Locus 2730

Sequence ID 3R_DroMel_CAF1
Location 7,324,510 – 7,324,697
Length 187
Max. P 0.966848
window4439 window4440

overview

Window 9

Location 7,324,510 – 7,324,621
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.75
Mean single sequence MFE -30.28
Consensus MFE -24.60
Energy contribution -24.44
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.81
SVM decision value 0.60
SVM RNA-class probability 0.797050
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7324510 111 - 27905053
AAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCAUCUCUUUUAGCCCUAAGUGAAUUCUG-------UUUUCAUCGCUGGCUGU-CGGUGAAUAGGGGUGCAGAAUUAUGAAAA
..........(((((((....))))).((((((.-((.((((.....(((((....(((((.....-------..)))))....))))).-.)))).))))))))))............. ( -31.00)
>DroSec_CAF1 835 118 - 1
AACUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCAUCUCUUUUAGCCCUAAGUGAAUUCUGUUUUCUGUUUUCAUCGCUGGCUGU-CGGUGAAUAGGGGUGCAGAAUUAUGAAAA
..........(((((((....))))).((((((.-((.((((.....(((((....(((((..(........)..)))))....))))).-.)))).))))))))))............. ( -32.20)
>DroSim_CAF1 4591 118 - 1
AAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCAUCUCUCUUAGCCCUAAGUGAAUUCUGUUUUCUGUUUUCAUCGCUGGCUGU-CGGUGAAUAGGGGUGCAAAAUUAUGAAAA
..........(((((((....))))).((((((.-((.((((.....(((((....(((((..(........)..)))))....))))).-.)))).))))))))))............. ( -32.20)
>DroEre_CAF1 4580 112 - 1
AAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUCCAUCAUUCUCCUUUAGCCCAAAGUGAAUUCUG-------UUUUCAUCGCUGGUUUU-CGGUGAAUAGGGGUGCAAAAUUAUGAAAA
..........(((((((....))))).((((((.....((((.((...((((....(((((.....-------..)))))....))))..-.)).))))))))))))............. ( -29.80)
>DroYak_CAF1 4705 112 - 1
AAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCAUCUGUUUUAGCCCUAAGUGAAUUCUG-------UUUUCAUCGCUGUUUUGCCAGUGAAUAGGGGUGCAAAAUUAUGAAAA
..........(((((((....))))).((((((.-......................((((.....-------..))))((((((......))))))..))))))))............. ( -26.20)
>consensus
AAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC_AUCCAUCUCUUUUAGCCCUAAGUGAAUUCUG_______UUUUCAUCGCUGGCUGU_CGGUGAAUAGGGGUGCAAAAUUAUGAAAA
..........(((((((....))))).((((((........................((((..............))))((((((......))))))..))))))))............. (-24.60 = -24.44 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 7,324,582 – 7,324,697
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.81
Mean single sequence MFE -28.01
Consensus MFE -24.11
Energy contribution -24.15
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -1.78
Structure conservation index 0.86
SVM decision value 1.60
SVM RNA-class probability 0.966848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7324582 115 - 27905053
CGAGCGGGCGC----CUCAGUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCA
.(((.((((..----......((((........))))(((((((......((((.........................))))......)))))))...........)))))))-..... ( -26.41)
>DroSec_CAF1 914 115 - 1
CGAGCGGGCGC----CUGAGUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAACUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCA
.(((.((((((----.((((((((((..(((.......)))(((....................))).......))))..))))))....))(((((....))))).)))))))-..... ( -28.95)
>DroSim_CAF1 4670 115 - 1
CGAGCGGGCGC----CUGAGUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCA
.(((.((((..----.(((((((((........))))....)))))..............................................(((((....))))).)))))))-..... ( -28.20)
>DroEre_CAF1 4652 120 - 1
CGAGCGGGUGAACGCCUGACUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUCCAUCAU
.((((((((....))))(((.((((........)))).))))))).............................................(((((((....))))).))........... ( -27.70)
>DroYak_CAF1 4778 115 - 1
CGAGCGGGCGUUCG----UGUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC-AUCCA
.(((.(((((((.(----(((((((...(((.......))).)))).........)))).))).............................(((((....))))).)))))))-..... ( -28.80)
>consensus
CGAGCGGGCGC____CUGAGUUGGGAUAGACCACCCACGUCGCUCAUAUUAUUUUACACUAACAAGCCAAACAUUCCUUAAAUUUAACAAGCGGCGACAUUUUGCCAGCCCCUC_AUCCA
.(((.((((............((((........))))(((((((......((((.........................))))......)))))))...........)))))))...... (-24.11 = -24.15 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:30 2006