pcwise 2.0.4b (Mon Mar 16 18:05:46 1998 release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyrights

Query protein:    |RabbitB|
Comp Matrix:      blosum62.bla
Gap open:         12
Gap extension:    2
Start/End         local
Target Sequence   tmp_seq
Strand:           both
Codon Table:      codon.table
Subs error:       1e-05
Indel error:      1e-05
Algorithm         333

pcwise output
Score 16.37 bits over entire alignment
Score reported as bits over a synchronised coding sequence model

|RabbitB|         58 GKGVLKAVEHINKTLGPAL                               
                     GK  L+A  H+ K + PA+                               
                     GKVDLEAFSHFTKIITPAI                               
tmp_seq          778 gaggcggtactaaaaacga                               
                     gatatactgatcattccct                               
                     agccgaccctcaaccaagt                               


//

pcwise output
Score 15.43 bits over entire alignment
Score reported as bits over a synchronised coding sequence model

|RabbitB|        370 HRSGETEDTFIADLVVGLCTGQIKTGAPCRSER                 
                     HR+  T    +++    LCT    +G P R  R                 
                     HRTRRTARPCLSNWGCSLCTSSPPSGRPGRWAR                 
tmp_seq         -328 ccaccagcctcaatgtactattcctgacgctgc                 
                     agcggccgcgtgaggggtgccccccggcgggcg                 
                     ccaacattttatcgatctcttttgtagtgcggc                 


//