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Multiple Alignment Results by GeneBee service

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Submitted Sequences:
>SQ1
MLPTAVLLVL AVSVAARDNA TCDGPCGLRF RQKLESGMRV
MYHNNRRYHT CGGILLNSHW VLTAAHCFKN KKKVT
>SQ2
IVGGRRAQPQ EFPFLASIQK QGRPFCAGAL VHPRFVLTAA
RQQEQSRQTF SIRSISQNGY DPRQNLNDVL
>SQ3
SRRTYTLTDY LKSTFR

The results of the alignment are sent to you in the folowing order:

1. REFINED ALIGNMENT - quality of alignment. This quality is measured:
a) in POWER of an alignment, and b) in PERCENT OF HOMOLOGY.
The notion of POWER is fundamental for this program.
POWER relates to the possibility of receiving a sum of mismatch weights along an alignment for random sequences of same length. As a rule, alignment is considered to be significant, if its POWER exceeds 7 SD (SD - Standard Deviation units). PERCENT OF HOMOLOGY is a measure of difference between a given alignment and an alignment of identical sequences.

2. PHYLOGENETIC TREES: built by topological and cluster algorithms.

3. Then the DISTANCE MATRIX is presented. These distances are calculated by counting residual change weights in aligned sequences.

4. You can also see the first - DRAFT - results of the alignment of your sequences (POWER and PERCENT OF HOMOLOGY are provided). The construction of the REFINED ALIGNMENT is based on this DRAFT one.

5. Finally, you can also see the detailed representation of the 5 BEST SUPERMOTIFS of your alignment.

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
In cluster algorithm the notion of distance between groups of sequences is used for the setting of the branching order. This distance is defined as the arithmetic mean of pairwise distances between elements of the two groups.

0.999999
_________________________________________________________ SQ1
|      |_________________________________________________ SQ2
|________________________________________________________ SQ3

2.2. BY TOPOLOGICAL ALGORITHM

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----