📄 showalign.txt
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10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSxHBB_HUMAN --------..Lt..E.S.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.HBB_HORSE --------..LS..E.a.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.HBA_HUMAN --------------..S.......K..-..kVG..A.......l......F..T......HBA_HORSE --------------..S.......K..-..kVGG.A.......l......F..T......MYG_PHYCA -------.......q.........e.d-....G...L..-L....P.....F..F..L..GLB5_PETMA ..........LS..E.t.i.S.W.......E..G..i........P..Q.FF..F..Lt.LGB2_LUPLU --------..Lt..q.a.V.S.W.e.N.............v..I.P..k..F......S.Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxHHBB_HUMAN .D.v.Gn.kVK.HGKKVL.A..D.l.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.nHBB_HORSE ...v.Gn.kVK.HGKKVL.s..e.V.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.nHBA_HUMAN .D...GS.QVK.HGKKV..AL.n.V.HvDDm....s.LSDLHA.KLR--VDP.NFKLL.HHBA_HORSE .D...GS.QVK.HGKKV..AL...V.HLDDL....s.LSDLHA.KLR--VDP.NFKLL.HMYG_PHYCA ...M..S..lK.HG..VL.AL...l......E.....La..HA.K.k--i.....e.i..GLB5_PETMA .D.l..S..Vr.H.erii.Av.D.V..mDD.E.....L.DL.....k--....d.q....LGB2_LUPLU ........Q........L.........v..v....A.L.nL.s..v...V...hF.vv..Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxxHBB_HUMAN .Lv.VLA.H...eFTP.V.Aa..K.vA.VA..L..KY.------HBB_HORSE .Lv.VLA.H...DFTPEl.AS..K.vA.VA..L..KY.------HBA_HUMAN .LL..LA.H...eFTP.V.ASl.K.LA.Vs..L..KY.------HBA_HORSE .LL..LA.H...DFTP.V.ASl.K.Ls.Vs..L..KY.------MYG_PHYCA .ii.VL......DF..d...aM.K.L......i..KY.......GLB5_PETMA ....i.......D...E...SM...L...A.-------------LGB2_LUPLU .iL..i.......ws.El.sa.......lA..i..e.....---Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx Output files for usage example 9 File: globins.showalign 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSxHBB_HUMAN --------VH..PE.K.A.T.L.G.V.-VD....E..GR-.LV.Y.WT.R..E..GD..THBB_HORSE --------VQ..GE.K.A.L.L.D.V.-EE....E..GR-.LV.Y.WT.R..D..GD..NHBA_HUMAN --------------VL.PADKTNV.AA-WG...AH.GEYGAEA.ERMFLS.PT.KTYFPHHBA_HORSE --------------VL.AADKTNV.AA-WS....H.GEYGAEA.ERMFLG.PT.KTYFPHMYG_PHYCA -------VLSEGEW.LVLHVWAKV.A.-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KTGLB5_PETMA PIVDTGSVAP..AA.K.K.R.A.APVYSTY.TS.VD.LVKFFTST.AA.E..PK.KG..TLGB2_LUPLU --------GA..ES.A.L.K.S.E.F.ANIPKHTHRFFIL.LE.A.AA.DL.SFLKGT.EConsensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxHHBB_HUMAN P.A.M..P...A......G.FS.G.A......GTF.T.....CD..H--...E.....G.HBB_HORSE PGA.M..P...A......H.FG.G.H......GTF.A.....CD..H--...E.....G.HBA_HUMAN F.LSH..A...G.....AD..T.A.A.....PNAL.A......H...--...V.....S.HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGAL.N......H...--...V.....S.MYG_PHYCA EAE.KA.ED..K..VT..T..GAI.KKKGHH.AELKP..QS..T.H.--.PIKYL.F.SEGLB5_PETMA A.Q.KK.AD..W.A....N..N.A.AS...T.KMSMK.R..SGKHA.--SFQV.P.YFKVLGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQ.TG.VVTD.T.K..G.VH.SKG.ADA..P..KEConsensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxxHBB_HUMAN V..C...H.FGK....P.Q..YQ.V..G..NA.AH..H------HBB_HORSE V..V...R.FGK......Q..YQ.V..G..NA.AH..H------HBA_HUMAN C..VT..A.LPA....A.H...D.F..S..TV.TS..R------HBA_HORSE C..ST..V.LPN....A.H...D.F..S..TV.TS..R------MYG_PHYCA A..H..HSRHPG..GA.AQG..N.A.ELFRKD.AA..KELGYQGGLB5_PETMA LAAV.ADTVAAG.AGF.KLM..ICI.LRS.Y-------------LGB2_LUPLU A..KT.KEVVGAK..E..N..WTIAYDE..IV.KK.MNDAA---Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx Output files for usage example 10 File: globins.showalign 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLSTHBB_HORSE --------.Q.sG...a..L...D...-Ee.........-............d......NHBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PTtKTYFPHHBA_HORSE --------------VL..ADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PTtKTYFPHMYG_PHYCA -------VlSEGEWqLVLHVWAKVeAd-.AGH.QdI.I.-.FKSh.E.LEK.dR.KH.K.GLB5_PETMA PIVDTGSVAP.sAA..tKiRsA.AP.YSTY.TS.VDiLVKFFTST.AA.E..PK.KG.t.LGB2_LUPLU --------GA..ESqAaL.KsS.EeF.ANIPKHTHRFFILv.EiA.AAkDL.SFLKGT.EHBB_HUMAN --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLSTConsensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGNHBB_HORSE .G................Hs.Ge.vH..........A..........--...........HBA_HUMAN F.LSH.sAq..G.....AD.LtnAv..v.dmPNALsA..d..AH..R--...V..k..ShHBA_HORSE F.LSH.sAq........GD.LtLAvG...d.P.ALsN..d..AH..R--...V..k..ShMYG_PHYCA EAEmKAsEDl.K..VT..T.LGAI.KKKGhHeAELKP.aqS.AT.HK--iPIkYLEFiSEGLB5_PETMA A.QlKKsAD.rW.AeriiN.Vn.Av.Sm.dTeKMSMK.Rd.SGKHAK--SFQVdPqYFKVLGB2_LUPLU VPQNNPELqAH.GKVFK.VYEaAIQLQvTGvVV.D...KN.GSVHvSKG.ADAh.PvvKEHBB_HUMAN PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGNConsensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------HBB_HORSE ...V...R....d...El..s.................------HBA_HUMAN C.lVT..A.LPA....A.H.sLD.Fl.S.sTV.TS..R------HBA_HORSE C.lST..V.LPNd...A.H.sLD.FlsS.sTV.TS..R------MYG_PHYCA AiiH..HSRHPGd.GADA.G.MN.AlELFRKDi.A..KELGYQGGLB5_PETMA lAAViADTVAAGdAGFEKLMsMICilLRS.Y-------------LGB2_LUPLU AilKTiKEVV.AkwsEElNs.wTIAYDEl.IViKKeMnDAA---HBB_HUMAN VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx Output files for usage example 11 File: globins.showalign 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlstHBB_HORSE --------.Q.SG...a..l...d...-ee.........-............d......nHBA_HUMAN --------------Vl.padktnv.aa-wgk..ah.geygaealermfls.pttktyfphHBA_HORSE --------------Vl..adktnv.aa-wsk...h.geygaealermflg.pttktyfphMYG_PHYCA -------vLSEGEWQlvlhvwakvead-.agh.qdi.i.-.fksh.e.lek.dr.kh.k.GLB5_PETMA pivdtgsvAP.SAA..tkirsa.ap.ysty.ts.vdilvkfftst.aa.e..pk.kg.t.LGB2_LUPLU --------GA..ESQaal.kss.eef.anipkhthrffilv.eia.aakdl.sflkgt.eHBB_HUMAN --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlst 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgnHBB_HORSE .g................hs.ge.vh..........a..........--...........HBA_HUMAN f.lsh.saq..g.....ad.ltnav..v.dmpnalsa..d..ah..r--...v..k..shHBA_HORSE f.lsh.saq........gd.ltlavg...d.p.alsn..d..ah..r--...v..k..shMYG_PHYCA eaemkasedl.k..vt..t.lgai.kkkghheaelkp.aqs.at.hk--ipikylefiseGLB5_PETMA a.qlkksad.rw.aeriin.vn.av.sm.dtekmsmk.rd.sgkhak--sfqvdpqyfkvLGB2_LUPLU vpqnnpelqah.gkvfk.vyeaaiqlqvtgvvv.d...kn.gsvhvskg.adah.pvvkeHBB_HUMAN pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgn 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----|HBB_HUMAN vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------HBB_HORSE ...v...r....d...el..s.................------HBA_HUMAN c.lvt..a.lpa....a.h.sld.fl.s.stv.ts..r------HBA_HORSE c.lst..v.lpnd...a.h.sld.flss.stv.ts..r------MYG_PHYCA aiih..hsrhpgd.gada.g.mn.alelfrkdi.a..kelgyqgGLB5_PETMA laaviadtvaagdagfeklmsmicillrs.y-------------LGB2_LUPLU ailktikevv.akwseelns.wtiaydel.ivikkemndaa---HBB_HUMAN vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------ Output files for usage example 12 File: globins.showalign 10 20 30 40 50 60 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSxGLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tTHBA_HORSE --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPHHBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPHHBB_HORSE --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..NHBB_HUMAN --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..TLGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.EMYG_PHYCA -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KTConsensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx 70 80 90 100 110 120 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxHGLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKVHBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.HBA_HUMAN F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.HBB_HORSE PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..GnHBB_HUMAN P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..GnLGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKEMYG_PHYCA EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSEConsensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH 130 140 150 160 170 180 ----:----|----:----|----:----|----:----|----:----|----:----|Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxxGLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------HBA_HORSE C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------HBA_HUMAN C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------HBB_HORSE V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------HBB_HUMAN V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---MYG_PHYCA AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQGConsensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxxData files showalign reads in scoring matrices to determine the consesnus sequence and to determine which matches are similar or not. EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run:% embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:% embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata". The directories are searched in the following order: * . (your current directory) * .embossdata (under your current directory) * ~/ (your home directory) * ~/.embossdataNotes None.References None.Warnings None.Diagnostic Error Messages None.Exit status It always exits with status 0.Known bugs None.⌨️ 快捷键说明
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