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

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

MAFFT-L-INS-i Result

CLUSTAL format alignment by MAFFT (v7.023b)


query           M--------------------------------IF-PGNLGYASSLQQS----AQASRSY
gi|365176835|em M--------------------------------IF-PGNLGYASSLQQS----AQASRSY
gi|220898177|gb M--------------------------------IF-PGNWGYSSSISPS----TQASRSL
LATCH|ENSLACP00 M--------------------------------IF-PGNWGYSSSISPS----TQASRSL
gi|255742469|gb MDSTALQYKLTLETSSDKTGTLQDGIRPMEMIPVL-STNFGFSSSMIPPSFKATASGRCH
gi|262263016|gb MDSTSLQYKLTLETSSDKTGILQDEARPMEIVPVL-STNFGISSAMCPTPLKTTSSGRCH
gi|301128894|em MDATSLQYKLTLETSSDETGIRQDEVRPTEMVPVLISPNFGMSSAMAPSPLKPLSSGKCH
gi|187936707|db M-----------------------------------------------------------
                *                                                           

query           PFNPDELGFTVIHPTYEMD----TLEAHRYSQLQ---NGESQFPPRVPHPTCSRAECPGV
gi|365176835|em PFNPDELGFTVIHPTYEMD----TLEAHRYSQLQ---NGESQFPPRVPHPTCSRAECPGV
gi|220898177|gb P-HTDELGFAAVHTSYEME----SLEGHRFTQLQ---NGETQFFPRASYSTCSRVEYPGV
LATCH|ENSLACP00 P-HTDELGFAAVHTSYEME----SLEGHRFTQLQ---NGETQFFPRASYSTCSRVEYPGV
gi|255742469|gb GLYPEDIATCGSYGGAEREIVALSPEAGRIAPNQFQSDSHISSFVSHRHNPCTRGEYPTG
gi|262263016|gb GLYSEGISTCESHGSADREIVAMSFEAGQFPTNQLQSDSHISSFTSYRHNPCTRGEYPTN
gi|301128894|em GFYSEDISTCGSLGSAARETVAMSPAVGQYPTNQFGNDSHISSFTSYRHNLCTRSEYPTN
gi|187936707|db ------------------------------------------------------------
                                                                            

query           SRVLPK-SMELPRFPHLT-QDQTDSVDPDFRLVFPH-SAYCGQQFTAGSLNPGTNNSPHS
gi|365176835|em SRVLPK-SMELPRFPHLT-QDQTDSVDPDFRLVFPH-SAYCGQQFTAGSLNPGTNNSPHS
gi|220898177|gb NRTLAM-PLELSRPANLTGQVQTDNVDQGLRMAFSH-SAYCGPHFTPGSLNPGMSNSPHS
LATCH|ENSLACP00 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
                                                 . * . *     : .::*    . .  

query           LGL-SFHSPWPAHQVM---QSRQRKKRVPYTKYQITELEKAFEVNRFLTPESRQHIAVKL
gi|365176835|em LGL-SFHSPWPAHQVM---QSRQRKKRVPYTKYQITELEKAFEVNRFLTPESRQHIAVKL
gi|220898177|gb LAL-SFHSSWPPQQVL---QIRQRKKRVPYSKHQITELERAFEENRFLTPEIRQNISVKL
LATCH|ENSLACP00 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
                *.* .: . *.          * ****:**:* **:*** *:: ******* *  *: :*

query           GLTERQVKIWFQNQRQKEKKLLLRQPAGISSS-VTSPIGPPEQ-------
gi|365176835|em GLTERQVKIWFQNQRQKEKKLLLRQPAGISSS-VTSPIGPPEQ-------
gi|220898177|gb GLTERQVKIWFQNQRQKEKKLLLRQPSGTSGPLVASTIGAGQT-------
LATCH|ENSLACP00 GLTERQVKIWFQNQRQKEKKLLLRQPSGTSGPLVASTIGAGQT-------
gi|255742469|gb GLTERQVKIWFQNQRQKEKKLLRVQQP--------VNPGGSGL-------
gi|262263016|gb GLTERQVKIWFQNQRQKEKKLLRVQQS--------INPSCPGL-------
gi|301128894|em GLTERQVKIWFQNQRQKEKKLLRVQQS--------VKAGYSGL-------
gi|187936707|db SLTERQVKIWFQNQRQKEKKLMRRQQSGAAANASNINNGSGGTTGSATLP
                .********************:  * .           .           

Method

% mafft --reorder --auto input 

References:
Katoh et al. (2002) describes FFT-NS-1, FFT-NS-2 and FFT-NS-i.
Katoh et al. (2005) describes G-INS-i, L-INS-i, E-INS-i and Mafft-homologs.
Katoh and Toh (2008) describes Q-INS-i.
Katoh and Frith (2012) describes *-fragment.
Q-INS-i uses the McCaskill routine from the Vienna RNA package (Hofacker et al. 2003) and MXSCARNA (Tabei et al. 2008).

MAFFT home:
http://mafft.cbrc.jp/alignment/software/