将排队对比的序列文件(以FASTA或GDE格式)拷贝到以下区域。如果包括已知三维结构蛋白序列，识别与类似性计算也将包括此序列。
>CbrigsFEM-2 MSGPPPPKTNEKSSQPVTG-RSQEPTRKGQLGPNYLRIIEEDEEYGHALL EPSEEQIKFEREALFEDLHLDRQRSARSFIEETFEEEMLGPQN-GIPPTT ESPQSYIPIRYRNPPAAAPVHDVFGDAVHAIFQKLMTRGPPVEYCHWMSY WIAKQID-KDSPVKYHECRFTPDQYVTENTAEAKKTYMDNMWKAAEKNLW MYTYNSPLLRTKWTGIHVSAEQIKGQRHKQEDRFVA-YPNSLYMDTSRSD HIALLGVFDGHGGHECSQYAAGHMWETWIETRASHFEE------PLEKQL KTSLDLLDERMTVRSTKE--CWKGGTTAVCCAIDMNKKELAFAWLGDSPG YIMDNLEVRKVTRDHSPSDPEEGRRVEEAGGQLFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNQAETCQRDIEVG---DYLVILACDGISD VFNTSDLYNLVQAYVNENPVEEYNDLAHYICHEAIAHGSTDNVTVV-IGF LRPPQDLWRMMKIDEESDEEEDEVDDE----------------------- ------------------------------------------- >CremFEM-2 ----MSDSLNHPSSSTVHADDGFEPPTSP----------EDNNK------ KPSLEQIKQEREALFTDLFADRRRSARSVIEEAFQNELMSAE--PVQPNV PNPHS-IPIRFRHQPVAGPAHDVFGDAVHSIFQKIMSRGVNADYSHWMSY WIALGID-KKTQMNYHMKPFCKDTYATEGSLEAKQTFTDKIRSAVEEIIW KSAEYCDILSEKWTGIHVSADQLKGQRNKQEDRFVA-YPNGQYMNRGQSD -ISLLAVFDGHGGHECSQYAAAHFWEAWSDAQHHHSQDM-----KLDELL EKALETLDERMTVRSVRE--SWKGGTTAVCCAVDLNTNQIAFAWLGDSPG YIMSNLEFRKFTTEHSPSDPEECRRVEEVGGQIFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNKPDTLLKTIEPA---DYLVLLACDGISD VFNTSDLYNLVQAFVNEYDVEDYHELARYICNQAVSAGSADNVTVV-IGF LRPPEDVWRVMK--TDSDDEESELEEEDDNE------------------- ------------------------------------------- >CeleFEM-2 -------------------------------------------------- ---MEKVNEERDAVFEDHIGDRRRSVRSLLEEAFADEMEKTSYDVEVADT PQPH--IPIRFRHPPIAGPVHDVFGDAIHDIFQKMMKRGQAVDFCHWVSH LIATEIDEKFSEVAFRDVQYNPDIYVTDSTTEAKKLFNDKIWPAIDKILQ QNAETCPILSEKWSGIHVSGDQLKGQRHKQEDRFLA-YPNGQYMDRGEDP -ISVLAVFDGHGGHECSQYAAGHLWETWLEVRKSRDPSD-----SLEDQL RKSLELLDERMTVRSVKE--CWKGGSTAVCCAIDMDQKLMALAWLGDSPG YVMSNIEFRQLTRGHSPSDEREARRVEEAGGQLFVIGGELRVNGVLNLTR ALGDV---------PGRPMISNEPETCQVPIESS---DYLVLLACDGISD VFNERDLYQLVEAFANDYPVEDYAELSRFICTKAIEAGSADNVSVV-IGF LRPPQDVWKLMK--HESDDEDSDVTDEE---------------------- -------------------------------------------

将对比的已知三维结构序列拷贝到以下区域（注意包括序列名称）生成的脚本文件仅能用于描述此序列的三维分子文件。
>humanPP2Calpha -------------------------------------------------- -------------------------------------------------- -------------------------------------------------- --------------------------------------------MGAFLD KPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLES---- -WSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGI RTGFLEIDEHMRVMSEKKHGADRSGSTAV--GVLISPQHTYFINCGDSRG LLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMI----QRVNGSLAVSR ALGDFDYKCVHGKGPTEQLVS--PEPEVHDIERSEEDDQFIILACDGIWD VMGNEELCDFVRSRLE--VTDDLEKVCNEVVDTCLYKGSRDNMSVILICF PNAPKVSPEAVK--KEAELDKYLECRVEEIIKKQGEGVPDLVHVMRTLAS ENIPSLPPGGELASKRNVIEAVYNRLNPYKNDDTDSTSTDDMW

使用以下两个选项以改变多序列对比图的外观。

• 每行显示 100 90 80 70 60 50 40 30 个残基
• 使用 加粗 常规 字母

选择你希望使用的颜色。缺口(已知三维结构序列与其它序列缺口对比的氨基酸）具有最高颜色优先级别，其后是相同氨基酸，再后是类似氨基酸。

• 缺口颜色 white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green ,相同氨基酸颜色 white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green , 类似氨基酸颜色 white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green
• Percentage of sequences that must agree for gap, identity, or similarity coloring to be added: 10 20 30 40 50 60 70 80 90 100
• 缺省颜色(用于非缺口、非相同、非类似氨基酸): white very light gray light gray medium gray dark gray very dark gray black lightest red very light red light red medium red dark red very dark red darkest red lightest yellow very light yellow light yellow medium yellow dark yellow very dark yellow darkest yellow lighest blue very light blue light blue medium blue dark blue very dark blue darkest blue lighest green very light green light green medium green dark green very dark green darkest green

输入所使用的类似性氨基酸组，以逗号分隔。
ILV,FWY,KRH,DE,GAS,P,C,TNQM