Locus 419

Sequence ID 2R_DroMel_CAF1
Location 2,458,579 – 2,458,718
Length 139
Max. P 0.983778
window815 window816

overview

Window 5

Location 2,458,579 – 2,458,678
Length 99
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -21.78
Consensus MFE -18.10
Energy contribution -18.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.83
SVM decision value 1.92
SVM RNA-class probability 0.982447
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2458579 99 + 20766785
AUUUUUAAUAAAACUAUUUUCUAAAUAUAAA---------------------AAAGAAAAUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGA
...............(((((((.........---------------------..)))))))..((....((((((.......))))))....((((((.....)))))).))........ ( -20.10)
>DroSec_CAF1 20663 111 + 1
AUUUUCCAUAAAACUAAUUUCAUAAUAUAAAAUGAAUAAGA---------AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGA
..............((((((((.................((---------((.......))))......((((((.......))))))....))))))))(((((.....)))))..... ( -21.60)
>DroSim_CAF1 21025 111 + 1
AUUUUCCAUAAAACUAACUUCAUAAUAUAAAAUGAAUAGGA---------AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGA
.((((((.((....))..(((((........)))))..)))---------)))....(((((((.....((((((.......))))))....))))))).(((((.....)))))..... ( -23.10)
>DroYak_CAF1 19866 111 + 1
AUUUUUAAUAAAAUAAU------A-AAGAA-UAAGCUAAUAAGCUAGAAAAAAAAU-CGUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGA
.................------.-.(((.-..((((....)))).((((......-..))))((....((((((.......))))))....((((((.....)))))).)))))..... ( -22.30)
>consensus
AUUUUCAAUAAAACUAAUUUCAUAAUAUAAAAUGAAUAAGA_________AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGA
...............................................................((....((((((.......))))))....((((((.....)))))).))........ (-18.10 = -18.10 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 6

Location 2,458,610 – 2,458,718
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.82
Mean single sequence MFE -33.66
Consensus MFE -31.50
Energy contribution -31.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.94
SVM decision value 1.95
SVM RNA-class probability 0.983778
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2458610 108 + 20766785
------------AAAGAAAAUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUGUGAAGAUCGCCGAUAAAAGC
------------.........((((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))....(((.....))).))....... ( -32.80)
>DroSec_CAF1 20703 111 + 1
A---------AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUGUGAAGAUCGCCGAUAAAAGC
.---------...........((((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))....(((.....))).))....... ( -32.80)
>DroSim_CAF1 21065 111 + 1
A---------AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUGUCAAGAUCGCCGAUAAAAGC
.---------.............((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))..(((((.........))))).... ( -32.70)
>DroEre_CAF1 20421 100 + 1
A---------AAAAAU-UGUCUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUG----------CGAUAAAAGC
.---------....((-(((...((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))....)----------))))...... ( -32.90)
>DroYak_CAF1 19898 119 + 1
AAGCUAGAAAAAAAAU-CGUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUGAGAUGAUCGCCGAUAAAAGC
..(((.........((-((((((((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))....))))))))..........))) ( -37.11)
>consensus
A_________AAAAAUAAAUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCACUUGUGAAGAUCGCCGAUAAAAGC
.......................((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))......................... (-31.50 = -31.50 +   0.00) 

alignment

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secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:38:08 2006