Failure to parse well formed clustal file

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WebLogo will not parse the following, well formed clustal file. 

'Error: Number of characters in each logo line is not consistent, starting at: 
AGO1___SCHPO'

The problem seems to be the last block. If you add gap characters to the last 
block so that all 
lines are the same length, then the file will parse. 


AGO1___SCHPO     ----IPKSNPLGN----------VPTLILGGDVYHPGVGATG-----------V---S-I
O02095_CAEEL     -----IGSEAFNK----------PNRLIVGFVTSQRVGGNPD-----------Y--PI-S
O16386_CAEEL     -----LRSGVFSN----------SKRLIIGFETSQR-GGLGD-----------A--PI-A
O16720_CAEEL     --LPNVRPR-IFN----------EPVIFLGCDITHPAAGDTR-----------K--PS-I
O48771_ARATH     GIEYSYNIPLINK----------IPTLILGMDVSHGPPGRAD-----------V--PS-V
O62275_CAEEL     --------------FVDAKKQL-DSHLIIGVGISAPPAGTKYAMEN---KGVLN--PN-V
O67434_AQUAE     -------LKEIEG----------KVDAFVGIDISRITRDGKT-----------------V
O76922_DROME     -------QVVIPL----------HGLMTVGFDVCHSPKNKNK-----------S-----
Y
PINH___ARATH     VDAISCRIPLVSD----------IPTIIFGADVTHPENGEES-----------S--PS-I
PIWI___ARCFU     --------------ILNVDPEK-GSDIIIGTGATRIDNVNLF-----------------C
PIWI___DROME     -------MIELPL----------SGLMTIGFDIAKSTRDRKR-----------A-----Y
PIWL1__HUMAN     -------RVDIPL----------KLVMIVGIDCYHDMTAGRR-----------S-----I
Q17567_CAEEL     -------KVNIPL----------KSTMIVGYDLYHDSTLKGK-----------T-----V
Q19645_CAEEL     -ADIPRDLACWNE----------VSTFVIGMDVAHPDRNAAR-------EG--N--PS-
T
Q21495_CAEEL     -----VNSETWND----------SGLLLIGLSTAPYLNSYSS-----------E--NVTT
Q21691_CAEEL     -VPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGARTRFDIQKVMFDG--D--PT-
V
Q23415_CAEEL     --------------VSDAKKSMTDEQLIIGVGVSAPPAGTKYMMDN---KGHLN--PQ-
I
Q9ZVD5_ARATH     SVERTPAFTVISK----------VPTIILGMDVSHGSPGQSD-----------V--PS-I
TAG76__CAEEL     IVADKITNKYLVD----------QPTMVVGIDVTHPTQAEMR-----------MNMPS-
V
Y1321__METJA     --------------ILDSKT---PYDYIMGLDTGLGIFGNHR-----------------V
YQ53___CAEEL     -IPNAVRGKAVCSNNETLRKKLLEHVQFIGFEISHGASRTLFDRSRSQMDG--E--PS-V


AGO1___SCHPO     ASIVASVD-LNGCKYTA-VSRSQPR------------HQIPK----SNPLGNVPTLILGG
O02095_CAEEL     VGFAANML-KHHQKFAG-GYVYVHR------------DRIGS-----EAFNKPNRLIVGF
O16386_CAEEL     IGFAANMM-SHSQQFAG-GYMFVKK------------SALRS-----GVFSNSKRLIIGF
O16720_CAEEL     AAVVGSMD-AHPSRYAA-TVRVQQH------------RQLPN---VRPRIFNEPVIFLGC
O48771_ARATH     AAVVGSKCWPLISRYRA-AVRTQSP------------RLGIEYSYNIPLINKIPTLILGM
O62275_CAEEL     IGYAYNA--QHNQEFSG-DFVLNSA------------SQFVD----AKKQL-DSHLIIGV
O67434_AQUAE     NAVAFTKIFNSKGELVR-YYLTSYP----AF------GELKE-------IEGKVDAFVGI
O76922_DROME     GAFVATMDQKESFRYFS-TVNEHIK------------GQQVV-------
IPLHGLMTVGF
PINH___ARATH     AAVVASQDWPEVTKYAG-LVCAQAH------------RQVDAISCRIPLVSDIPTIIFGA
PIWI___ARCFU     FAMVFK---KDGTMLWN-EISPIVT------------SSILN-----VDPEKGSDIIIGT
PIWI___DROME     GALIASMDLQQNSTYFS-TVTE-CS------------AFMIE-------LPLSGLMTIGF
PIWL1__HUMAN     AGFVASIN-EGMTRWFS-RCIFQDR------------GQRVD-------IPLKLVMIVGI
Q17567_CAEEL     GACVSTTS-NDFTQFYS-QTRPHEN------------PTKVN-------IPLKSTMIVGY
Q19645_CAEEL     VGLSCNSA-ENPYSFIG-DFLYTDP-------RR---ADIPR---DLACWNEVSTFVIGM
Q21495_CAEEL     IGFVSNTM-DHPQKFAG-GYKYVKS------------GSVNS-----ETWNDSGLLLIGL
Q21691_CAEEL     VGVAYSL--KHSAQLGGFSYFQESRLVPESVGHRVVCNNSAE----MRAKLYAKTQFIGF
Q23415_CAEEL     IGFASNA--VANHEFVG-DFVLAPS------------GQVSD----AKKSMTDEQLIIGV
Q9ZVD5_ARATH     AAVVSSREWPLISKYRA-SVRTQPS------------KASVERTPAFTVISKVPTIILGM
TAG76__CAEEL     AAIVANVD-LLPQSYGA-NVKVQKK------------CRIVADKITNKYLVDQPTMVVGI
Y1321__METJA     GGCTVVY--DSEGKIRR-IQPIETP-AP---------GEILD-------SKTPYDYIMGL
YQ53___CAEEL     VGVSYSL--TNSTQLGGFTYLQTQK-IPNAVRGKAVCSNNET----LRKKLLEHVQFIGF


AGO1___SCHPO     PVYYAHLVSNLARYQDV
O02095_CAEEL     PLYIADRYSQRGAMVLA
O16386_CAEEL     PLHIAGTYSERGSQMLA
O16720_CAEEL     PAYYAHLVAFRARYHLV
O48771_ARATH     PVRYAHLAAAQVAQFTK
O62275_CAEEL     PLYVANEYAKRGRNLWN
O67434_AQUAE     TVHYSDKITKLMLRGIE
O76922_DROME     VCHYAHKLAFLVAESIN
PINH___ARATH     PAYYAHLAAFRARFYLE
PIWI___ARCFU     TVNYPKLVAGIIANVNR
PIWI___DROME     VCQYAKKLATLVGTNLH
PIWL1__HUMAN     PCQYAHKLAFLVGQSIH
Q17567_CAEEL     PCQYAHKLAFLTAQSLH
Q19645_CAEEL     PVYVAHELAKRGTGLYK
Q21495_CAEEL     PLYLTAEMAERGTKNLA
Q21691_CAEEL     VSYAAQNLAKRGHNNYK
Q23415_CAEEL     PLYVANEYAKRGRDLWS
Q9ZVD5_ARATH     PICYAHLAAAQLGTFMK
TAG76__CAEEL     PVYYADLVATRARCHVK
Y1321__METJA     PIHYADKFVKALGKNWK
YQ53___CAEEL     VLYAAENLAKRGRNNYK

Original issue reported on code.google.com by [e-mail] on 4 Mar 2010 at 5:17

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Original comment by [e-mail] on 31 Mar 2010 at 10:22

• Added labels: Milestone-Release3.1

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Actually, the real problem may be that this clustal file doesn't have the 
customary (but not universal) clustal header line.

Original comment by [e-mail] on 14 Feb 2011 at 8:20

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Fixed in revision 84

Original comment by [e-mail] on 14 Feb 2011 at 10:04

• Changed state: Fixed

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This situation is still happening

Original comment by [e-mail] on 25 Feb 2011 at 6:30