to GCG, PHYLIP, MSF, NEXUS, uppercase/lowercase, etc. with Readseq

computes the residue-wise confidence scores and extracts well-aligned residues. Beta

Given alignment

CLUSTAL format alignment by MAFFT (v7.023b)


gi|365176835|em M--------------------------------IF-PGNLGYASSLQQS----AQASRSY
gi|220898177|gb M--------------------------------IF-PGNWGYSSSISPS----TQASRSL
gi|255742469|gb MDSTALQYKLTLETSSDKTGTLQDGIRPMEMIPVL-STNFGFSSSMIPPSFKATASGRCH
gi|262263016|gb MDSTSLQYKLTLETSSDKTGILQDEARPMEIVPVL-STNFGISSAMCPTPLKTTSSGRCH
gi|301128894|em MDATSLQYKLTLETSSDETGIRQDEVRPTEMVPVLISPNFGMSSAMAPSPLKPLSSGKCH
gi|187936707|db M-----------------------------------------------------------
                *                                                           

gi|365176835|em PFNPDELGFTVIHPTYEMD----TLEAHRYSQLQ---NGESQFPPRVPHPTCSRAECPGV
gi|220898177|gb P-HTDELGFAAVHTSYEME----SLEGHRFTQLQ---NGETQFFPRASYSTCSRVEYPGV
gi|255742469|gb GLYPEDIATCGSYGGAEREIVALSPEAGRIAPNQFQSDSHISSFVSHRHNPCTRGEYPTG
gi|262263016|gb GLYSEGISTCESHGSADREIVAMSFEAGQFPTNQLQSDSHISSFTSYRHNPCTRGEYPTN
gi|301128894|em GFYSEDISTCGSLGSAARETVAMSPAVGQYPTNQFGNDSHISSFTSYRHNLCTRSEYPTN
gi|187936707|db ------------------------------------------------------------
                                                                            

gi|365176835|em SRVLPK-SMELPRFPHLT-QDQTDSVDPDFRLVFPH-SAYCGQQFTAGSLNPGTNNSPHS
gi|220898177|gb NRTLAM-PLELSRPANLTGQVQTDNVDQGLRMAFSH-SAYCGPHFTPGSLNPGMSNSPHS
gi|255742469|gb TQIYQHWPLEYPRAAPV--QNQTDHNSLGTS-AFSH-SQYYGAPISGGAFNTAMPSVSRA
gi|262263016|gb SSFYQHWPLEYPRAAPV--QNQTDSNNLGMP-AFSH-PQYCGAPFSGGALNTTMPGVPRH
gi|301128894|em CPIYQHCPLEYPRAVPA--QTQTDPSNQRMP-AFSH-SQYCEAPFTGAALNTAMAGVTRH
gi|187936707|db -------------------------GPYGHHHHHHHAAPYYSPPYSSGALNHGLANMSSA
                                                 . * . *     : .::*    . .  

gi|365176835|em LGL-SFHSPWPAHQVM---QSRQRKKRVPYTKYQITELEKAFEVNRFLTPESRQHIAVKL
gi|220898177|gb LAL-SFHSSWPPQQVL---QIRQRKKRVPYSKHQITELERAFEENRFLTPEIRQNISVKL
gi|255742469|gb LAL-GFASQWSTSQNQ---VNRQRKKRIPYSKLQITELEKAFENNRFLTPEIRLNISLKL
gi|262263016|gb LAL-GFTSQWSTSQNS---IHRQRKKRVPYSKQQIAELEMAYENNRFLTPEVRLNISFKL
gi|301128894|em LAL-GFASQWSTSQNP---IHRQRKKRIPYSKQQITELEMAFENNRFLTPEVRLNISFKL
gi|187936707|db LALGGIAGHWSQAAQGTSCASRPRKKRVPYSKQQISELERAFDENRFLTPELRLSISHRL
                *.* .: . *.          * ****:**:* **:*** *:: ******* *  *: :*

gi|365176835|em GLTERQVKIWFQNQRQKEKKLLLRQPAGISSS-VTSPIGPPEQ-------KKKK
gi|220898177|gb GLTERQVKIWFQNQRQKEKKLLLRQPSGTSGPLVASTIGAGQT-------KKKK
gi|255742469|gb GLTERQVKIWFQNQRQKEKKLLRVQQP--------VNPGGSGL-------KKKK
gi|262263016|gb GLTERQVKIWFQNQRQKEKKLLRVQQS--------INPSCPGL-------KKKK
gi|301128894|em GLTERQVKIWFQNQRQKEKKLLRVQQS--------VKAGYSGL-------KKKK
gi|187936707|db SLTERQVKIWFQNQRQKEKKLMRRQQSGAAANASNINNGSGGTTGSATLPKKKK
                .********************:  * .           .           ****