Example for alignment in MSF format
MSF of: 1atf.hssp from: 1 to: 37
1atf.msf MSF: 37 Type: P 1-Sep-95 23:57:2 Check: 4754 ..
Name: 1atf Len: 37 Check: 9032 Weight: 1.00
Name: anpa_pseam Len: 37 Check: 9032 Weight: 1.00
Name: anpy_pseam Len: 37 Check: 7396 Weight: 1.00
Name: anp3_pseam Len: 37 Check: 7162 Weight: 1.00
Name: anp4_pseam Len: 37 Check: 7320 Weight: 1.00
Name: anpx_pseam Len: 37 Check: 7591 Weight: 1.00
Name: anp_limfe Len: 37 Check: 7149 Weight: 1.00
Name: anp3_myosc Len: 37 Check: 6165 Weight: 1.00
Name: cyg4_human Len: 37 Check: 6763 Weight: 1.00
Name: sox3_human Len: 37 Check: 7741 Weight: 1.00
Name: anp5_myoae Len: 37 Check: 6918 Weight: 1.00
Name: e74b_drome Len: 37 Check: 8042 Weight: 1.00
Name: e74a_drome Len: 37 Check: 8042 Weight: 1.00
Name: brn1_mouse Len: 37 Check: 7423 Weight: 1.00
Name: vglh_prvn3 Len: 37 Check: 9736 Weight: 1.00
Name: vglh_prvka Len: 37 Check: 9736 Weight: 1.00
Name: els_human Len: 37 Check: 6485 Weight: 1.00
Name: pum_drome Len: 37 Check: 6403 Weight: 1.00
Name: hmcu_drome Len: 37 Check: 9094 Weight: 1.00
Name: myb3_horvu Len: 37 Check: 3005 Weight: 1.00
Name: vglh_prvri Len: 37 Check: 9598 Weight: 1.00
Name: dcor_leido Len: 37 Check: 805 Weight: 1.00
Name: anp8_myosc Len: 37 Check: 7939 Weight: 1.00
Name: salm_drome Len: 37 Check: 8751 Weight: 1.00
Name: yr21_trsvr Len: 37 Check: 9744 Weight: 1.00
Name: olec_brana Len: 37 Check: 7470 Weight: 1.00
Name: icp4_hsv11 Len: 37 Check: 7757 Weight: 1.00
Name: hmen_drovi Len: 37 Check: 9511 Weight: 1.00
Name: els_chick Len: 37 Check: 8551 Weight: 1.00
Name: hm1d_droan Len: 37 Check: 7224 Weight: 1.00
Name: hme1_mouse Len: 37 Check: 7877 Weight: 1.00
Name: h1_paran Len: 37 Check: 9757 Weight: 1.00
Name: sox4_human Len: 37 Check: 9029 Weight: 1.00
Name: evx1_mouse Len: 37 Check: 8592 Weight: 1.00
Name: sfa1_strfr Len: 37 Check: 7786 Weight: 1.00
Name: anp8_myoae Len: 37 Check: 7340 Weight: 1.00
Name: ul25_hsv11 Len: 37 Check: 8003 Weight: 1.00
Name: otx1_mouse Len: 37 Check: 423 Weight: 1.00
Name: hme1_human Len: 37 Check: 6890 Weight: 1.00
Name: salm_drovi Len: 37 Check: 8527 Weight: 1.00
Name: hunb_drovi Len: 37 Check: 8821 Weight: 1.00
Name: al60_poapr Len: 37 Check: 7048 Weight: 1.00
Name: reb1_yeast Len: 37 Check: 666 Weight: 1.00
Name: tegu_hsveb Len: 37 Check: 9389 Weight: 1.00
Name: tola_ecoli Len: 37 Check: 8296 Weight: 1.00
Name: vsi2_trybb Len: 37 Check: 2993 Weight: 1.00
Name: tri_drome Len: 37 Check: 8874 Weight: 1.00
Name: syv_neucr Len: 37 Check: 9059 Weight: 1.00
Name: ch38_drome Len: 37 Check: 185 Weight: 1.00
Name: els_bovin Len: 37 Check: 8190 Weight: 1.00
Name: mlev_mouse Len: 37 Check: 8058 Weight: 1.00
Name: sr14_human Len: 37 Check: 7514 Weight: 1.00
Name: anp3_pagbo Len: 37 Check: 7234 Weight: 1.00
Name: ul14_hcmva Len: 37 Check: 8486 Weight: 1.00
Name: dgdr_burce Len: 37 Check: 1353 Weight: 1.00
Name: icp4_hsvek Len: 37 Check: 472 Weight: 1.00
Name: cina_drome Len: 37 Check: 8074 Weight: 1.00
Name: icp4_hsveb Len: 37 Check: 472 Weight: 1.00
Name: csp_plama Len: 37 Check: 8083 Weight: 1.00
Name: mer3_strli Len: 37 Check: 9978 Weight: 1.00
Name: rla_metva Len: 37 Check: 8691 Weight: 1.00
Name: csp_plabr Len: 37 Check: 8083 Weight: 1.00
Name: fsh_drome Len: 37 Check: 354 Weight: 1.00
Name: ul25_hsveb Len: 37 Check: 9935 Weight: 1.00
Name: eya_drome Len: 37 Check: 5839 Weight: 1.00
Name: bccp_pseae Len: 37 Check: 8437 Weight: 1.00
Name: icp0_hsvbk Len: 37 Check: 9894 Weight: 1.00
Name: lkta_actac Len: 37 Check: 2547 Weight: 1.00
Name: macs_chick Len: 37 Check: 8928 Weight: 1.00
Name: atpx_rhoru Len: 37 Check: 89 Weight: 1.00
Name: elav_drome Len: 37 Check: 1343 Weight: 1.00
Name: dsxm_drome Len: 37 Check: 999 Weight: 1.00
Name: dsxf_drome Len: 37 Check: 999 Weight: 1.00
Name: muc1_xenla Len: 37 Check: 1818 Weight: 1.00
Name: kdtk_drome Len: 37 Check: 9950 Weight: 1.00
Name: sos_drome Len: 37 Check: 935 Weight: 1.00
Name: h82_neigo Len: 37 Check: 8048 Weight: 1.00
Name: pgkh_wheat Len: 37 Check: 1462 Weight: 1.00
Name: rla0_mouse Len: 37 Check: 8930 Weight: 1.00
Name: sryc_drome Len: 37 Check: 1699 Weight: 1.00
Name: notc_drome Len: 37 Check: 9115 Weight: 1.00
Name: id4_mouse Len: 37 Check: 5085 Weight: 1.00
Name: guna_celfi Len: 37 Check: 686 Weight: 1.00
Name: sapa_strco Len: 37 Check: 1013 Weight: 1.00
Name: pgkc_crifa Len: 37 Check: 9505 Weight: 1.00
Name: cu38_locmi Len: 37 Check: 465 Weight: 1.00
Name: rla3_leiin Len: 37 Check: 8742 Weight: 1.00
Name: acsb_acexy Len: 37 Check: 9646 Weight: 1.00
Name: hlya_serma Len: 37 Check: 106 Weight: 1.00
Name: ykel_drome Len: 37 Check: 9869 Weight: 1.00
Name: h8_neime Len: 37 Check: 9000 Weight: 1.00
Name: algp_pseae Len: 37 Check: 9519 Weight: 1.00
Name: h12_arath Len: 37 Check: 1562 Weight: 1.00
Name: i3ms_brana Len: 37 Check: 9297 Weight: 1.00
Name: vco7_ade02 Len: 37 Check: 9329 Weight: 1.00
Name: tali_mouse Len: 37 Check: 764 Weight: 1.00
Name: anp_notco Len: 37 Check: 9497 Weight: 1.00
Name: vp26_ebv Len: 37 Check: 464 Weight: 1.00
Name: h1_echcr Len: 37 Check: 15 Weight: 1.00
Name: 5hta_drome Len: 37 Check: 9310 Weight: 1.00
Name: odp2_bacst Len: 37 Check: 85 Weight: 1.00
Name: h81_neigo Len: 37 Check: 9096 Weight: 1.00
Name: ic18_prvif Len: 37 Check: 8084 Weight: 1.00
Name: hles_drome Len: 37 Check: 9305 Weight: 1.00
Name: fusa_burce Len: 37 Check: 9707 Weight: 1.00
Name: r167_yeast Len: 37 Check: 7821 Weight: 1.00
Name: cmf_drome Len: 37 Check: 5327 Weight: 1.00
Name: imp2_drome Len: 37 Check: 8306 Weight: 1.00
//
1 37
1atf DTASDAAAAA ALTAANAKAA AELTAANAAA AAAATAR
anpa_pseam DTASDAAAAA ALTAANAKAA AELTAANAAA AAAATAR
anpy_pseam DTASDAAAAA AATAATAAAA AalTAANAAA AAAATA.
anp3_pseam DTASDAAAAA ALTAABAAAA AKLTABBAAA AAAATA.
anp4_pseam STASDAAAAA AATAATAAAA AAATAATAAA AAAATA.
anpx_pseam ATAATAAAAA AATAATAAKA AALTAANAAA AAAATA.
anp_limfe DTASDAAAAA AATAAAAAKA AADTAAAAAK AAADTA.
anp3_myosc ..MNAPARAA AKTAADALAA AKKTAADAAA AAAAA..
cyg4_human .EPSPAAAAA A.......AA PAPTPAASAA AAAATAG
sox3_human ..MNVAAAAA AAsaPSATAA AAatAAAAAA AAAAMS.
anp5_myoae ..MDAPAIAA AKTAADALAA AKKTAADAAA AAAKP..
e74b_drome HTHSTIAAAA AAAAasAVAA AAMLSASAAA AATAAA.
e74a_drome HTHSTIAAAA AAAAasAVAA AAMLSASAAA AATAAA.
brn1_mouse .TALPHAAAA AAAAAAAAVE ASsaAAAAAA AAAAAAH
vglh_prvn3 .TAERAAAAA ELtlANLGAA ARLALAPAGA PGAAAAT
vglh_prvka .TAERAAAAA ELtlANLGAA ARLALAPAGA PGAAAAT
els_human ..PQAAAAAA AKAAAKFGAG AAgpAAAAAA AAAAKA.
pum_drome GTAAVAAAAA AAAAANSRQV AATAAAAAAV AAAA...
hmcu_drome .EAAAAAAAA ALqpTEQPAA TVATGAAAAA AAAATP.
myb3_horvu ASADTATAAA ALPDAeaGFA EELGAANAAA .......
vglh_prvri .TAERAAAAA ELTRAALSPA AalAPAGAPG AAAATDE
dcor_leido .PASPAALAA AQraPINKSA IEtdAASAAD AAATTAT
anp8_myosc QKAARLAAAA ALAAKTAADA AAKAAAKAAA IAAAAAS
salm_drome QQAAVAAAAA AQhaAEAQQK AAAAAAAAAA AAAAQRQ
yr21_trsvr .AARRGASCA ALTA..ARAA AFLALAMAAY LAALRAR
olec_brana ..AGGAAAPA AEPAPAAEAA PAAEAAPAAA PAAAPA.
icp4_hsv11 .LPSSAAAAA ADlpLLAAAA SAPDAADALA AAAASA.
hmen_drovi .SVSAAAAAA SIfaAAATPS aeFSRQQQAA AAAATA.
els_chick ..GPAAAAAA AKAAAKAGAY GAgtPAGAAA AAAKAAK
hm1d_droan NVAQYAAAMQ QHYAAAAAAA AARNSAAAAA AAAAAA.
hme1_mouse ATAVGAGASK AGNPAAAAAA AAAAAAAAVA AAAAAAS
h1_paran AKAKKAKAAA AKKARKAKAA AKRKAALAKK KAAAAKR
sox4_human ..KAAAAAAA SFAAEQAGAA ALlsASSAAS ASAALA.
evx1_mouse ..ASAAAAAA AGplACHSGP ANGLAPRAAA AAAASD.
sfa1_strfr .TVTTEAAAA KVRAAGarGA AELDAAMAAL EARAK..
anp8_myoae .DGETPAQKA ARLAAAAAAL AAKTAADAAA KAAAIA.
ul25_hsv11 .QAQRTAAAA ALENAAMQAA EllEALETAA AAAEEA.
otx1_mouse ASANPAAAAA AGLGGNPVAA ASsvAAGAAT AAASYP.
hme1_human DGSQPAAAGA GASKAGNPAA AAAAAAAAVA AAAAAA.
salm_drovi QQXAVAAAAA AQheVQQKAA QEVQQKAAAA AAAAAA.
hunb_drovi ...SNASAAA AQQQQQppAA AAGTAAGAAG TAAPAA.
al60_poapr .TAMSQAQKA AKPAAAatAT AAVGAATGAA TAAA...
reb1_yeast DTASAAAAAA AAIQEQQQLL QQkdDAIAAA AAAASSS
tegu_hsveb APAKSAAAPA AAPAKSAAAP AAAPAKSAAA PAAAPAK
tola_ecoli EAEAAKAAAE AQKKAEAAAA ALKKKAEAAE AAAAEAR
vsi2_trybb QKSKGAAALA AytAANVKAA SglTAASLLR QRAANVS
tri_drome AAAAKPAAPA AAPAANGKAA PAANGKAAPA AAAAPAG
syv_neucr PAAAPAAAPA AQDAPGakAK ADKAAKFAAK QAAAKAK
ch38_drome ADAASAAAAA AGGaaNAGAG ALESGADAAG VAQAGQS
els_bovin GVGPQAAAAA AKAAAKLGAG GavGAPDAAA AAAAAAK
mlev_mouse EPKKDDAKAA APKAAPAPAA AP...AAAPA AAPEPER
sr14_human TKKTKAAAAA AAAAPAAAAT AATTAATTAA TAAQ...
anp3_pagbo ...AATAATA ATAATAATAA TAATAATAAT AATA...
ul14_hcmva .....AAGSV ALttEEESEA AEETAAGEAS AVAAAA.
dgdr_burce ..VSAAAAAA VFEPASASAG DRRNRMRADA AAARTAR
icp4_hsvek .PAQAAAAAA SQQQPEAPaa ALGPRRKAAA AAAAPGT
cina_drome EAAEEEAIRE AEEAAAAKAA KLEERANAQA QAAADA.
icp4_hsveb .PAQAAAAAA SQQQPEAPaa ALGPRRKAAA AAAAPGT
csp_plama NAAGNAAGNA AGNAadAGNA AGNAAGNAAG NAAGNA.
mer3_strli ALALAAAATA ALtgTDTKAN TPATRAGSGN AAAAKA.
rla_metva NDARVKALVA ALeeAIAKAA IAPVAAAAPV AAAAAP.
csp_plabr NAAGNAAGNA AGNAadAGNA AGNAAGNAAG NAAGNA.
fsh_drome .TSAAVAQAA AIAAATAAAA VTLGAAAAAA LASSASN
ul25_hsveb .AARHRAAAA AIdvADALAA LEDAARAAES ADAATPQ
eya_drome NSSAVAAAAA AVyaATAARQ AKMEPGAAAA AAA....
bccp_pseae ...AQAPAFA APVAAPAPAA AAPAAAAAES APAAPK.
icp0_hsvbk ARPADPAPAA ALGPALAGAQ IGTPAAAAAV TAAAAAP
lkta_actac DTATKAAAAA ELtgNIGKAI TQYLIAQRAA AGLSTTG
macs_chick ESEGGAAAAA EGGKEEAAAA APeaAAEEAS AAAAGSR
atpx_rhoru TEAAIAAYET ALAEARARAH DEIRAVTEAA AKAAEAR
elav_drome QLMQSAAAAA AVAATNAAAA PVQNAAAVAA AAQLQQQ
dsxm_drome HQQAAAAAAA APSAPASHLG GSSTAAsaAA AAASVAQ
dsxf_drome HQQAAAAAAA APSAPASHLG GSSTAAsaAA AAASVAQ
muc1_xenla PTAAVAATGE DATTAAATAA AETTAAAGEA PTTTTAP
kdtk_drome EAQMHAAAAA AVAAAGseHE MEMSLAAAAA AAAMHQR
sos_drome STSSVAAAAA ASSTATSIAT ASasIMDAPT AAAANAG
h82_neigo TEAPAAEAPA AEAPAAEAAA AEAPAAEAPA AEAPAAE
pgkh_wheat STAAPPAALV ARRAASASVA APlpARSLAF AAGADPR
rla0_mouse EKVKAFLADP SAFAAAAPAA AATTAAPAAA AAPAKAE
sryc_drome AQKAAAAAAA AAAASSAVNP NELSASsaAP APAKQAR
notc_drome ......KASS KKTSAASKKA ANlsAVQAAA AAAAAV.
id4_mouse HSLGGSAAAA A.....AAAA ARCKAAEAAA DEPAL..
guna_celfi ..MSTRRTAA ALLAAAAVAV GGLTALTTTA AQAAPG.
sapa_strco ...SMQAVGA TLTAVGAIGA GLLVTAPAAG AATAGAT
pgkc_crifa .TNKDAKAPA A..AAAAGGD CPCGSGCAAV PAAATAT
cu38_locmi .AAPAIAAAP ALGYARYAAA APVAVAHAAV PAAASV.
rla3_leiin .IAEGAAKMS AMPAASSGAA AGVTASAAGD AAPAAA.
acsb_acexy .PPLPAAASQ AATPAAASAD QPATTAPAAD AASASA.
hlya_serma .....AAALA IILAASAGaa AEIVAANGAN GPGVST.
ykel_drome .APAGGAAAA AAPAAPAQAP QPnaAAIANA NAPANAE
h8_neime .SQEPAAPAA EATPAAEAPA SEAPAAEAAP ADAAEAP
algp_pseae KPAAKAAAKP AVKTVAANAA AKPAAKPAAK PAAKTA.
h12_arath .AKPKGKVAA AVAPAKAKAA AKGtaAKVVA KAKVTAK
i3ms_brana AAAPRAAPAA APAAAPAAAP AAAPAPKPAA APAPKP.
vco7_ade02 NRARRTGRRA AMRAARRLAA GIVtrAAAAA AAAISA.
tali_mouse .MATNAAAQN AIkhAAKQAA ASATQTIAAA QHAASAP
anp_notco TAALNFAATA ATPATAATPA LIFAAAAATA ATPATA.
vp26_ebv PVQQAQAAAS AGTGALASSA PslRAATSGA TAAASA.
h1_echcr .KATREKARA RAKAKKAKAA ARRKAAAAKR KAAAAKR
5hta_drome TTAGSPLATA ALAAAAASAS VAAAAARITA KAAHWA.
odp2_bacst .LKEDIDAFL AGGAKPAPAA AEEKAAPAAA KPATTEG
h81_neigo .SQEPAAPAA EATPAGEAPA SEAPAAEAAP ADAAEAP
ic18_prvif DEARRGRALA ALAAVDAAEA REAEAASTAA AGAEAG.
hles_drome AAAAAAAAAA RLSPQSAYHA FAYNGVGAAV AAAAAA.
fusa_burce ESAAGAAAPA AASGAKPVAA AARPAQVAAA GAAGVP.
r167_yeast ..AAQPAAQY GTAAAVGTAA AVGTAAGAAA GAVP...
cmf_drome SHAANSAAAA AAQASIAAAA AGQWDQLAAL AA.....
imp2_drome ........QP QPAAAAAPAA AQVQADDAAA AAPATP.