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COMMENTS ON OUTPUTSIMPLE QUERY FORM Multiple Alignment Results by GeneBee serviceYour E-mail address: Submitted Sequences: Search Parameters (default values): The results of the alignment are sent to you in the folowing order: 1. REFINED ALIGNMENT -- quality of alignment. This quality is measured: Results 1.REFINED ALIGNMENT
Power 4.27
Homology percent 5.3
Symbols used in the alighnment charts:
' ' - average weight of column pair exchanges is less than
weight matrix mean value
'.' - is less than mean value plus one SD
'+' - is less than mean value plus two SD
'*' - is greater than mean value plus two SD
.. ... ... ......... .... .. . .... . ..++.* ..
SQ1(1) ML----PTAVLLVLAVSVAARDNATCDGP-CGLRFrqkLESGMRVMYHNNRRYhtcgGIL
SQ2(1) IVggrrAQPQEFPFLASIQKQGRPFCAGAlVHPRF---VLTAARQQEQSRQTF----SIR
SQ3(1) ------------------------------------------------SRRTY-------
.. ... .+ ++.. .
SQ1( 56) LNSHWVLTAAHCFKNKKKvt
SQ2( 54) SISQNGYDPRQNLNDVL---
SQ3( 6) -------TLTDYLKSTFR--
2. PHYLOGENETIC TREES 2.1.BY CLUSTER ALGORITHM 0.999999 _________________________________________________________ SQ1 | |_________________________________________________ SQ2 |________________________________________________________ SQ3 The main feature of the topological algorithms is the fact that they optimize the tree structure (i.e. the way the tree nodes are connected) first without consideration of branch lengths, that are reconstituted once the topological structure have been established. _________________________________________________________ SQ3 | |__________________________ SQ2 |__________________ SQ1 3. DISTANCE MATRIX 1 2 3 SQ1 0.000 0.890 1.000 SQ2 0.890 0.000 1.000 SQ3 1.000 1.000 0.000 4. DRAFT ALIGNMENT
Power 2.11
Percent of homology 2.1
. ... .. .. ... . .......
SQ1( 1) mlptavllvlavsvaardnatcdgpCGLRFRQKLESGMRVMYHNNRRYHTCGGILLN---
SQ2( 1) -------------------------IVGGRRAQPQEFPFLASIQKQGRPFCAGALVHprf
SQ3( 1) ------------------------------------------------------------
++.... .+ ++.. .
SQ1( 58) --------------------SHWVLTAAHCFKNKKKvt
SQ2( 36) vltaarqqeqsrqtfsirsiSQNGYDPRQNLNDVL---
SQ3( 1) --------------------SRRTYTLTDYLKSTFR--
5. FIVE BEST LOCAL ALIGNMENTS (SUPERMOTIFS)
1ST LOCAL SUPERMOTIF, power 5.13
. ... . *.+.*++.+.+*++++ ...+..
SQ1 ( 41) myhnnrryhtCGGILLNSHWVLTAAHcfknkkkvt-
SQ2 ( 16) asiqkqgrpfCAGALVHPRFVLTAARqqeqsrqtfs
2ND LOCAL SUPERMOTIF, power 3.67
+*.+*.+... ...*.
SQ2 ( 36) vltaarqqeqSRQTFSIrsisqngydp
SQ3 ( 1) ----------SRRTYTLtdylkstfr-
3RD LOCAL SUPERMOTIF, power 3.59
.. .. +.. *+.*...+
SQ1 ( 21) tcdgpcglrfRQKLESGMrvmyhnnrry
SQ2 ( 53) rsisqngydpRQNLNDVL----------
4TH LOCAL SUPERMOTIF, power 3.24
.. .. ++.... .+ ++.. .
SQ1 ( 48) yhtcggillnSHWVLTAAHCFKNKkkvt
SQ2 ( 46) srqtfsirsiSQNGYDPRQNLNDVL---
SQ3 ( 1) ----------SRRTYTLTDYLKSTFr--
5TH LOCAL SUPERMOTIF, power 2.51
+ *... ..* ...
SQ2 ( 43) qeqsrqtfsiRSISQNGYdprqnlndvl
SQ3 ( 1) --------srRTYTLTDYlkstfr----
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