Incossistent output for big `--amplicon` values

[phlaster]

I was messing with --amplicon parameter constructing degenerate primers for my aligned genes. And I found some output inconsistencies. For example, for single alignment file I got following outputs:

No --amplicon parameter:

$ degenprime --degenerate --input_file:NodA_galegae.afa --output_file:NodA.csv
Output details saved to NodA.csv
Program complete.

$ cat NodA.csv 
Pair #,Forward,Reverse,Amplicon,Temp. Diff
1,ACCTATGGCCCAACCGGGAA,ACGGCCAGTCGCTCATTGTG,465,0.291779
2,ACGAGGAGCTGGCATCATTC,CCCAACCGGCACTACAACAA,472,0.622589
3,GAAACTGAGTTGGCTTCCTC,TAAAACGTCTTCGGTTCGAG,476,0.372711
4,GAGCTGGCATCATTCTTTCG,TCCGCAAGGGTAGACTCTAC,403,0.813354
5,TGTCTTCCGGGGTGCATTGG,GACGGCCAGTCGCTCATTGT,552,0.498199

Big --amplicon parameter: (failure type #1, quite reasonable message)

$ degenprime --degenerate --input_file:NodA_galegae.afa --output_file:NodA.csv --amplicon:560
At least one of the forward or reverse primer lists was empty.

Even bigger --amplicon parameter: (failure type #2, wow)

$ degenprime --degenerate --input_file:NodA_galegae.afa --output_file:NodA.csv --amplicon:580
                          %%%%%%%%%%%%%%%%%%%%%%%%                          
                          % Sequence Information %                          
                          %%%%%%%%%%%%%%%%%%%%%%%%                          

                             Sequence Count: 17                             

                Sequence(0001):[NodA|unitig_1_co] Size:[588]                
                Sequence(0002):[NodA|unitig_1_co] Size:[588]                
                Sequence(0003):[NodA|unitig_1_co] Size:[588]                
                Sequence(0004):[NodA|unitig_1_co] Size:[588]                
                Sequence(0005):[NodA|unitig_1_co] Size:[588]                
                Sequence(0006):[NodA|unitig_1_co] Size:[588]                
                Sequence(0007):[NodA|unitig_1_co] Size:[588]                
                Sequence(0008):[NodA|unitig_1_co] Size:[588]                
                Sequence(0009):[NodA|unitig_1_co] Size:[588]                
                Sequence(0010):[NodA|unitig_1_co] Size:[588]                
                Sequence(0011):[NodA|unitig_1_co] Size:[588]                
                Sequence(0012):[NodA|unitig_2_co] Size:[588]                
                Sequence(0013):[NodA|unitig_1_co] Size:[588]                
                Sequence(0014):[NodA|unitig_1_co] Size:[588]                
                Sequence(0015):[NodA|unitig_1_co] Size:[588]                
                Sequence(0016):[NodA|unitig_1_co] Size:[588]                
                Sequence(0017):[NodA|unitig_1_co] Size:[588]                

                            %%%%%%%%%%%%%%%%%%%%%                           
                            % Conserved Regions %                           
                            %%%%%%%%%%%%%%%%%%%%%                           

                           %%%%%%%%%%%%%%%%%%%%%%                           
                           % Consensus Sequence %                           
                           %%%%%%%%%%%%%%%%%%%%%%                           

                       Conserved regions capitalized.                       
 (00000-00059): ATGTCTTCCGGGGTGCATTGGAAATTACATTGGGAAACTGAGTTGGCTTCCTCCGACCAC
 (00060-00119): GAGGAGCTGGCATCATTCTTTCGAAATACCTATGGCCCAACCGGGAAGTTTAACGCCAAA
 (00120-00179): CCCTTCGAGGATGGTCGTAGCTGGGCCGGCGCACGGCCTGAGCTTCGCGCCATTGCCTAC
 (00180-00239): GATTCCAAGGGAATAGCCGGTCATCTAGGGTTGTTACGGCGTTTCATCAGAGTGGGTGAG
 (00240-00299): ACAGAAGTACTTGTGGCTGAGTTGGGGTTATATGGTGTTCGACCGGATTTAGAAAAATTG
 (00300-00359): GGCATCGCTCACTCCATTCGAGCCATGGCTCCGGTCGTGGACGACCTTGGCGTGCCTTTC
 (00360-00419): GCATTCGGAACTGTGCGATACGCGATGCGAAATCACATCGAGAGATTCTGCAGGGATGGC
 (00420-00479): GCGGCAAATATCGTGTCCGGCATTCGAGTAGAGTCTACCCTTGCGGATGTCTATCGTGAC
 (00480-00539): TGCCCGGCCACTCGAACCGAAGACGTTTTAGTTGTTGTAGTGCCGGTTGGGCGCACAATG
 (00540-00587): AGCGACTGGCCGTCGGGGTCCCTGATACagcgacgcgggccggaacta

There were insufficient primers found for this data.                        
Insufficient primers found for this data.

Now for another alignment file I got:
No --amplicon parameter:

$ degenprime --degenerate --input_file:ActR_galegae.afa --output_file:ActR.csv
Output details saved to ActR.csv
Program complete.

$ cat ActR.csv 
Pair #,Forward,Reverse,Amplicon,Temp. Diff
1,TGACCCTTCGCTGCTGATCG,GTCACGGCGGTDGCGATATT,269,0.708435
2,CTGACCCTTCGCTGCTGATC,GGCTTGGCGAGATAGTCGAG,309,0.446228
3,ACACACCCGGAACCGACCAA,ACGTTGCGCTCGCACATCTC,493,0.168365
4,CGCTGCTGATCGTCGATGAC,CGCMGACATCGGGTTTTCCG,382,0.349274
5,GCTGCTGATCGTCGATGACG,CGCTCGCACATCTCGTAGAC,431,0.605988

Big --amplicon parameter: (failure type #3, quite reasonable message again, but different from #1)

$ degenprime --degenerate --input_file:ActR_galegae.afa --output_file:ActR.csv --amplicon:540
No primer pairs were found for these specifications.
Output details saved to ActR.csv
Program complete.

Even bigger --amplicon parameter: (failure type #2, this again)

$ degenprime --degenerate --input_file:ActR_galegae.afa --output_file:ActR.csv --amplicon:550
                          %%%%%%%%%%%%%%%%%%%%%%%%                          
                          % Sequence Information %                          
                          %%%%%%%%%%%%%%%%%%%%%%%%                          

                             Sequence Count: 18                             

                Sequence(0001):[ActR|unitig_0_87] Size:[582]                
                Sequence(0002):[ActR|unitig_0_87] Size:[582]                
                Sequence(0003):[ActR|unitig_0_87] Size:[582]                
                Sequence(0004):[ActR|unitig_0_87] Size:[582]                
                Sequence(0005):[ActR|unitig_0_87] Size:[582]                
                Sequence(0006):[ActR|unitig_0_87] Size:[582]                
                Sequence(0007):[ActR|unitig_0_87] Size:[582]                
                Sequence(0008):[ActR|unitig_0_87] Size:[582]                
                Sequence(0009):[ActR|unitig_0_87] Size:[582]                
                Sequence(0010):[ActR|unitig_0_87] Size:[582]                
                Sequence(0011):[ActR|unitig_0_87] Size:[582]                
                Sequence(0012):[ActR|unitig_0_87] Size:[582]                
                Sequence(0013):[ActR|unitig_0_37] Size:[582]                
                Sequence(0014):[ActR|unitig_0_87] Size:[582]                
                Sequence(0015):[ActR|unitig_0_87] Size:[582]                
                Sequence(0016):[ActR|unitig_0_87] Size:[582]                
                Sequence(0017):[ActR|unitig_0_87] Size:[582]                
                Sequence(0018):[ActR|unitig_0_87] Size:[582]                

                            %%%%%%%%%%%%%%%%%%%%%                           
                            % Conserved Regions %                           
                            %%%%%%%%%%%%%%%%%%%%%                           

                           %%%%%%%%%%%%%%%%%%%%%%                           
                           % Consensus Sequence %                           
                           %%%%%%%%%%%%%%%%%%%%%%                           

                       Conserved regions capitalized.                       
 (00000-00059): ---------ATGGAAACACACCCGGAACCGACCAAGGTTCATGCCGACCCCGAACTCGGG
 (00060-00119): CCTGACCCTTCGCTGCTGATCGTCGATGACGACGGVCCGTTCCTGCGHCGGCTGGCnCGV
 (00120-00179): GCSATGGAGACCCGCGGCTTCCTBGTCGAHACGGCGGAGTCCGTCGCGGAAGGTATCGCH
 (00180-00239): AAGACVAAGGCGCGGCCGCCGAAATATGCVGTGGTCGACCTGCGBCTCGGCGACGGCAAC
 (00240-00299): GGDCTGGAYGTVATCGAAGCDATCCGCCAGAGCCGCGAGGAYACCAAGGTGATCGTGCTG
 (00300-00359): ACBGGCTACGGCAATATCGCHACCGCCGTGACGGCVGTGAAGCTCGGGGCGCTCGACTAT
 (00360-00419): CTCGCCAAGCCBGCBGACGCCGACGACATHTTYGGCGCDCTGACVCAGCGGCCGGGCGAG
 (00420-00479): CGGGCDGACGTGCCGGAAAACCCGATGTCKGCGGATCGCGTGCGCTGGGAACATATCCAG
 (00480-00539): CGBGTCTACGAGATGTGCGAGCGCAACGTBTCSGAGACGGCVCGCCGGCTCAACATGCAT
 (00540-00581): CGCCGCACGCTGCAGCGCATCCtcgccaagcgcgcvccgaaa

There were insufficient primers found for this data.                        
Insufficient primers found for this data.

So when primer construction fails there are at least 3 different kinds of output, which is somewhat confusing. I attached the files discussed so that you look at them.

alignments.zip