Color Align Conservation

Sequence Manipulation Suite:

Color Align Conservation accepts a group of aligned sequences (in FASTA or GDE format) and colors the alignment. The program examines each residue and compares it to the other residues in the same column. Residues that are identical among the sequences are given a black background, and those that are similar among the sequences are given a gray background. The remaining residues receive a white background. You can specify the percentage of residues that must be identical and similar for the coloring to be applied. Use Color Align Conservation to enhance the output of sequence alignment programs.

Paste the aligned sequences in FASTA or GDE format into the text area below. Input limit is 20000 characters.

>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--

Please check the browser compatibility page before using this program.

Show residues per line.
Percentage of sequences that must agree for identity or similarity coloring to be added:
Used colored .

Enter the groups of similar amino acids separated by commas to be used for the similarity calculation. If you are coloring a DNA alignment, leave this text area empty.

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

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