This is an example of a pima alignment displayed with GCG pretty.
Plurality: 8.00 Threshold: 1.00 AveWeight 1.00 AveMatch 0.54 AvMisMatch -0.40
PRETTY of: * September 1, 1997 15:14 ..
1 50
hiv1bz163b6 MGAraSvLsG gklDaWEkIR LRPgGKKKYs lKHlVWAsrE LERFainpgL
hiv2rod27 MGArnSvLrG kkaDeLErIR LRPgGKKKYr lKHiVWAank LDRFgLaesL
hivlbv217346 MGAraSvLsG gklDeWEkIR LRPgGKKKYr mKHlVWAsrE LERFaLnpgL
hivug26846 MGAraSvLrG gklDtWEkIk LRPgGKKcYm mKHlVWAsrE LgRFaLnsgL
hivvi557346 MGAraSvLsG gklDaWEkIR LRPgGKKKYr lKHlVWAsrE LERFaLnpdL
sivagm357 MGAatSaLnr rqlDkFEhIR LRPtGKKKYq iKHlIWAgkE MERFgLherL
sivagm67757 MGgghSaLsG rslDtFEkIR LRPnGKKKYq iKHlIWAgkE MERFgLhekL
sivmm251r127 MGArnSvLsG kkaDeLEkIR LRPgGKKKYm lKHvVWAanE LDRFgLaesL
sivstm127 MGArsSvLsG kkaDeLEkVR LRPgGKKKYm lKHvVWAanE LDRFgLaesL
Consensus MGA--S-L-G ---D-WE-IR LRP-GKKKY- -KH-VWA--E LERF-L---L
51 100
hiv1bz163b6 LEtsEGCqkI igqLqsslqT GsEeLrSLYN tvavlYfVHq rveVKdTkEA
hiv2rod27 LEskEGCqkI ltvLdPmvpT GsEnLkSLFN tvcviWCIHa eekVKdTegA
hivlbv217346 LEttEGCqqI lqqLqPslqT GtEeLkSLFN avavlWCIHq rigVKdTkEA
hivug26846 LEtsEGCkqI mkqLqPalqT GtDeLrSLYN tvatlYCVHk gieVrdTkEA
hivvi557346 LDtaEGClql ieqLqPalkT GtEeLqSLFN llatlYCVHq ridVKdTkEA
sivagm357 LEseEGCkkI ievLyPlepT GsEgLkSLFN lvcvlFCVHk dkeVKdTeEA
sivagm67757 LEtkEGCqkI ievLtPlepT GsEgLkaLFN lccviWCIHa eqkVKdTeEA
sivmm251r127 LEnkEGCqkI lsvLaPlvpT GsEnLkSLYN tvcviWCIHa eekVKhTeEA
sivstm127 LEskEGCqkI itvLePlvpT GsEnLkSLFN tvcviWCIHa eekVKhTeEA
Consensus LE--EGC--I ---L-P---T G-E-L-SLFN -----WCIH- ---VK-T-EA
101 150
hiv1bz163b6 ldkleeeqnk sqqktkqa** **aadkgvsq nypiv***** *******Qnl
hiv2rod27 kqivrrhlva etgtaekmps tsrptapsse kggnypv*** *******Qhv
hivlbv217346 leevekrqkn sqqkiqqa** dkgdnsqvsq nypiv***** *******Qna
hivug26846 ldkieeeqnk iqqkteta** ***dkgkvsq nypiv***** *******Qnl
hivvi557346 leklkeaqnk sqnrtqqatg dkgngnkisq nypiv***** *******Qna
sivagm357 vaivrqcchl vekernaern ttetssgqkk ndkgvtvppg gsqnfpaQqq
sivagm67757 vvtvkqhyhl vdknekaakk knettappgg esrnypv*** *******vnq
sivmm251r127 kqivqrhlvv etgtaetmpk tsrptapssg rggnypv*** *******Qqi
sivstm127 kqvvkrhlvv etgtankmpa tsrptappsg rggnypv*** *******Qqv
Consensus ---------- ---------- ---------- ---------- -------Q--
151 200
hiv1bz163b6 qgqmVHqsiS PRTLNAWVKv IEEKaFspEV IPmFsALSEG aTPqDlNtML
hiv2rod27 ggnytHiplS PRTLNAWVKl VEEKkFgaEV VPgFqALSEG cTPyDiNqML
hivlbv217346 qgqmVHqpiS PRTLNAWVKv VEEKaFspEV IPmFsALSEG aTPqDlNtML
hivug26846 qgqmVHqalS PRTLNAWVKv IEEKaFspEV IPmFtALSEG aTPqDlNtML
hivvi557346 qgqpVHqaiS PRTLNAWVKv VEEKaFspEV IPmFsALSEG aTPqDlNaML
sivagm357 gnawIHvplS PRTLNAWVKa VEEKkFgaEI VPmFqALSEG cTPyDiNqML
sivagm67757 nnawVHqplS PRTLNAWVKc VEEKrWgaEV VPmFqALSEG clsyDvNqML
sivmm251r127 ggnyVHlplS PRTLNAWVKl IEEKkFgaEV VPgFqALSEG cTPyDiNqML
sivstm127 ggnyVHlplS PRTLNAWVKl VEEKkFgaEV VPgFqALSEG cTPyDiNqLL
Consensus ----VH---S PRTLNAWVK- VEEK-F--EV VP-F-ALSEG -TP-D-N-ML
201 250
hiv1bz163b6 NtVGgHQaAM QmlkDtINEE AA*ewdrlhp vqagpippgq ireprgsdia
hiv2rod27 NcVGdHQaAM QiirEiINEE AA*ewdvqhp ipgplpagql reprgsdiag
hivlbv217346 NtVGgHQaAM QmlkDtINEE AA*ewdrihp qqagpippgq irdprgsdia
hivug26846 NtVGgHQaAM QmlkDtINEE AA*ewdrlhp vhagpvapgq mreprgsdia
hivvi557346 NiVGgHQaAM QmlkDtINEE AA*ewdrvhp vhagpippgq mreprgsdia
sivagm357 NvlGdHQgAL QivkEiINEE AAqwdiahpp pagplpagql rdprgsdiag
sivagm67757 NvIGdHQgAL QilkEvINEE AAewdrthrp pagplpagql rdptgsdiag
sivmm251r127 NcVGdHQaAM QiirDiINEE AA**dwdlqh pqpapqqgql repsgsdiag
sivstm127 NcVGeHQaAM QiikEiINEE AAdwdmqhpq ppgplpagql repsgsdiag
Consensus N-VG-HQ-AM Q---D-INEE AA-------- ---------- ----------
251 300
hiv1bz163b6 gTtstlqeqi qwmtsnppVp VGeIYkRWIi LGLnKiVrMY sPvsILDIrQ
hiv2rod27 tTstveeqiq wmfrpqnpVp VGnIYrRWIq iGLqKcVrMY nPtnILDIkQ
hivlbv217346 gTtstlqeqi rwmtsnppIp VGeIYkRWIi LGLnKiVrMY sPvsILDIrQ
hivug26846 gTtstlqeqi nwmtsnppIp VGeIYkRWIi LGLnKiVrMY sPvsILDIkQ
hivvi557346 gTtstlqeqi awmtsnppIp VGdIYkRWIi LGLnKiVrMY sPvsILDIrQ
sivagm357 tTstvqeqle wiytanprVd VGaIYrRWIi LGLqKcVkMY nPvsVLDIrQ
sivagm67757 tTssiqeqie wtfnanprId VGaqYrkWVi LGLqKvVqMY nPqkVLDIrQ
sivmm251r127 tTssvdeqiq wmyrqqnpIp VGnIYrRWIq LGLqKcVrMY nPtnILDVkQ
sivstm127 tTsspeeqiq wmyrqqnpIp VGnIYrRWIq LGLqKcVrMY nPvnILDVkQ
Consensus -T-------- --------I- VG-IY-RWI- LGL-K-V-MY -P--ILDI-Q
301 350
hiv1bz163b6 GPKEpFrdYV DRFFKtLRAE QatqeVKgWM TdTLLVQNAN PDCqtILkaL
hiv2rod27 GPKEpFqsYV DRFYKsLRAE QtdpaVKnWM TqTLLVQNAN PDCKlVLkgL
hivlbv217346 GPKEpFrdYV DRFFKtLRAE QatqdVKnWM TdTLLVQNAN PDCKtILkaL
hivug26846 GPKEpFrdYV DRFFKtLRAE QatqdVKnWM TdTLLVQNAN PDCKtILraL
hivvi557346 GPKEpFrdYV DRFFKaLRAE QatqeVKgWM TdTLLVQNAN PDCKtILraL
sivagm357 GPKEaFkdYV DRFYKaiRAE QasgeVKqWM TesLLIQNAN PDCKvILkgL
sivagm67757 GPKEpFqdYV DRFYKaLRAE QapqdVKnWM TqTLLIQNAN PDCKlILkgL
sivmm251r127 GPKEpFqsYV DRFYKsLRAE QtdaaVKnWM TqTLLIQNAN PDCKlVLkgL
sivstm127 GPKEtFqsYV DRFYKsLRAE QadpsVKnWM TrTLLIQNAN PDCKlVLkgL
Consensus GPKE-F--YV DRFYK-LRAE Q----VK-WM T-TLLVQNAN PDCK-IL--L
351 400
hiv1bz163b6 Gpgat***** ********** ********** ********** **********
hiv2rod27 GmnptlEEML tACQGVGGPg qKArlmaeal kevigpapip faaa***qqr
hivlbv217346 GpgatlEEMM tACQGVGGPs hKArvlaeam sqasgtatai mmqkgnfkgp
hivug26846 GpgaslEEMM tACQGVGGPg hKArvlaeam sqannin**i mmqrsnfkgp
hivvi557346 GqgasiEEMM tACQGVGGPg hKAkvlaeam sqvntnav*m mmqkgnfkgq
sivagm357 GmhptlEEML tACQGVGGPs yKAkvm*aem mqnmqsqnmm qqggqrgrpr
sivagm67757 GmnptlEEML iACQGVGGPq hKAkl***mv emmsngqnmv qvgpqkkgpr
sivmm251r127 GvnptlEEML tACQGVGGPg qKArlmaeal kealapvpip faaaqkrgpr
sivstm127 GmnptlEEML tACQGVGGPg qKArlmaeal kevfqpdplp faaa*qqqgr
Consensus G-----EEML -ACQGVGGP- -KA------- ---------- ----------
401 450
hiv1bz163b6 ********** ********** ********** ********** **********
hiv2rod27 kafkcWncgk eghsarqcra prrqgcwkcg kpghimtncp drqagflglg
hivlbv217346 rknikCfdcg keghlarncr aprkrgcwkc gkeghqmkdc terqanflgk
hivug26846 kriikCfncg keghlarncr aprkkgcwkc greghqmkdc terqanflgk
hivvi557346 rriikCfncg keghlarncr aprkkgcwkc gkeghqlkdc terqanflgk
sivagm357 ppvkcYncgk fghmqrqcpe prkmrclkcg kpghlakdcr gqvnflgygr
sivagm67757 gplkcFncgk fghmqrecka prqikcfkcg kighmakdck ngqanflgyg
sivmm251r127 kpikcWncgk eghsarqcra prrqgcwkcg kmdhvmakcp drqagflglg
sivstm127 rtvkcWncgk aghtakqckg prrqgcwkcg qqghqmakcp erqvgflgfg
Consensus ---------- ---------- ---------- ---------- ----------
451 500
hiv1bz163b6 ********** ********** ********** ********** **********
hiv2rod27 pwgk**kprn fpvaqvpqgl tPtAppvdpa vDllekymqq gkrqreqrer
hivlbv217346 iwpshkgrpg nflqnrpeps aPpAeslgfg eEiapspkqe pkelypltsl
hivug26846 iwppnkgrpg nflqsrpept aPpAeptapp aEsfrfegtt pppkqepkdr
hivvi557346 iwspnkgrpg nflqsrpept aPpAesfgfg eEmtpppkqe rkdaesplts
sivagm357 wmga****kp rnfpaatlgv ePtAppppsp yDpakkllqq yadkgkqlre
sivagm67757 hwggakprnf vqyrgdtvgl ePtAppmeta yDpakkllqq yaekgqrlre
sivmm251r127 pwgk**kprn fpmaqvhqgl tPtAppedpa vDllknymql gkqqresrek
sivstm127 pwgk**kphn fpmaqipqgl tPtAppedpa aDllrsymql gkkqresrkt
Consensus ---------- ---------- -P-A------ -D-------- ----------
501 538
hiv1bz163b6 ********** ********** ********** ********
hiv2rod27 pykevtedll hleqgetpyr epptedllhl nslfgkdq
hivlbv217346 ks******** ********** ********** ********
hivug26846 eplislks** ********** ********** ********
hivvi557346 lks******* ********** ********** ********
sivagm357 qrkkppavnp dwtegyslns lfgedq**** ********
sivagm67757 ereqtrkqke kevedvslss lfggdq**** ********
sivmm251r127 pykevtedll hlnslfggdq ********** ********
sivstm127 pykevtedll hlnslfgedq ********** ********
Consensus ---------- ---------- ---------- --------
Instructions on how to create this pretty format with pima output.