base numbers starting from the first displayed
• With gene name ...plus full comments (seq name in bold) Sequence only
• Format ( block size , line size ) Single line Unformat remove gaps
• Pattern search : unmatched strings in grey, dots, lower case
  ... OR matched strings in green, bold/black*, underline/red*, double underline/blue* (colours in "diagram" format)
• Show residue/base numbers to LEFT RIGHT when mouse over (output may take long) No numbers
• Properties hydropathy charges at pH ( window ) red/blue enhanced r/b magenta/green cysteine / proline aromatic (FHWY) positive (HKR) negative (DE) phosphorylatable (STY) large (FHRWY) small (GASC) polar (DENQHKRSTWY)
• Identity/similarity identical on black background identical with asterisks display differences only first seq + different residues -- hereafter amino acids only -- black/grey background asterisks (id)/dots (sim) red/orange background black/grey characters ("asterisks" if properties/pattern is selected)
  ... if the residues at the position of at least % seqs seqences are identical/similar (% excluding gaps)
• Diagram (without residue names) 1 pixel / residue(s), Homology score in window average max min
  ... bar height pixels, between bars pixels, background colour flushright png output (properties only)
  ... scale bar

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• Title font size% line height px