Look at the alignment of the first hit:
Q: 34 KIPGATCPNNNNNNNNNNNNNNNNNNNNNNNNNNNN 69 . K T PNNNNNNNNNNNNNNNNNNNNNNNNNNNN S: 48 KTSNITTPNNNNNNNNNNNNNNNNNNNNNNNNNNNN 83 |
That shows it all. The long line of N-s gives more points than the "normal" alignment for crambin that is found by BLAST approximately as hit number 5:
Q: 2 SCCPSIKVRSNYELCRLPGTPEDLCASFEGCIKIPGATCPNNNNN 46 . +CCPSI RSN+ +CRLPGTPE LCA++ GCI IPGATCP + N S: 2 TCCPSIVARSNFNVCRLPGTPEALCATYTGCIIIPGATCPGDYAN 46 |