Locus 2961

Sequence ID 2L_DroMel_CAF1
Location 8,500,439 – 8,500,593
Length 154
Max. P 0.973851
window4702 window4703

overview

Window 2

Location 8,500,439 – 8,500,559
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.89
Mean single sequence MFE -24.04
Consensus MFE -21.30
Energy contribution -21.42
Covariance contribution 0.12
Combinations/Pair 1.13
Mean z-score -1.46
Structure conservation index 0.89
SVM decision value 0.96
SVM RNA-class probability 0.889790
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8500439 120 + 22407834
UUAUCCUUCACACACGCUGGCCUAAAAGGUCACGUCAUAAACCAAGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUAGCGUUAAAAGAACUGUGGAAAAACUUUUGCCCGCUCC
...(((.......(((.(((((.....))))))))..........(((((..((.(((((((((((((......)))))))))..)))).))..)))))))).................. ( -24.30)
>DroSec_CAF1 9876 119 + 1
UUAUCCUUCACACAUGCUGGCCUAAAAGGUCACGUCAUAAACC-AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGCUAAAAUAACUGUGGAAAAACUUUUGCCCGUUCC
......((((((.(((((((((.....))))).).))).....-(((.(((..........(((((((......)))))))))).)))........)))))).................. ( -21.80)
>DroSim_CAF1 9085 119 + 1
UUAUCCUUCACACACGCUGGCCUAAAAGGUCACGUCAUAAACC-AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGCUAAAAGAACUGUGGAAAAACUUUUGCCCGUUCC
.............(((.(((((.....))))))))........-(((.(((..........(((((((......)))))))))).)))....((((.(..(((....)))..)..)))). ( -23.30)
>DroEre_CAF1 9495 119 + 1
UUAUCCUUCACACACGCUGGCCUAAAAGGUCACGUCAUAAACC-ACUAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCAUUAAAAGAGCUGUGGAAAAACUUUAGCCCGUUCC
.............(((.(((((.....))))))))......((-((.(((..((.((((.((((((((......)))..))))).)))).))..)))))))................... ( -24.60)
>DroYak_CAF1 10075 119 + 1
UUAUCCAUCACACACGCUGGCCUAAAAGGUCACGUCAUAAACC-ACUAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCAUUAAAAGAGCUGUGGAAAAACUUUGGCCCGUUCC
....(((......(((.(((((.....))))))))......((-((.(((..((.((((.((((((((......)))..))))).)))).))..)))))))........)))........ ( -26.20)
>consensus
UUAUCCUUCACACACGCUGGCCUAAAAGGUCACGUCAUAAACC_AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGUUAAAAGAACUGUGGAAAAACUUUUGCCCGUUCC
...(((.......(((.(((((.....))))))))..........(((((..((.((((.((((((((......)))..))))).)))).))..)))))))).................. (-21.30 = -21.42 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,500,479 – 8,500,593
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.87
Mean single sequence MFE -34.64
Consensus MFE -26.08
Energy contribution -27.00
Covariance contribution 0.92
Combinations/Pair 1.13
Mean z-score -2.93
Structure conservation index 0.75
SVM decision value 1.72
SVM RNA-class probability 0.973851
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8500479 114 + 22407834
ACCAAGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUAGCGUUAAAAGAACUGUGGAAAAACUUUUGCCCGCUCCUCGCGGGAGCUGAACUUUGGGGCGAAAG------UUUUCU
.((..(((((..((.(((((((((((((......)))))))))..)))).))..))))))).((((((((((((((((((.....))))).........)))))))))------)))).. ( -38.10)
>DroSec_CAF1 9916 113 + 1
ACC-AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGCUAAAAUAACUGUGGAAAAACUUUUGCCCGUUCCUCGCGGGAGCUGAACUUUGGGGCGAAAG------UUUUCU
.((-(.((((.(((.((..(((((((((......)))))))))....)).))).))))))).(((((((((((((((((...((....)).))))....)))))))))------)))).. ( -35.50)
>DroSim_CAF1 9125 113 + 1
ACC-AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGCUAAAAGAACUGUGGAAAAACUUUUGCCCGUUCCUCGCGGGAGCUGAACUUUGGGGCGAAAG------UUUUCU
.((-(.((((..((.((..(((((((((......)))))))))....)).))..))))))).(((((((((((((((((...((....)).))))....)))))))))------)))).. ( -34.60)
>DroEre_CAF1 9535 119 + 1
ACC-ACUAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCAUUAAAAGAGCUGUGGAAAAACUUUAGCCCGUUCCCCGCGGGAGGCGAACUUUGGGGCGAAAGCGAAAGUUUCCU
.((-((.(((..((.((((.((((((((......)))..))))).)))).))..)))))))..(((((((..(((((((.((......)).))))...)))((....)).)))))))... ( -34.70)
>DroYak_CAF1 10115 114 + 1
ACC-ACUAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCAUUAAAAGAGCUGUGGAAAAACUUUGGCCCGUUCCUCGCGGGAUCUGAACUUUGGAGCGAAAGU-----UUUCCU
.((-((.(((..((.((((.((((((((......)))..))))).)))).))..))))))).((((((((.((((((.....))))..((..(...)..)))).)))))-----)))... ( -30.30)
>consensus
ACC_AGCAGUAAUUAUAAUUGUAUAACCUAUAAUGGUUAUGUACCGUUAAAAGAACUGUGGAAAAACUUUUGCCCGUUCCUCGCGGGAGCUGAACUUUGGGGCGAAAG______UUUUCU
.....(((((..((.((((.((((((((......)))..))))).)))).))..)))))(((((..((((((((((((((.....))))).........)))))))))......))))). (-26.08 = -27.00 +   0.92)

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 10:40:40 2006