|   | prophet | 
Note: prophet does NOT use the 'simple frequency matrices' produced by prophecy. If you have a 'simple frequency matrix'you should use the program profit to scan sequences.
| % prophet Gapped alignment for profiles Input sequence(s): tsw:h* Profile or weight matrix file: globins.gribskov Gap opening coefficient [1.0]: Gap extension coefficient [1.0]: Output alignment [hd_fugru.prophet]: | 
Go to the input files for this example
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
  [-infile]            infile     Profile or weight matrix file
   -gapopen            float      [1.0] Gap opening coefficient (Number from
                                  0.000 to 100.000)
   -gapextend          float      [1.0] Gap extension coefficient (Number from
                                  0.000 to 100.000)
  [-outfile]           align      [*.prophet] Output alignment file name
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name
   "-outfile" associated qualifiers
   -aformat3           string     Alignment format
   -aextension3        string     File name extension
   -adirectory3        string     Output directory
   -aname3             string     Base file name
   -awidth3            integer    Alignment width
   -aaccshow3          boolean    Show accession number in the header
   -adesshow3          boolean    Show description in the header
   -ausashow3          boolean    Show the full USA in the alignment
   -aglobal3           boolean    Show the full sequence in alignment
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required | 
| [-infile] (Parameter 2) | Profile or weight matrix file | Input file | Required | 
| -gapopen | Gap opening coefficient | Number from 0.000 to 100.000 | 1.0 | 
| -gapextend | Gap extension coefficient | Number from 0.000 to 100.000 | 1.0 | 
| [-outfile] (Parameter 3) | Output alignment file name | Alignment output file | <*>.prophet | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
| # Gribskov Protein Profile # Columns are amino acids A->Z # Last column is indel penalty # Rows are alignment positions 1->n Gribskov Name globins Matrix pprofile Length 164 Max_score 645.45 Threshold 75 Gap_open 3.00 Gap_extend 0.30 Consensus PIVDTGSVVSLSEEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLEFFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLASKYRELGYQG 0.15 0.00 0.03 0.03 0.03 -0.18 0.09 0.06 -0.06 0.00 0.03 -0.09 -0.06 0.00 0.00 0.45 0.09 0.09 0.12 0.09 0.00 0.03 -0.24 0.00 -0.24 0.00 0.87 0.87 0.00 0.00 0.06 -0.06 -0.06 0.18 -0.09 -0.09 0.45 0.00 -0.06 0.24 0.18 -0.09 0.00 -0.06 -0.09 -0.09 -0.03 0.06 0.00 0.33 -0.15 0.00 0.03 0.00 0.87 0.87 0.06 0.00 0.06 -0.06 -0.06 0.06 0.06 -0.09 0.33 0.00 -0.06 0.24 0.18 -0.09 0.00 0.03 -0.06 -0.09 -0.03 0.06 0.00 0.45 -0.24 0.00 -0.03 0.00 0.87 0.87 0.09 0.00 -0.15 0.45 0.30 -0.30 0.18 0.12 -0.06 0.00 0.09 -0.15 -0.12 0.18 0.00 0.03 0.18 0.00 0.06 0.06 0.00 -0.06 -0.33 0.00 -0.15 0.00 0.87 0.87 0.12 0.00 0.06 0.06 0.06 -0.09 0.12 -0.03 0.06 0.00 0.06 -0.03 0.00 0.06 0.00 0.09 -0.03 -0.03 0.09 0.45 0.00 0.06 -0.18 0.00 -0.09 0.00 0.87 0.87 0.18 0.00 0.06 0.18 0.15 -0.18 0.45 -0.06 -0.09 0.00 -0.03 -0.15 -0.09 0.12 0.00 0.09 0.06 -0.09 0.18 0.12 0.00 0.06 -0.30 0.00 -0.18 0.00 0.87 0.87 0.12 0.00 0.18 0.06 0.06 -0.09 0.18 -0.06 -0.03 0.00 0.06 -0.12 -0.09 0.09 0.00 0.12 -0.03 0.03 0.45 0.09 0.00 -0.03 0.09 0.00 -0.12 0.00 0.87 0.87 0.13 0.00 0.13 -0.13 -0.13 0.13 0.13 -0.19 0.69 0.00 -0.13 0.50 0.38 -0.19 0.00 0.06 -0.13 -0.19 -0.06 0.13 0.00 0.94 -0.50 0.00 -0.06 0.00 0.87 0.87 0.59 0.00 -0.06 -0.07 -0.02 0.24 0.31 -0.25 0.68 0.00 -0.20 0.72 0.60 -0.14 0.00 0.14 -0.03 -0.39 0.03 0.23 0.00 0.97 -0.55 0.00 -0.12 0.00 0.87 0.87 0.52 0.00 0.12 0.35 0.35 -0.54 0.38 0.41 -0.22 0.00 0.20 -0.30 -0.22 0.31 0.00 0.76 0.53 0.27 0.61 0.20 0.00 -0.08 -0.38 0.00 -0.48 0.00 0.87 0.87 0.01 0.00 -0.88 -0.10 0.24 0.83 -0.26 -0.04 0.62 0.00 -0.16 1.19 0.96 -0.18 0.00 -0.22 0.11 -0.34 -0.28 -0.02 0.00 0.62 0.07 0.00 0.09 0.00 0.87 0.87 0.54 0.00 0.44 0.37 0.34 -0.45 0.94 -0.20 -0.08 0.00 0.14 -0.40 -0.25 0.35 0.00 0.41 -0.02 -0.08 1.07 0.80 0.00 0.08 -0.38 0.00 -0.51 0.00 0.87 0.87 0.82 0.00 -0.13 0.71 0.92 -0.68 0.80 0.16 -0.20 0.00 0.14 -0.34 -0.20 0.38 0.00 0.56 0.45 -0.09 0.42 0.36 0.00 0.03 -1.13 0.00 -0.61 0.00 0.87 0.87 0.37 0.00 -0.47 0.17 0.38 -0.05 0.14 0.07 -0.26 0.00 0.19 -0.05 -0.22 0.21 0.00 -0.01 0.13 0.35 0.52 0.05 0.00 -0.30 -0.16 0.00 0.01 0.00 0.87 0.87 0.41 0.00 -0.61 0.90 1.26 -0.71 0.55 0.42 0.25 0.00 0.31 0.13 0.15 0.40 0.00 0.26 1.04 0.04 0.05 0.19 0.00 0.49 -1.41 0.00 -0.69 0.00 4.55 4.55 0.13 0.00 -1.04 -0.15 0.01 0.48 -0.39 -0.11 0.51 0.00 0.83 0.99 1.12 -0.01 0.00 -0.10 0.23 0.20 -0.13 0.12 0.00 0.54 0.36 0.00 -0.23 0.00 4.55 4.55 1.00 0.00 0.64 0.24 0.24 -0.41 0.81 -0.30 0.35 0.00 0.13 -0.08 -0.01 0.24 0.00 0.58 -0.09 -0.17 1.23 0.86 0.00 0.56 -0.52 0.00 -0.50 0.00 4.55 4.55 1.09 0.00 -0.33 0.08 0.18 -0.09 0.21 -0.09 0.27 0.00 0.33 0.48 0.58 0.07 0.00 0.55 0.27 -0.09 0.23 0.35 0.00 0.48 -0.45 0.00 -0.42 0.00 4.55 4.55 0.81 0.00 0.28 0.11 0.11 0.02 0.25 0.19 0.96 0.00 -0.14 0.57 0.42 0.00 0.00 0.30 0.09 -0.24 0.04 0.33 0.00 1.16 -1.02 0.00 -0.07 0.00 4.55 4.55 0.18 0.00 -0.48 0.64 0.44 -0.46 0.23 0.20 0.36 0.00 0.51 0.16 0.35 0.23 0.00 0.18 0.36 0.36 0.10 0.44 0.00 0.49 -0.41 0.00 -0.54 0.00 4.55 4.55 0.54 0.00 -0.30 0.00 0.00 -0.24 0.14 -0.11 -0.31 0.00 0.85 -0.20 -0.13 0.31 0.00 0.17 0.07 0.74 1.03 0.20 0.00 -0.32 0.34 0.00 -0.23 0.00 4.55 4.55 1.15 0.00 0.04 0.11 0.19 -0.01 0.45 -0.22 0.41 0.00 0.00 0.45 0.45 0.10 0.00 0.39 0.02 -0.39 0.45 0.98 0.00 0.54 -0.54 0.00 -0.27 0.00 4.55 4.55 -0.59 0.00 -1.37 -0.55 -0.60 0.59 -0.70 0.19 -0.64 0.00 0.77 0.14 -0.34 0.60 0.00 -0.65 -0.10 1.43 0.47 -0.35 0.00 -0.90 1.17 0.00 0.70 0.00 4.55 4.55 0.84 0.00 0.10 0.51 0.46 -0.41 0.84 -0.17 0.76 0.00 -0.08 0.37 0.31 0.10 0.00 0.33 0.15 -0.39 0.23 0.43 0.00 1.25 -1.48 0.00 -0.47 0.00 4.55 4.55 0.29 0.00 -0.79 0.77 1.01 -1.00 0.24 0.34 -0.33 0.00 1.52 -0.50 0.03 0.60 0.00 0.59 0.73 0.81 0.39 0.36 0.00 -0.24 -0.67 0.00 -1.02 0.00 4.55 4.55 1.29 0.00 0.37 -0.04 0.02 -0.05 0.55 -0.31 0.87 0.00 -0.23 0.66 0.50 -0.12 0.00 0.39 -0.09 -0.53 0.21 0.43 0.00 1.26 -1.05 0.00 -0.13 0.00 4.55 4.55 0.85 0.00 0.11 0.82 0.60 -0.46 0.53 0.45 -0.20 0.00 0.14 -0.35 -0.33 1.10 0.00 0.04 0.34 -0.27 0.31 0.28 0.00 -0.17 -0.59 0.00 0.08 0.00 4.55 4.55 0.33 0.00 0.22 0.10 0.10 -0.16 0.27 -0.07 -0.03 0.00 0.06 -0.13 -0.09 0.12 0.00 0.19 0.00 -0.01 0.51 0.15 0.00 0.00 -0.02 0.00 -0.16 0.00 3.49 3.49 -0.07 0.00 -0.59 -0.28 -0.19 0.40 -0.10 -0.08 0.31 0.00 0.12 0.51 0.09 0.08 0.00 -0.22 -0.19 0.46 0.27 0.34 0.00 0.38 -0.15 0.00 0.27 0.00 4.55 4.55 0.76 0.00 0.40 0.62 0.60 -0.23 0.69 0.08 0.07 0.00 -0.05 -0.21 -0.21 0.39 0.00 0.11 0.11 -0.36 0.62 0.32 0.00 0.13 -0.59 0.00 -0.08 0.00 4.55 4.55 0.48 0.00 -0.64 1.07 1.40 -1.00 0.84 0.30 -0.37 0.00 0.92 -0.57 -0.17 0.68 0.00 0.43 0.73 0.33 0.49 0.41 0.00 -0.16 -1.18 0.00 -0.96 0.00 4.55 4.55 0.27 0.00 0.12 0.05 0.05 -0.03 0.22 0.21 0.92 0.00 0.13 0.58 0.47 0.01 0.00 0.26 0.04 -0.02 -0.04 0.63 0.00 1.28 -0.92 0.00 -0.17 0.00 4.55 4.55 0.84 0.00 0.41 0.85 0.73 -0.84 1.99 -0.09 -0.44 0.00 -0.05 -0.76 -0.50 0.65 0.00 0.52 0.30 -0.27 1.16 0.57 0.00 0.17 -1.15 0.00 -0.81 0.00 4.55 4.55 1.04 0.00 0.09 0.88 0.78 -1.00 1.73 -0.04 -0.37 0.00 0.06 -0.56 -0.30 0.60 0.00 0.54 0.72 -0.24 0.69 0.66 0.00 0.20 -1.41 0.00 -0.90 0.00 4.55 4.55 0.22 0.00 -0.42 1.10 1.14 -0.58 0.34 1.15 -0.01 0.00 0.23 -0.17 -0.22 0.63 0.00 0.23 0.76 0.22 -0.01 0.15 0.00 0.11 -1.12 0.00 -0.21 0.00 4.55 4.55 1.40 0.00 0.14 0.65 0.50 -0.62 0.58 0.00 0.39 0.00 0.14 -0.03 0.11 0.28 0.00 0.46 0.32 -0.15 0.40 0.47 0.00 0.44 -1.03 0.00 -0.47 0.00 4.55 4.55 0.15 0.00 -0.45 -0.28 -0.13 0.99 0.18 -0.35 0.98 0.00 -0.42 1.28 1.00 -0.26 0.00 -0.22 -0.18 -0.60 -0.08 0.14 0.00 1.05 -0.09 0.00 0.15 0.00 4.55 4.55 [Part of this file has been deleted for brevity] 0.16 0.00 -0.11 0.88 0.64 -0.34 0.31 0.88 -0.34 0.00 0.27 -0.44 -0.47 1.57 0.00 -0.20 0.43 -0.04 0.17 0.13 0.00 -0.41 -0.25 0.00 0.30 0.00 4.55 4.55 -0.40 0.00 -0.34 -1.18 -0.69 1.78 -0.70 -0.11 0.83 0.00 -0.69 1.65 0.86 -0.65 0.00 -0.27 -0.78 -0.56 -0.32 -0.26 0.00 0.50 1.18 0.00 1.21 0.00 4.55 4.55 0.11 0.00 -0.78 0.67 0.83 -1.02 0.09 0.60 -0.41 0.00 1.29 -0.48 0.09 0.52 0.00 0.51 1.05 1.17 0.23 0.13 0.00 -0.33 -0.04 0.00 -1.00 0.00 4.55 4.55 -0.32 0.00 -0.42 -0.96 -0.65 1.99 -0.80 -0.17 1.10 0.00 -0.68 1.95 1.30 -0.60 0.00 -0.69 -0.56 -0.75 -0.59 -0.25 0.00 0.97 1.06 0.00 1.13 0.00 4.55 4.55 -0.21 0.00 -0.66 -0.84 -0.54 1.76 -0.70 -0.35 1.55 0.00 -0.54 2.09 1.51 -0.65 0.00 -0.50 -0.46 -0.65 -0.50 -0.09 0.00 1.36 0.53 0.00 0.68 0.00 4.55 4.55 0.57 0.00 0.31 0.54 0.50 -0.76 1.07 -0.20 -0.29 0.00 0.79 -0.67 -0.28 0.59 0.00 0.49 0.18 0.31 1.56 0.50 0.00 -0.09 -0.13 0.00 -0.84 0.00 4.55 4.55 0.24 0.00 -0.40 0.85 1.05 -0.48 0.36 1.03 -0.03 0.00 0.30 -0.16 -0.18 1.01 0.00 0.17 0.68 0.19 0.09 0.19 0.00 0.09 -0.93 0.00 -0.16 0.00 4.55 4.55 0.91 0.00 0.71 -0.33 -0.32 0.16 0.31 -0.28 0.79 0.00 -0.46 0.35 0.32 -0.30 0.00 0.24 -0.31 -0.53 0.32 0.34 0.00 1.05 -1.14 0.00 0.39 0.00 4.55 4.55 0.36 0.00 -0.54 -0.45 -0.27 1.21 -0.41 -0.35 1.43 0.00 -0.36 1.70 1.36 -0.44 0.00 -0.21 -0.17 -0.59 -0.29 0.12 0.00 1.30 -0.03 0.00 0.23 0.00 4.55 4.55 0.47 0.00 -0.26 -0.37 -0.25 0.88 -0.15 -0.38 1.45 0.00 -0.34 1.51 1.20 -0.41 0.00 -0.06 -0.18 -0.56 -0.21 0.21 0.00 1.55 -0.42 0.00 0.09 0.00 4.55 4.55 0.28 0.00 0.49 -0.02 -0.04 -0.07 0.27 0.21 0.69 0.00 0.04 0.21 0.17 0.02 0.00 0.28 -0.04 0.03 0.42 0.26 0.00 0.98 -0.76 0.00 0.03 0.00 4.55 4.55 0.40 0.00 0.33 -0.08 -0.08 0.14 0.31 -0.38 1.39 0.00 -0.08 0.77 0.63 -0.19 0.00 0.20 -0.30 -0.38 0.08 1.15 0.00 1.57 -1.12 0.00 -0.23 0.00 4.55 4.55 0.33 0.00 -0.86 -0.55 -0.31 1.41 -0.48 -0.32 1.20 0.00 -0.40 1.93 1.56 -0.47 0.00 -0.25 -0.11 -0.62 -0.39 0.03 0.00 1.20 0.30 0.00 0.29 0.00 4.55 4.55 1.41 0.00 0.00 0.89 0.74 -0.87 0.64 0.54 -0.19 0.00 0.34 -0.35 -0.19 0.58 0.00 0.56 0.61 0.01 0.38 0.42 0.00 -0.01 -1.07 0.00 -0.41 0.00 4.55 4.55 0.59 0.00 0.21 0.36 0.43 -0.45 0.47 0.27 0.17 0.00 0.31 -0.13 0.02 0.31 0.00 0.47 0.22 0.28 0.65 0.68 0.00 0.32 -0.37 0.00 -0.45 0.00 4.55 4.55 -0.10 0.00 -0.10 0.27 0.27 -0.17 -0.19 1.38 0.12 0.00 0.26 0.04 0.06 0.35 0.00 0.32 0.58 0.81 -0.19 -0.03 0.00 0.30 -0.02 0.00 0.03 0.00 4.55 4.55 0.19 0.00 -0.34 -0.46 -0.20 1.05 -0.35 0.28 0.70 0.00 -0.39 1.24 0.78 -0.22 0.00 -0.16 -0.15 -0.37 -0.28 -0.06 0.00 0.65 0.35 0.00 0.68 0.00 4.55 4.55 1.19 0.00 0.28 0.51 0.45 -0.97 1.26 0.02 -0.33 0.00 0.03 -0.55 -0.33 0.28 0.00 1.54 0.42 -0.01 0.78 0.59 0.00 0.25 -1.45 0.00 -1.08 0.00 4.55 4.55 0.97 0.00 -0.10 0.77 0.68 -0.94 1.22 0.02 -0.35 0.00 0.67 -0.58 -0.19 0.90 0.00 0.41 0.47 0.06 0.68 0.53 0.00 0.03 -0.95 0.00 -0.76 0.00 4.55 4.55 0.46 0.00 -0.89 2.13 1.78 -1.45 0.86 0.63 -0.33 0.00 0.67 -0.72 -0.50 0.93 0.00 0.17 0.97 0.11 0.33 0.33 0.00 -0.33 -1.67 0.00 -0.85 0.00 4.55 4.55 -0.28 0.00 -0.20 -1.30 -0.80 1.86 -0.70 -0.17 0.67 0.00 -0.72 1.52 0.57 -0.60 0.00 -0.70 -0.99 -0.52 -0.21 -0.33 0.00 0.19 1.45 0.00 1.66 0.00 4.55 4.55 0.79 0.00 0.39 0.59 0.52 -0.69 1.39 -0.24 -0.02 0.00 0.15 -0.46 -0.23 0.47 0.00 0.52 0.02 -0.26 0.86 1.64 0.00 0.29 -1.13 0.00 -0.70 0.00 4.55 4.55 0.84 0.00 0.07 0.03 0.22 -0.34 0.36 0.17 -0.03 0.00 -0.05 0.01 -0.06 -0.01 0.00 1.35 0.18 0.02 0.43 0.34 0.00 0.19 -0.78 0.00 -0.50 0.00 4.55 4.55 1.12 0.00 -0.39 1.32 1.48 -1.09 0.88 0.39 -0.24 0.00 0.32 -0.47 -0.30 0.62 0.00 0.64 0.75 -0.09 0.47 0.45 0.00 -0.08 -1.63 0.00 -0.80 0.00 4.55 4.55 0.59 0.00 -0.23 -0.13 -0.06 0.22 0.13 -0.28 0.98 0.00 0.21 0.96 0.90 -0.16 0.00 0.16 0.01 -0.21 -0.02 0.29 0.00 1.32 -0.60 0.00 -0.24 0.00 4.55 4.55 0.10 0.00 -0.78 0.58 0.62 -0.35 -0.04 1.19 -0.17 0.00 0.31 0.22 0.17 0.63 0.00 0.23 1.43 0.43 -0.25 -0.12 0.00 -0.10 -0.31 0.00 -0.22 0.00 4.55 4.55 1.60 0.00 0.24 0.38 0.40 -0.54 1.03 -0.27 0.07 0.00 0.06 0.05 0.31 0.26 0.00 0.55 0.23 -0.29 0.68 0.53 0.00 0.41 -1.10 0.00 -0.55 0.00 4.55 4.55 1.41 0.00 0.80 0.40 0.40 -0.64 1.00 -0.27 -0.10 0.00 0.20 -0.47 -0.30 0.43 0.00 0.74 0.03 -0.10 1.77 0.57 0.00 0.03 -0.24 0.00 -0.60 0.00 4.55 4.55 -0.29 0.00 -0.52 -0.86 -0.64 1.61 -0.82 -0.18 0.74 0.00 -0.25 1.68 1.44 -0.47 0.00 -0.72 -0.37 -0.13 -0.51 -0.26 0.00 0.61 0.72 0.00 0.86 0.00 4.55 4.55 0.35 0.00 -0.50 1.14 0.87 -0.84 0.47 0.50 0.16 0.00 0.41 -0.19 -0.11 0.89 0.00 0.16 0.94 0.09 0.17 0.40 0.00 0.08 -1.08 0.00 -0.54 0.00 4.55 4.55 0.09 0.00 -0.26 0.19 0.16 -0.68 -0.11 0.05 0.03 0.00 1.63 -0.49 0.15 0.36 0.00 0.12 0.27 0.85 0.41 0.33 0.00 -0.03 -0.31 0.00 -0.42 0.00 4.55 4.55 0.55 0.00 0.24 -0.49 -0.29 0.76 -0.02 -0.31 1.20 0.00 -0.43 1.11 0.67 -0.36 0.00 -0.07 -0.47 -0.60 -0.03 0.19 0.00 1.14 -0.28 0.00 0.48 0.00 4.55 4.55 -0.07 0.00 -0.67 -0.71 -0.49 1.61 -0.56 -0.30 1.36 0.00 -0.50 2.05 1.57 -0.58 0.00 -0.41 -0.28 -0.66 -0.54 -0.07 0.00 1.50 0.38 0.00 0.51 0.00 4.55 4.55 1.16 0.00 -0.16 0.64 0.79 -0.38 0.64 0.01 0.12 0.00 0.11 0.11 0.16 0.34 0.00 0.38 0.35 -0.28 0.63 0.40 0.00 0.24 -0.79 0.00 -0.44 0.00 4.55 4.55 0.36 0.00 -0.06 0.32 0.42 -0.24 0.73 -0.04 -0.03 0.00 0.24 -0.07 0.16 0.28 0.00 0.32 0.21 0.24 0.90 0.28 0.00 0.18 0.13 0.00 -0.60 0.00 4.55 4.55 0.12 0.00 0.21 -0.52 -0.36 0.75 0.09 -0.39 1.27 0.00 -0.36 1.21 0.79 -0.40 0.00 -0.03 -0.49 -0.46 0.20 0.16 0.00 1.50 -0.16 0.00 0.26 0.00 4.55 4.55 1.38 0.00 0.45 0.35 0.35 -0.74 0.71 -0.02 -0.15 0.00 0.36 -0.41 -0.08 0.35 0.00 0.72 0.25 0.28 1.10 0.46 0.00 0.02 -0.11 0.00 -0.65 0.00 4.55 4.55 0.19 0.00 0.10 0.27 0.22 -0.07 0.10 0.24 0.15 0.00 0.55 -0.11 0.00 0.78 0.00 -0.09 0.03 0.03 0.20 0.82 0.00 0.03 -0.12 0.00 0.08 0.00 4.55 4.55 0.85 0.00 0.09 0.49 0.33 -0.41 0.57 -0.10 0.63 0.00 -0.03 0.30 0.25 0.09 0.00 0.30 0.15 -0.31 0.17 0.36 0.00 0.96 -1.20 0.00 -0.35 0.00 0.92 0.92 -0.09 0.00 -0.63 -0.54 -0.36 1.36 -0.59 -0.32 1.43 0.00 -0.36 1.73 1.36 -0.50 0.00 -0.36 -0.23 -0.50 -0.41 0.00 0.00 1.24 0.21 0.00 0.32 0.00 0.92 0.92 1.31 0.00 0.23 0.36 0.36 -0.60 0.63 -0.11 0.07 0.00 0.31 -0.17 0.03 0.30 0.00 0.53 0.16 -0.16 0.47 1.05 0.00 0.22 -0.87 0.00 -0.45 0.00 0.92 0.92 0.65 0.00 0.26 0.40 0.40 -0.44 0.39 0.51 -0.20 0.00 0.35 -0.35 -0.24 0.48 0.00 0.46 0.32 0.27 0.81 0.26 0.00 -0.14 -0.14 0.00 -0.25 0.00 0.92 0.92 0.04 0.00 -0.82 0.51 0.58 -0.82 -0.05 0.18 -0.27 0.00 1.89 -0.41 0.22 0.56 0.00 0.14 0.58 0.98 0.27 0.27 0.00 -0.27 -0.03 0.00 -0.81 0.00 0.92 0.92 -0.37 0.00 1.14 -0.67 -0.64 1.67 -0.78 0.33 0.21 0.00 -0.71 0.54 0.09 -0.17 0.00 -1.01 -0.74 -0.71 -0.53 -0.37 0.00 -0.04 1.31 0.00 1.83 0.00 0.92 0.92 -0.16 0.00 -0.43 0.35 0.34 -0.55 -0.20 0.97 -0.38 0.00 0.98 -0.43 0.00 0.60 0.00 0.26 0.63 1.21 0.07 0.00 0.00 -0.38 0.58 0.00 -0.38 0.00 0.92 0.92 0.14 0.00 -0.27 0.54 0.64 -0.34 0.25 0.19 -0.09 0.00 0.14 -0.17 -0.12 0.25 0.00 0.05 0.28 0.00 0.09 0.09 0.00 -0.09 -0.52 0.00 -0.24 0.00 0.92 0.92 0.18 0.00 -0.22 -0.12 -0.06 0.32 -0.08 -0.08 0.26 0.00 -0.10 0.48 0.39 -0.10 0.00 -0.03 0.00 -0.17 -0.07 0.02 0.00 0.29 0.05 0.00 0.06 0.00 0.92 0.92 0.41 0.00 0.11 0.24 0.21 -0.27 0.58 -0.08 -0.10 0.00 -0.03 -0.18 -0.10 0.16 0.00 0.17 0.09 -0.14 0.25 0.19 0.00 0.09 -0.44 0.00 -0.24 0.00 0.92 0.92 -0.10 0.00 0.33 -0.16 -0.16 0.43 -0.20 0.10 0.03 0.00 -0.20 0.10 -0.03 -0.03 0.00 -0.26 -0.20 -0.20 -0.13 -0.10 0.00 -0.03 0.36 0.00 0.49 0.00 0.92 0.92 0.07 0.00 -0.20 0.20 0.20 -0.26 0.07 0.20 -0.10 0.00 0.13 -0.03 0.00 0.13 0.00 0.10 0.49 0.13 -0.03 -0.03 0.00 -0.07 -0.16 0.00 -0.20 0.00 0.92 0.92 0.20 0.00 0.07 0.20 0.16 -0.20 0.49 -0.07 -0.10 0.00 -0.03 -0.16 -0.10 0.13 0.00 0.10 0.07 -0.10 0.20 0.13 0.00 0.07 -0.33 0.00 -0.20 0.00 0.92 0.92 | 
| 
########################################
# Program: prophet
# Rundate: Sun 15 Jul 2007 12:00:00
# Commandline: prophet
#    -sequence "tsw:h*"
#    -infile ../../data/globins.gribskov
# Align_format: simple
# Report_file: hd_fugru.prophet
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HD_FUGRU
# Matrix: EBLOSUM62
#
# Length: 167
# Identity:      20/167 (12.0%)
# Similarity:    46/167 (27.5%)
# Gaps:           6/167 ( 3.6%)
# Score: 74.34
# 
#
#=======================================
globins            3 VDTGSV-VSLS-EEELSAVDKAWVKANSVAEVGGHALERGLFASEPMTLE     50
                     :....| ..|| .|..:.........:.:......:....|...|....:
HD_FUGRU        2289 LQQPCVWNKLSTPEYNTHTCSLIYCLHHIILAVAVSPGDQLLHPERKKTK   2338
globins           51 FFDTFKYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGT-LAALS     99
                     ...........|....:..::....:::..|.:.:..:..|... ..|..
HD_FUGRU        2339 ALRHSDDEDQVDSVHDNHTLEWQACEIMAELVEGLQSVLSLGHHRNTAFP   2388
globins          100 DLHAHKLKKGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASV    149
                     ......|:..:..::...|.:....|........::|:........|..:
HD_FUGRU        2389 AFLTPTLRNIIISLSRLPLVNSHTRVPPLVWKLGWSPQPGGEFGTTLPEI   2438
globins          150 ATV-LASK--YRELGYQ    163
                     ... |..|  :||..|:
HD_FUGRU        2439 PVDFLQEKDVFREFLYR   2455
#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HIRA_FUGRU
# Matrix: EBLOSUM62
#
  [Part of this file has been deleted for brevity]
                     :|.|:.||.|||...|.|.| . .||||.||. . |....|.|..||::|
HBB_PANPA          1 MVHLTPEEKSAVTALWGKVNVD-DEVGGEALGRL-LLVVYPWTQRFFESF     48
globins           56 KYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHK    105
                     ..|||.|...|:..|||||||||.|..|.:||||:|:||.|.||:||..|
HBB_PANPA         49 GDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDK     98
globins          106 LK-KGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLA    154
                     |. .  ||.||:||.:.|:.|||.|...:|||.|||:..|.:|.||..||
HBB_PANPA         99 LHVD--DPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALA    146
globins          155 SKYR    158
                     .||.
HBB_PANPA        147 HKYH    150
#=======================================
#
# Aligned_sequences: 2
# 1: globins
# 2: HBB_PANTR
# Matrix: EBLOSUM62
#
# Length: 154
# Identity:      77/154 (50.0%)
# Similarity:    92/154 (59.7%)
# Gaps:           7/154 ( 4.5%)
# Score: 178.67
# 
#
#=======================================
globins            8 VVSLSEEELSAVDKAWVKAN-SVAEVGGHALE-RGLFASEPMTLEFFDTF     55
                     :|.|:.||.|||...|.|.| . .||||.||. . |....|.|..||::|
HBB_PANTR          1 MVHLTPEEKSAVTALWGKVNVD-DEVGGEALGRL-LLVVYPWTQRFFESF     48
globins           56 KYLSTFDLSKGSADVKAHGKKVLDALGDAVAHLDDLEGTLAALSDLHAHK    105
                     ..|||.|...|:..|||||||||.|..|.:||||:|:||.|.||:||..|
HBB_PANTR         49 GDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDK     98
globins          106 LK-KGVDPVNFKLLSHCLLVVLASHLPGDFTPEVQASMDKFLASVATVLA    154
                     |. .  ||.||:||.:.|:.|||.|...:|||.|||:..|.:|.||..||
HBB_PANTR         99 LHVD--DPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALA    146
globins          155 SKYR    158
                     .||.
HBB_PANTR        147 HKYH    150
#---------------------------------------
#---------------------------------------
 | 
EMBOSS An error in prophet.c at line 110: Unrecognised profile/matrix file format
then you have probably given prophet a 'simple frequency matrix' and not a a GRIBSKOV or HENIKOFF profile produced by prophecy.
If you see something like:
Uncaught exception Allocation Failed raised at prophet.c:147
then you have run out of memory. This will occur if your sequence and/or your profile are large.
prophet allocates space based on the length of the sequence and the size of the profile (8 x seqlen x profilelen)
| Program name | Description | 
|---|---|
| profit | Scan a sequence or database with a matrix or profile | 
| prophecy | Creates matrices/profiles from multiple alignments |