Multiple Align Show

Multiple Align Show accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to your specifications. You can specify the number of residues per line, and the font size and font style. You can also set a consensus level, which specifies the fraction of residues that need to be identical or similar in a column of the alignment for highlighting to be added. Use Multiple Align Show to enhance the output of sequence alignment programs.

Paste the aligned sequences in FASTA or GDE format into the text area below. >CremaneiFEM-2 -------------------MSDSLNHPSSSTVHADDGFEPPTSPEDNNKK PSLEQIKQEREALFTDLFADRRRSARSVIEEAFQNELMSAEPVQPNVPN- -PHSIPIRFRHQPVAGPAHDVFGDAVHSIFQKIMSRGVNADYSHWMSYWI ALGIDKKT-QMNYHMKPFCKDTYATEGSLEAKQTFTDKIRSAVEEIIWKS AEYCDILSEKWTGIHVSADQLKGQRNKQEDRFVAYPNGQYMNRGQ-SDIS LLAVFDGHGGHECSQYAAAHFWEAWSDAQHHHSQDMKLDELLEKALETLD ERMTVRSVRESWKGGTTAVCCAVDLNTNQIAFAWLGDSPGYIMSNLEFRK FTTEHSPSDPEECRRVEEVGGQIFVIGGELRVNGVLNLTRALGDVPGRPM ISNKPDTLLKTIEPADYLVLLACDGISDVFNTSDLYNLVQAFVNEYDVED YHELARYICNQAVSAGSADNVTVVIGFLRPPEDVWRVMKTDSDDEESELE EEDDNE >CelegansFEM-2 -------------------------------------------------- --MEKVNEERDAVFEDHIGDRRRSVRSLLEEAFADEMEKTSYDVEVADTP -QPHIPIRFRHPPIAGPVHDVFGDAIHDIFQKMMKRGQAVDFCHWVSHLI ATEIDEKFSEVAFRDVQYNPDIYVTDSTTEAKKLFNDKIWPAIDKILQQN AETCPILSEKWSGIHVSGDQLKGQRHKQEDRFLAYPNGQYMDRGE-DPIS VLAVFDGHGGHECSQYAAGHLWETWLEVRKSRDPSDSLEDQLRKSLELLD ERMTVRSVKECWKGGSTAVCCAIDMDQKLMALAWLGDSPGYVMSNIEFRQ LTRGHSPSDEREARRVEEAGGQLFVIGGELRVNGVLNLTRALGDVPGRPM ISNEPETCQVPIESSDYLVLLACDGISDVFNERDLYQLVEAFANDYPVED YAELSRFICTKAIEAGSADNVSVVIGFLRPPQDVWKLMKHESDDEDSDVT DEE--- >CbriggsaeFEM-2 MSGPPPPKTNEKSSQPVTGRSQEPTRKGQLGPNYLRIIEEDEEYGHALLE PSEEQIKFEREALFEDLHLDRQRSARSFIEETFEEEMLGPQNGIPPTTES PQSYIPIRYRNPPAAAPVHDVFGDAVHAIFQKLMTRGPPVEYCHWMSYWI AKQIDKDS-PVKYHECRFTPDQYVTENTAEAKKTYMDNMWKAAEKNLWMY TYNSPLLRTKWTGIHVSAEQIKGQRHKQEDRFVAYPNSLYMDTSRSDHIA LLGVFDGHGGHECSQYAAGHMWETWIETRASHFEEP-LEKQLKTSLDLLD ERMTVRSTKECWKGGTTAVCCAIDMNKKELAFAWLGDSPGYIMDNLEVRK VTRDHSPSDPEEGRRVEEAGGQLFVIGGELRVNGVLNLTRALGDVPGRPM ISNQAETCQRDIEVGDYLVILACDGISDVFNTSDLYNLVQAYVNENPVEE YNDLAHYICHEAIAHGSTDNVTVVIGFLRPPQDLWRMMKIDEESDEEEDE VDDE--

• Show 100 90 80 70 60 50 40 30 residues per line.
• Font style: Arial Arial Black Arial Narrow Courier New Times New Roman
• Font size: 8 10 12 14 18 24 36
• Use colored backgrounds text to highlight residues.

Choose the colors you wish to use for highlighting. Identical amino acids have the highest priority for coloring, followed by similar amino acids.

• Color identical amino acids by amino acid 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 and similar amino acids by amino acid 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 identity or similarity coloring to be added: 10 20 30 40 50 60 70 80 90 100
• The default color (the color used if no identity or similarity coloring is added): 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
• The color of all gaps: 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

Enter the groups of similar amino acids separated by commas to be used for the similarity calculation.
ILV,FWY,KRH,DE,GAS,P,C,TNQM

Enter the colors to be used for the by amino acid color scheme if it is selected from any of the above lists. Each amino acid is described by two colors separated by a blank space. Each color pair is followed by a comma, except for the last pair. The first color in each pair is used for the text if colored text is used, or the background if colored backgrounds are used. The second color in each pair is used for the text when colored backgrounds are used. The colors are entered as hexadecimal color codes.
A=#999999 #000000, C=#FFFF00 #000000, D=#33CCFF #000000, E=#33CCFF #000000, F=#FF9900 #000000, G=#999999 #000000, H=#CC0000 #000000, I=#FF6666 #000000, K=#CC0000 #000000, L=#FF6666 #000000, M=#3366FF #000000, N=#3366FF #000000, P=#CC33CC #000000, Q=#3366FF #000000, R=#CC0000 #000000, S=#999999 #000000, T=#3366FF #000000, V=#FF6666 #000000, W=#FF9900 #000000, Y=#FF9900 #000000

Enter the starting positions of the sequences separated by commas (to alter residue numbering). An example entry is: 3,200,5,1. If no numbers are given, the default starting position of 0 is used for each sequence.