Locus 3549

Sequence ID 2L_DroMel_CAF1
Location 10,344,029 – 10,344,146
Length 117
Max. P 0.876761
window5608 window5609

overview

Window 8

Location 10,344,029 – 10,344,122
Length 93
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.40
Mean single sequence MFE -20.27
Consensus MFE -14.61
Energy contribution -14.50
Covariance contribution -0.11
Combinations/Pair 1.33
Mean z-score -1.14
Structure conservation index 0.72
SVM decision value 0.26
SVM RNA-class probability 0.655864
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10344029 93 + 22407834
GUUAGCCUUUAGUUA--------------------AGUGGUGGUAAUUAAUCAUUCAACUUAUGAGGAUUAUUUCUUAAAGGCCU-CUGGCUCGGAAAUAGUCUGAACCUUAUU
....((((((((((.--------------------((((((........)))))).))))...(((((....)))))))))))..-..((.(((((.....))))).))..... ( -22.00)
>DroVir_CAF1 2110 113 + 1
GUUUCUCUUUAAAAAAAAAAUGUUAAUUUAGUUUUUGUGAAGCGAAUUGACUAUUCAACUUAUGAUUACUAUUUCAUAAAGGCUU-CUGGCUGGGAAAUAUUAUGAACGGUUUU
(((((((..((((((..((((....))))..)))))).(((((((((.....))))...((((((........))))))..))))-).....)))))))............... ( -20.50)
>DroSec_CAF1 679 93 + 1
GUUAGCCUGUAGAUA--------------------AGUGGUGGUAAUUAAUUAUUCAACUUAUGAGGAUUAUUUCUUAAAGGCCU-CUGGCUCGGAAAUAGUCUGAACUUUAUU
(((.........(((--------------------(((.(((((.....)))))...))))))..(((((((((((....((((.-..)))).))))))))))).)))...... ( -18.80)
>DroSim_CAF1 626 93 + 1
GUUAGCCUGUAGAUA--------------------AGUGGUGGUAAUUAAUUAUUCAACUUAUGAAGAUUAUUUCUUAAAGGCCU-CUGGCUCGGAAAUGGUCUGAACUUUGUU
(((.........(((--------------------(((.(((((.....)))))...))))))..(((((((((((....((((.-..)))).))))))))))).)))...... ( -18.40)
>DroEre_CAF1 629 90 + 1
----GCCUUUAGUUA--------------------GGUGGUGCAAAUUAAUUAUUCAACCUAUGAGGAUUAUUUCAUAAAGGCCUUCUGGCUCGGAAAUAGUCUGAAAUUUAUU
----((((......)--------------------)))(((...(((.....)))..))).....((((((((((.....((((....))))..)))))))))).......... ( -20.30)
>DroYak_CAF1 625 92 + 1
GUUAGCCUUUAGUUA--------------------AGUGAUACAAAUUAAUUAUUCAACUUAUGAGGACUAUUUCUUAAAGGCCU--UGGCUCGGAAAUAGUCUGAACAUUAUU
(((...(((.((((.--------------------((((((........)))))).))))...)))((((((((((....(((..--..))).))))))))))..)))...... ( -21.60)
>consensus
GUUAGCCUUUAGAUA____________________AGUGGUGCUAAUUAAUUAUUCAACUUAUGAGGAUUAUUUCUUAAAGGCCU_CUGGCUCGGAAAUAGUCUGAACUUUAUU
.................................................................(((((((((((....((((....)))).))))))))))).......... (-14.61 = -14.50 +  -0.11)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 10,344,044 – 10,344,146
Length 102
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.27
Mean single sequence MFE -24.70
Consensus MFE -15.83
Energy contribution -15.34
Covariance contribution -0.49
Combinations/Pair 1.55
Mean z-score -1.57
Structure conservation index 0.64
SVM decision value 0.90
SVM RNA-class probability 0.876761
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10344044 102 + 22407834
-AGUGGUGGUAAUUAAUCAUUCAACUUAUGAGGAUUAUUUCUUAAAGGCCU-CUGGCUCGGAAAUAGUCUGAACCUUAUUGUA----CACGCG---------AUAAUUUUGAUGAUU
-.............((((((.(((.......(((((((((((....((((.-..)))).))))))))))).....(((((((.----...)))---------))))..))))))))) ( -22.00)
>DroVir_CAF1 2144 116 + 1
UUGUGAAGCGAAUUGACUAUUCAACUUAUGAUUACUAUUUCAUAAAGGCUU-CUGGCUGGGAAAUAUUAUGAACGGUUUUAUGUGUAAAUAUAAAAUGUUUGAUAUUUAGUUUGAUU
....(((((((((.....))))...((((((........))))))..))))-).(((((...((((((..(((((.((((((((....))))))))))))))))))))))))..... ( -22.70)
>DroSec_CAF1 694 111 + 1
-AGUGGUGGUAAUUAAUUAUUCAACUUAUGAGGAUUAUUUCUUAAAGGCCU-CUGGCUCGGAAAUAGUCUGAACUUUAUUGUA----CACGCGAGGUUUGCAAUAAUUUUGAUGAUU
-.............((((((.(((.......(((((((((((....((((.-..)))).))))))))))).....((((((((----..(....)...))))))))..))))))))) ( -23.70)
>DroEre_CAF1 640 112 + 1
-GGUGGUGCAAAUUAAUUAUUCAACCUAUGAGGAUUAUUUCAUAAAGGCCUUCUGGCUCGGAAAUAGUCUGAAAUUUAUUGUA----CAUGCGAGGUGUGCAAUAAUUUUGAUGAUU
-.............(((((((..........((((((((((.....((((....))))..)))))))))).(((.((((((((----(((.....))))))))))).)))))))))) ( -28.50)
>DroYak_CAF1 640 110 + 1
-AGUGAUACAAAUUAAUUAUUCAACUUAUGAGGACUAUUUCUUAAAGGCCU--UGGCUCGGAAAUAGUCUGAACAUUAUUGUA----CAUGAGAGGUGUGCAAUAAUUUUGAUAAUU
-.............((((((.(((.......(((((((((((....(((..--..))).)))))))))))....(((((((((----(((.....)))))))))))).))))))))) ( -29.50)
>DroAna_CAF1 646 109 + 1
-UUUGGAAUAUAUUAAUCAUUCAUCUUAUGAUGAUUAUUUUAUAAAGGCU---UAGCCAGGAAAUAAUCUGAAAUUUAUUGUA----CGCUUGGACUGUAUAAUAAUCAUGAUGAUU
-...................(((((..((((((((((((((.....(((.---..)))..))))))))).......(((((((----((.......))))))))))))))))))).. ( -21.80)
>consensus
_AGUGGUGCAAAUUAAUUAUUCAACUUAUGAGGAUUAUUUCAUAAAGGCCU_CUGGCUCGGAAAUAGUCUGAACUUUAUUGUA____CACGCGAGGUGUGCAAUAAUUUUGAUGAUU
..............(((((((..........((((((((((.....((((....))))..)))))))))).....((((((((...............))))))))....))))))) (-15.83 = -15.34 +  -0.49)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:17 2006