FASTM - Nucleotide Fragment Search

• NUCLEOTIDE DATABASES
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  • Structure
    • Nucleotide Structure Sequences
• OTHER TYPES

  General

  • Protein Databases

  Specialised

  • Proteomes Databases
  • LGIC Protein Databases

Enter or paste a DNA RNA sequence in any supported format:

or upload a file:

• PROGRAM
  FASTM

• MATRIX
  N/A
• MATCH/MISMATCH SCORES
  +2/-2 +5/-4 +3/-2 N/A
• GAP OPEN
  -23 -22 -21 -20 -19 -18 -17 -16 -15 -14 -13 -12 -11 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0
• GAP EXTEND
  0 -1 -2 -3 -4 -5 -6 -7 -8
• KTUP
  6 5 4 3 2 N/A
• EXPECTATION UPPER VALUE
  1e-600 1e-300 1e-100 1e-50 1e-10 1e-5 0.001 0.1 1 2 5 10 20 50
• EXPECTATION LOWER VALUE
  0 (default) 1e-300 1e-100 1e-50 1e-10 1e-5 0.001 0.1 1 2 5 10 20 50
• DNA STRAND
  N/A both top bottom
• HISTOGRAM
  no yes
• FILTER
  none dust
• STATISTICAL ESTIMATES
  Regress MLE Altshul-Gish Regress/shuf. MLE/shuf.
• SCORES
  10 20 30 40 50 60 70 80 90 100 150 200 250 500 750 1000
• ALIGNMENTS
  10 20 30 40 50 60 70 80 90 100 150 200 250 500 750 1000
• SEQUENCE RANGE
• DATABASE RANGE
• MULTI HSPs
  no yes
• SCORE FORMAT
  Default -m 9 -- with coordinates scores and %identity -m 9C -- with CIGAR alignment -m 9c -- with encoded alignment -m 9i -- with identity and length