inconsistent CAP3 assembly and alignment

[ysnapus]

I have 5 related EST sequences and I want to assemble contigs. I am using the sequence assembly program CAP3. Here is my data:

>ES981358
GTTACTGTCCAGAGATTCGAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGAATGCACGCGTGGCAGGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTGCCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCTTGACCTTTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAAACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTGCAGCTGTGATCTCACTTCGCAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGTTTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAAAGTTATAGGAGATGTTTTCTTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTTAGTCCAA
>EV115773
ACTGNGGTCGCCTGCAGGTACCGGTCTCGGATTCCCGGGTCGACCCACGCGTCCGACCGTTGCCGCGCCTCGTTACTCTCTGGCCTCTCTGCAATCATCCATCACCATGTTCATGTTCATCGCTGCAGATTCTGCTCTGAGGTTCACATTGGTAAGGAAGGTCATGGAATAAGGACTTGCATTGGCCCCGGGAGCGGTTCAAGAAGTGCGACTCATGTATGGAAAAGAGGAAGAGCTAGCGACGTCGTATTGTTCCCAAAATGTTTCCACCTCTATGACCGTGCTGTCAAACCGCGAGTTATCCACGACGAGAGGTTCGCCGTCCCTAAGATCTCTGCGGTTCTTGAGCTATGCATACAGGCAGGCGTGGACATCGATAAGTTCCCAGCGAAGCGAAGATCCAAACCTGTTTACAGCATCGAAGGACGGATCGTAGATTTCGAGGAAGTCAACAACGGGAACTCAGAAACCGCAGTTACTAATTCTACTACTACGGCTACACCTTTACAAGAAGATTATCATTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGGTCACAGGGGTCAAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTACTGTCCAGAGATTCAAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCNGTTGTGGAGTTGTGTGTGCAAGGTGGGTGCACCGTGCCTGACCAGTC
>EV115686
GGTATATGAAACCTTTGAACAAACTATTGGACTAAAATGGATTCCACAATCTTGTTTTGTTTATATGAAAGGAAGAAAACATCTCCTATAACTTTTTATGAAGTTATATAACATTTTTGCCTTAATGGTACAAAACCTCAACGGGAATGTTGAAATTGCATTAACCTCAAAGCTATTGAGAAGCTGCGAAACTGCGAAGTGAGATCACAGCTGCACGGAGCAGAAGAATCAAACATCTAACTATGTTTCCTAATATGTATATGGAGCTTTCGTTTATTCATATCAATTGTTTCTTGATGCTGAATCACATTGAAAGGTCAAGCGACTAGATCGACTTCATCACGTTGAGGGTAAACCACATCGAGTCTCATCATACTCTTGTACTGGTCAGGCACCGGTGCACCACCTTGCACACACAACTCCACAACCGCAGGAGCTTTCCCATAAAACCTCTGCAAGCTATTGTCAAGAGCAGAAGAATCTGGATCCCGAACATGCCAAACATAGTTTGGACCGACCACGTCGTCAATAGTCGCTTCTTGCCACGCGTGCATTCCGTCTCGCATCTGATGTTTTGTCGCTTTACACATCTTCACTTTGTGTCCCTTTGGACCCACTTGAATCTCTGGACAGTAACCACATGTCCACACTTTGTATCTCTCCATCAGTTTCTTGACCCCTGTGACCATTTCAAACCATGAGTCCATCGTCTCAACGCTTAACTCCTTCAAGCTCTTCTTCTCTGTACTGTAATGA
>EV005953
GAACTCAGAAACCGCAGTTACTAGTGTTAGCACGGCTACACCTTTACAAGAAGATGATCATTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTAAGACAATGGATTCATGGTTTGAAATGGTCACAGGGGTCAAGGAACTGATGGAGAAATACAAAGTGTGGACTTGTGGTTACTGTCCAGAGGTTCAAGTGGGTCCCAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAGCATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTGTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCGGTCGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTACCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCGTGACCTTTCAAGGTGATTCAGCATCAAGAAACAATTGATATGAAAAAACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGGTTCTTCTGCTCCGTGCAGCTTCTCACTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGTTTTGTACCA
>EE435034
TTATATTGAGGAGATCCCCCGGTGGAGGATGTTAACCGAGATATCTCGGAGAAATATTCGTGCGGGATTTAGCATGATAACGAGGCTCAAAAAATGAAAAGTAGTCTAGCAATTGTAAGCTGAGGACTCTTTCACACAGGAAATAGCTATGATCATGATCATCGCTGGAGATTCTGCTCTGAGGATCACATTGTTTAAGGAAGGTCATGGAATAAGGACTTGCATTGGCCCCGGGAGCGGTTCAAGAAGTGCGACTCATGTATGGAAAAGAGGAAGAGCTAGCGACGTCGTATTGTTCCCAAAATGTTTCCACCTCTATGACCGTGCTGTCAAACCGCGAGTTATCCACGACGAGAGGTTCGCCGTCCCTAAGATCTCTGCGGTTCTTGAGCTATGCATACAGGCAGGCGTGGACATCGATAAGTTCCCAGCGAAGCGAAGATCCAAACCTGTTTACAGCATCGAAGGACGGATCGGTAGATTTCGAGGAAGTCAACAAACGGGAACTCAGAAACCGCAGTTACTAATTCTACTACTACGGCTACACCTTTACAAGAAGATTATCATTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGTTCACAGGGGTCA

When I run this through CAP3, I get a contig of EV005953+, EV115686-, and ES981358+, shown below:

EV005953+             GAACTCAGAAACCGCAGTTACTAGTGTTAGCACGGCTACACCTTTACAAGAAGATGATCA
EV115686-                                                                      TCA
                      ____________________________________________________________
consensus             GAACTCAGAAACCGCAGTTACTAGTGTTAGCACGGCTACACCTTTACAAGAAGATGATCA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             TTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTAAGACAATGGATTCATGGTT
EV115686-             TTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTT
                      ____________________________________________________________
consensus             TTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTAAGACAATGGACTCATGGTT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             TGAAATGGTCACAGGGGTCAAGGAACTGATGGAGAAATACAAAGTGTGGACTTGTGGTTA
EV115686-             TGAAATGGTCACAGGGGTCAAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTA
ES981358+                                                                     GTTA
                      ____________________________________________________________
consensus             TGAAATGGTCACAGGGGTCAAGAAACTGATGGAGAAATACAAAGTGTGGACATGTGGTTA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             CTGTCCAGAGGTTCAAGTGGGTCCCAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAA
EV115686-             CTGTCCAGAGATTCAAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAA
ES981358+             CTGTCCAGAGATTCGAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAA
                      ____________________________________________________________
consensus             CTGTCCAGAGATTCAAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             GCATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGG
EV115686-             ACATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGG
ES981358+             ACATCAGATGCGAGACGGAATGCACGCGTGGCAGGAAGCGACTATTGACGACGTGGTCGG
                      ____________________________________________________________
consensus             ACATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             TCCAAACTATGTGTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCA
EV115686-             TCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCA
ES981358+             TCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCA
                      ____________________________________________________________
consensus             TCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             GAGGTTTTATGGGAAAGCTCCTGCGGTCGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGT
EV115686-             GAGGTTTTATGGGAAAGCTCCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGT
ES981358+             GAGGTTTTATGGGAAAGCTCCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGT
                      ____________________________________________________________
consensus             GAGGTTTTATGGGAAAGCTCCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             ACCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGT
EV115686-             GCCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGT
ES981358+             GCCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGT
                      ____________________________________________________________
consensus             GCCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             CGATCTAGTCGCGTGACCTTTCAAGGTGATTCAGCATCAAGAAACAATTGATATGAAAAA
EV115686-             CGATCTAGTCGCTTGACCTTTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAA
ES981358+             CGATCTAGTCGCTTGACCTTTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAA
                      ____________________________________________________________
consensus             CGATCTAGTCGCTTGACCTTTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             ACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGGTTCTTCTGCTCCGTG
EV115686-             ACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTG
ES981358+             ACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTG
                      ____________________________________________________________
consensus             ACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             CAGCT                                                       
EV115686-             CAGCTGTGATCTCACTTCGCAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATT
ES981358+             CAGCTGTGATCTCACTTCGCAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATT
                      ____________________________________________________________
consensus             CAGCTGTGATCTCACTTCGCAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             TCAACATTCCCGTTGAGGTTTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAA
ES981358+             TCAACATTCCCGTTGAGGTTTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAA
                      ____________________________________________________________
consensus             TCAACATTCCCGTTGAGGTTTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             AGTTATAGGAGATGTTTTCTTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTT
ES981358+             AGTTATAGGAGATGTTTTCTTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTT
                      ____________________________________________________________
consensus             AGTTATAGGAGATGTTTTCTTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             AGTCCAATAGTTTGTTCAAAGGTTTCATATACC
ES981358+             AGTCCAA                          
                      ____________________________________________________________
consensus             AGTCCAATAGTTTGTTCAAAGGTTTCATATACC

However, I saw somewhere else that actually EV115773 should also align with the other sequences. To test this I gave just the relevant 4 sequences as the input:

>ES981358
GTTACTGTCCAGAGATTCGAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGAATGCACGCGTGGCAGGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTGCCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCTTGACCTTTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAAACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTGCAGCTGTGATCTCACTTCGCAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGTTTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAAAGTTATAGGAGATGTTTTCTTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTTAGTCCAA
>EV115773
ACTGNGGTCGCCTGCAGGTACCGGTCTCGGATTCCCGGGTCGACCCACGCGTCCGACCGTTGCCGCGCCTCGTTACTCTCTGGCCTCTCTGCAATCATCCATCACCATGTTCATGTTCATCGCTGCAGATTCTGCTCTGAGGTTCACATTGGTAAGGAAGGTCATGGAATAAGGACTTGCATTGGCCCCGGGAGCGGTTCAAGAAGTGCGACTCATGTATGGAAAAGAGGAAGAGCTAGCGACGTCGTATTGTTCCCAAAATGTTTCCACCTCTATGACCGTGCTGTCAAACCGCGAGTTATCCACGACGAGAGGTTCGCCGTCCCTAAGATCTCTGCGGTTCTTGAGCTATGCATACAGGCAGGCGTGGACATCGATAAGTTCCCAGCGAAGCGAAGATCCAAACCTGTTTACAGCATCGAAGGACGGATCGTAGATTTCGAGGAAGTCAACAACGGGAACTCAGAAACCGCAGTTACTAATTCTACTACTACGGCTACACCTTTACAAGAAGATTATCATTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGGTCACAGGGGTCAAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTACTGTCCAGAGATTCAAGTGGGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCNGTTGTGGAGTTGTGTGTGCAAGGTGGGTGCACCGTGCCTGACCAGTC
>EV115686
GGTATATGAAACCTTTGAACAAACTATTGGACTAAAATGGATTCCACAATCTTGTTTTGTTTATATGAAAGGAAGAAAACATCTCCTATAACTTTTTATGAAGTTATATAACATTTTTGCCTTAATGGTACAAAACCTCAACGGGAATGTTGAAATTGCATTAACCTCAAAGCTATTGAGAAGCTGCGAAACTGCGAAGTGAGATCACAGCTGCACGGAGCAGAAGAATCAAACATCTAACTATGTTTCCTAATATGTATATGGAGCTTTCGTTTATTCATATCAATTGTTTCTTGATGCTGAATCACATTGAAAGGTCAAGCGACTAGATCGACTTCATCACGTTGAGGGTAAACCACATCGAGTCTCATCATACTCTTGTACTGGTCAGGCACCGGTGCACCACCTTGCACACACAACTCCACAACCGCAGGAGCTTTCCCATAAAACCTCTGCAAGCTATTGTCAAGAGCAGAAGAATCTGGATCCCGAACATGCCAAACATAGTTTGGACCGACCACGTCGTCAATAGTCGCTTCTTGCCACGCGTGCATTCCGTCTCGCATCTGATGTTTTGTCGCTTTACACATCTTCACTTTGTGTCCCTTTGGACCCACTTGAATCTCTGGACAGTAACCACATGTCCACACTTTGTATCTCTCCATCAGTTTCTTGACCCCTGTGACCATTTCAAACCATGAGTCCATCGTCTCAACGCTTAACTCCTTCAAGCTCTTCTTCTCTGTACTGTAATGA
>EV005953
GAACTCAGAAACCGCAGTTACTAGTGTTAGCACGGCTACACCTTTACAAGAAGATGATCATTACAGTACAGAGAAGAAGAGCTTGAAGGAGTTAAGCGTTAAGACAATGGATTCATGGTTTGAAATGGTCACAGGGGTCAAGGAACTGATGGAGAAATACAAAGTGTGGACTTGTGGTTACTGTCCAGAGGTTCAAGTGGGTCCCAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAGCATCAGATGCGAGACGGAATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTGTGGCATGTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCTCCTGCGGTCGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTACCTGACCAGTACAAGAGTATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCGTGACCTTTCAAGGTGATTCAGCATCAAGAAACAATTGATATGAAAAAACGAAAGCTCCATATACATATTAGGAAACATAGTTAGATGTTTGGTTCTTCTGCTCCGTGCAGCTTCTCACTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGTTTTGTACCA

Now, I get an alignment where all the 4 sequences align:

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             ACTGNGGTCGCCTGCAGGTACCGGTCTCGGATTCCCGGGTCGACCCACGCGTCCGACCGT
                      ____________________________________________________________
consensus             ACTGNGGTCGCCTGCAGGTACCGGTCTCGGATTCCCGGGTCGACCCACGCGTCCGACCGT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             TGCCGCGCCTCGTTACTCTCTGGCCTCTCTGCAATCATCCATCACCATGTTCATGTTCAT
                      ____________________________________________________________
consensus             TGCCGCGCCTCGTTACTCTCTGGCCTCTCTGCAATCATCCATCACCATGTTCATGTTCAT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             CGCTGCAGATTCTGCTCTGAGGTTCACATTGGTAAGGAAGGTCATGGAATAAGGACTTGC
                      ____________________________________________________________
consensus             CGCTGCAGATTCTGCTCTGAGGTTCACATTGGTAAGGAAGGTCATGGAATAAGGACTTGC

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             ATTGGCCCCGGGAGCGGTTCAAGAAGTGCGACTCATGTATGGAAAAGAGGAAGAGCTAGC
                      ____________________________________________________________
consensus             ATTGGCCCCGGGAGCGGTTCAAGAAGTGCGACTCATGTATGGAAAAGAGGAAGAGCTAGC

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             GACGTCGTATTGTTCCCAAAATGTTTCCACCTCTATGACCGTGCTGTCAAACCGCGAGTT
                      ____________________________________________________________
consensus             GACGTCGTATTGTTCCCAAAATGTTTCCACCTCTATGACCGTGCTGTCAAACCGCGAGTT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             ATCCACGACGAGAGGTTCGCCGTCCCTAAGATCTCTGCGGTTCTTGAGCTATGCATACAG
                      ____________________________________________________________
consensus             ATCCACGACGAGAGGTTCGCCGTCCCTAAGATCTCTGCGGTTCTTGAGCTATGCATACAG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             GCAGGCGTGGACATCGATAAGTTCCCAGCGAAGCGAAGATCCAAACCTGTTTACAGCATC
                      ____________________________________________________________
consensus             GCAGGCGTGGACATCGATAAGTTCCCAGCGAAGCGAAGATCCAAACCTGTTTACAGCATC

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             GAAGGACGGATCGTAGATTTCGAGGAAGTCAACAACGGGAACTCAGAAACCGCAGTTACT
                      ____________________________________________________________
consensus             GAAGGACGGATCGTAGATTTCGAGGAAGTCAACAACGGGAACTCAGAAACCGCAGTTACT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             AATTCTACTACTACGGCTACACCTTTACAAGAAGATTATCATTACAGTACAGAGAAGAAG
EV005953+                         ACGGCTACACCTTTACAAGAAGATGATCATTACAGTACAGAGAAGAAG
EV115686-                                                   TCATTACAGTACAGAGAAGAAG
                      ____________________________________________________________
consensus             AATTCTACTACTACGGCTACACCTTTACAAGAAGATGATCATTACAGTACAGAGAAGAAG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             AGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGGTCACAGGGGTC
EV005953+             AGCTTGAAGGAGTTAAGCGTTAAGACAATGGATTCATGGTTTGAAATGGTCACAGGGGTC
EV115686-             AGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGGTCACAGGGGTC
                      ____________________________________________________________
consensus             AGCTTGAAGGAGTTAAGCGTTGAGACGATGGACTCATGGTTTGAAATGGTCACAGGGGTC

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             AAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTACTGTCCAGAGATTCAAGTG
EV005953+             AAGGAACTGATGGAGAAATACAAAGTGTGGACTTGTGGTTACTGTCCAGAGGTTCAAGTG
EV115686-             AAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTACTGTCCAGAGATTCAAGTG
ES981358+                                                  GTTACTGTCCAGAGATTCGAGTG
                      ____________________________________________________________
consensus             AAGAAACTGATGGAGAGATACAAAGTGTGGACATGTGGTTACTGTCCAGAGATTCAAGTG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             GGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGA
EV005953+             GGTCCCAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAGCATCAGATGCGAGACGGA
EV115686-             GGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGA
ES981358+             GGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGA
                      ____________________________________________________________
consensus             GGTCCAAAGGGACACAAAGTGAAGATGTGTAAAGCGACAAAACATCAGATGCGAGACGGA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             ATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCAT
EV005953+             ATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTGTGGCAT
EV115686-             ATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCAT
ES981358+             ATGCACGCGTGGCAGGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCAT
                      ____________________________________________________________
consensus             ATGCACGCGTGGCAAGAAGCGACTATTGACGACGTGGTCGGTCCAAACTATGTTTGGCAT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             GTTCGGGATCCAGATTCTTCTGCTCTTGACA-TAGCTTGCAGAGGTTTTATGGGAAAGCT
EV005953+             GTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCT
EV115686-             GTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCT
ES981358+             GTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCT
                      ____________________________________________________________
consensus             GTTCGGGATCCAGATTCTTCTGCTCTTGACAATAGCTTGCAGAGGTTTTATGGGAAAGCT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115773+             CCTGCNGTTGTGGAGTTGTGTGTGCAAGGTGG                            
EV005953+             CCTGCGGTCGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTACCTGACCAGTACAAGAGT
EV115686-             CCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTGCCTGACCAGTACAAGAGT
ES981358+             CCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTGCCTGACCAGTACAAGAGT
                      ____________________________________________________________
consensus             CCTGCGGTTGTGGAGTTGTGTGTGCAAGGTGGTGCACCGGTGCCTGACCAGTACAAGAGT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             ATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCGTGACCT
EV115686-             ATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCTTGACCT
ES981358+             ATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCTTGACCT
                      ____________________________________________________________
consensus             ATGATGAGACTCGATGTGGTTTACCCTCAACGTGATGAAGTCGATCTAGTCGCTTGACCT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             TTCAAGGTGATTCAGCATCAAGAAACAATTGATATGAAAAAACGAAAGCTCCATATACAT
EV115686-             TTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAAACGAAAGCTCCATATACAT
ES981358+             TTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAAACGAAAGCTCCATATACAT
                      ____________________________________________________________
consensus             TTCAATGTGATTCAGCATCAAGAAACAATTGATATGAATAAACGAAAGCTCCATATACAT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV005953+             ATTAGGAAACATAGTTAGATGTTTGGTTCTTCTGCTCCGTGCAGCT              
EV115686-             ATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTGCAGCTGTGATCTCACTTCG
ES981358+             ATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTGCAGCTGTGATCTCACTTCG
                      ____________________________________________________________
consensus             ATTAGGAAACATAGTTAGATGTTTGATTCTTCTGCTCCGTGCAGCTGTGATCTCACTTCG

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             CAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGT
ES981358+             CAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGT
                      ____________________________________________________________
consensus             CAGTTTCGCAGCTTCTCAATAGCTTTGAGGTTAATGCAATTTCAACATTCCCGTTGAGGT

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             TTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAAAGTTATAGGAGATGTTTTC
ES981358+             TTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAAAGTTATAGGAGATGTTTTC
                      ____________________________________________________________
consensus             TTTGTACCATTAAGGCAAAAATGTTATATAACTTCATAAAAAGTTATAGGAGATGTTTTC

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             TTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTTAGTCCAATAGTTTGTTCAA
ES981358+             TTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTTAGTCCAA            
                      ____________________________________________________________
consensus             TTCCTTTCATATAAACAAAACAAGATTGTGGAATCCATTTTAGTCCAATAGTTTGTTCAA

                          .    :    .    :    .    :    .    :    .    :    .    :
EV115686-             AGGTTTCATATACC
                      ____________________________________________________________
consensus             AGGTTTCATATACC

This seems to be correct. So why did the first run not align EV115773 ut gave it as a singlet? How can we correctly run CAP3 to give consistent results? All of this can be checked using the online CAP3 page at http://pbil.univ-lyon1.fr/cap3.php or by downloading CAP3 from http://seq.cs.iastate.edu/cap3.html