matcher output bug ?

[David Bauer]

Hi,

it seems that matcher somtimes forgets to label the matches with the
usual ":" in the output if the matching region is very short.
Example1 shows no label at all and Example2 the labeling starts somwhere
in the middle of the matching region.

Example1:
########################################
# Program:  matcher
# Rundate:  Fri Jan 11 16:40:50 2002
# Report_file: 
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: c1
# 2: AW370204
# Matrix: EDNAFULL
# Gap_penalty: 12
# Extend_penalty: 4
#
# Length: 166
# Identity:     165/166 (99.4%)
# Similarity:     1/166 ( 0.6%)
# Gaps:         165/166 (99.4%)
# Score: 809
# 
#
#=======================================


      200       210       220       230       240        
    c1 GTGTCCGAGTTGGAGAGTGCTCTGCAGATGGAGCCAGCTGCCTTCCAGGC
                                                         
AW3702 GTGTCCGAGTTGGAGAGTGCTCTGCAGATGGAGCCAGCTGCCTTCCAGGC
          40        50        60        70        80     

      250       260       270       280       290        
    c1 TTTATATTCTGCTGAGAAGCCAAAGCTGGAAGATGAGCATCTCGTTTTCT
                                                         
AW3702 TTTATATTCTGCTGAGAAGCCAAAGCTGGAAGATGAGCATCTCGTTTTCT
          90       100       110       120       130     

      300       310       320        330       340       
    c1 TCTGTCAGATGGGCAAGCGGGGCCTCCA-GGCCACGCAGCTGGCCCGGAG
                                                         
AW3702 TCTGTCAGATGGGCAAGCGGGGCCTCCAAGGCCACGCAGCTGGCCCGGAG
         140       150       160       170       180     

       350       360   
    c1 TCTTGGATACACTGGG
                       
AW3702 TCTTGGATACACTGGG
         190       200 

#---------------------------------------
#---------------------------------------

Example 2:
########################################
# Program:  matcher
# Rundate:  Fri Jan 11 16:43:55 2002
# Report_file: 
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: c1
# 2: BE695392
# Matrix: EDNAFULL
# Gap_penalty: 12
# Extend_penalty: 4
#
# Length: 230
# Identity:     222/230 (96.5%)
# Similarity:     4/230 ( 1.7%)
# Gaps:         222/230 (96.5%)
# Score: 1030
# 
#
#=======================================


         140       150       160       170       180     
    c1 TTCGACGTGCGCTCTCGCGAGGAGGCGGCAGCTGGGACCATCCCAGGGGC
                                                         
BE6953 TGCGATGTGCGCTCTCGCGAGGAG-CGGCAGCTGGGACCATCCCAGGG-C
        20        30        40         50        60      

         190       200       210       220       230     
    c1 GCTCAACATCCCGGTGTCCGAGTTGGAGAGTGCTCTGCAGATGGAGCCAG
                                                         
BE6953 GCTCAACATCCCGGTGTCCGAGTTGGAGAGTGCTCTGCAGACTGAGCCAG
          70        80        90       100       110     

         240       250        260       270       280    
    c1 CTGCCTTCCAGGCTTTATATTCT-GCTGAGAAGCCAAAGCTGGAAGATGA
                                            :::::::::::::
BE6953 CTGCCTTCCAGGCTTTATATTCTCGCTGAGAAGCCAAAGCTGGAAGATGA
         120       130       140       150       160     

          290       300       310       320       330    
    c1 GCATCTCGTTTTCTTCTGTCAGATGGGCAAGCGGGGCCTCCAGGCCACGC
       ::::::::::::::::::::::::::::::::::::::::::::::::::
BE6953 GCATCTCGTTTTCTTCTGTCAGATGGGCAAGCGGGGCCTCCAGGCCACGC
         170       180       190       200       210     

          340        350       360   
    c1 AGCTGGCCCGGA-GTCTTGGATACACTGGG
       :::::::::::: :::::::::::::::::
BE6953 AGCTGGCCCGGAAGTCTTGGATACACTGGG
         220       230       240     

#---------------------------------------
#---------------------------------------

-- 
Dr. David Bauer
GenProfile AG, Max-Delbrueck-Center, Erwin-Negelein-Haus 
Robert-Roessle-Str. 10, D-13125 Berlin, Germany
bauer at genprofile.com, Tel:49-30-94892165, FAX:49-30-94892151