Color Align Properties

Format Conversion

-Combine FASTA
-EMBL to FASTA
-EMBL Feature Extractor
-EMBL Trans Extractor
-Filter DNA
-Filter Protein
-GenBank to FASTA
-GenBank Feature Extractor
-GenBank Trans Extractor
-One to Three
-Range Extractor DNA
-Range Extractor Protein
-Reverse Complement

-Split Codons

-Split FASTA
-Three to One

Sequence Analysis

Sequence Figures

-Color Align Conservation
-Color Align Properties
-Group DNA
-Group Protein
-Primer Map
-Restriction Map
-Translation Map

Random Sequences

-Mutate DNA
-Mutate Protein
-Random Coding DNA
-Random DNA Sequence
-Random DNA Regions
-Random Protein Sequence
-Random Protein Regions
-Sample DNA
-Sample Protein
-Shuffle DNA
-Shuffle Protein

Miscellaneous

-IUPAC codes
-Genetic codes
-Browser compatibility
-Mirror this site
-Use this site off-line
-About this site
-Acknowledgments
-Reference

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Sequence Manipulation Suite:

Color Align Properties

Color Align Properties 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 or similar among the sequences are given a colored background. The color is chosen according to the biochemical properties of the residue. You can specify the percentage of residues that must be identical and similar for the coloring to be applied. Use Color Align Properties to highlight protein regions with conserved biochemical properties.

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

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