Locus 2708

Sequence ID 3L_DroMel_CAF1
Location 7,546,666 – 7,546,808
Length 142
Max. P 0.699782
window4244 window4245

overview

Window 4

Location 7,546,666 – 7,546,768
Length 102
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 86.32
Mean single sequence MFE -33.35
Consensus MFE -24.18
Energy contribution -27.18
Covariance contribution 3.00
Combinations/Pair 1.00
Mean z-score -2.65
Structure conservation index 0.73
SVM decision value -0.00
SVM RNA-class probability 0.532840
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7546666 102 - 23771897
GUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCUUUUGCUGC-AAAAGCAAAAGCAAAAGG
......((.....((.(((((.(..(((((((((((....)))))))...))))...).))))).))......(((((((((..-...)))))))))....)) ( -36.60)
>DroSec_CAF1 16108 102 - 1
GUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCUUUUGCAGC-AAAAGCAAAAGCAAAAGG
......((.....((.(((((.(..(((((((((((....)))))))...))))...).))))).))......((((((((...-....))))))))....)) ( -34.30)
>DroSim_CAF1 16035 102 - 1
GUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCUUUUGCAGC-AAAAGCAAAAGCAAAAGG
......((.....((.(((((.(..(((((((((((....)))))))...))))...).))))).))......((((((((...-....))))))))....)) ( -34.30)
>DroEre_CAF1 16239 96 - 1
GUUAAGCCGAUUGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCUUUUGCUGC-------AAAAGCAAAAGG
.....((..(((((..(((((.(..(((((((((((....)))))))...))))...).))))).)))))))..((((((((..-------...)))))))). ( -34.90)
>DroYak_CAF1 16178 102 - 1
GUUAAGCCGAUUGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCAUUUGCUGC-AUAAGCAAAAGCAAAAGG
......((.(((((..(((((.(..(((((((((((....)))))))...))))...).))))).)))))...((.((((((..-...)))))).))....)) ( -35.00)
>DroAna_CAF1 8204 84 - 1
GUUAACCCG------------GUCAUUUGUCAGCAGGAAGCUGCUGGAAUUGUGGAAAGCCACUGCCGAGGAAA-------GGCAAAAAGCAAAAUGCAAAGG
(((..((((------------((......(((((((....)))))))....((((....)))).)))).))...-------))).....((.....))..... ( -25.00)
>consensus
GUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGCCAAUGCCGCUUUUGCUGC_AAAAGCAAAAGCAAAAGG
......((.....((.(((((.((.....(((((((....))))))).......))...))))).))......((((((((........))))))))....)) (-24.18 = -27.18 +   3.00)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 7,546,702 – 7,546,808
Length 106
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -32.85
Consensus MFE -22.47
Energy contribution -22.97
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.68
SVM decision value 0.35
SVM RNA-class probability 0.699782
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7546702 106 - 23771897
AGAACUUUUCUUUGCCACAACAAGAAGCAAACACCAGUGGGUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
....((((((((.......(((((..((..((.((.((.((.....)).)).))...))..))..)))))((((((....)))))).....))))))))....... ( -28.90)
>DroSec_CAF1 16144 106 - 1
AGAACUUUCCUUGGCCACAGCAAGAAGCAAACACCAGUGGGUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
....((((((((((((((.((.....)).....((.((.((.....)).)).))...))))........(((((((....)))))))..))))))))))....... ( -37.30)
>DroSim_CAF1 16071 106 - 1
AGAACUUUCCUUGGCCACAGCAAGAAGCAAACACCAGUGGGUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
....((((((((((((((.((.....)).....((.((.((.....)).)).))...))))........(((((((....)))))))..))))))))))....... ( -37.30)
>DroEre_CAF1 16269 89 - 1
---------------GGCA--AAGAACCAAACACCAGUGGGUUAAGCCGAUUGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
---------------(((.--..((.(((....(((((.((.....)).)))))....))).)).....(((((((....)))))))...........)))..... ( -32.90)
>DroYak_CAF1 16214 98 - 1
--------CUGUCGCGACAACAAGAACCAAACACCAGUGGGUUAAGCCGAUUGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
--------..((.(((((((...((.(((....(((((.((.....)).)))))....))).))..)))))(((((....))))).............)).))... ( -31.30)
>DroAna_CAF1 8234 94 - 1
AGAGCUCUGCGAGUUAUUGGCAAGAACCAAUUGUCAGUGGGUUAACCCG------------GUCAUUUGUCAGCAGGAAGCUGCUGGAAUUGUGGAAAGCCACUGC
..(((((...)))))((((((((.......))))))))(((....))).------------........(((((((....)))))))....((((....))))... ( -29.40)
>consensus
AGAACUUUCCUUGGCCACAGCAAGAACCAAACACCAGUGGGUUAAGCCGAUGGGGAGGUGGGUCAUUUGUCAGCAGGAAGCUGCUGGAAUCGAGGAAAGCCACUGC
..................................((((((.((..(((........)))...((.....(((((((....))))))).......)))).)))))). (-22.47 = -22.97 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:39:56 2006