Locus 4111

Sequence ID 2R_DroMel_CAF1
Location 13,515,873 – 13,515,976
Length 103
Max. P 0.999077
window6621 window6622

overview

Window 1

Location 13,515,873 – 13,515,976
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 78.27
Mean single sequence MFE -31.82
Consensus MFE -17.85
Energy contribution -20.98
Covariance contribution 3.12
Combinations/Pair 1.11
Mean z-score -1.88
Structure conservation index 0.56
SVM decision value -0.02
SVM RNA-class probability 0.521187
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13515873 103 + 20766785
AACCGACGGUUUUCCCAUAUGCCCGGAUACGGAUUUGGAUCCUGGUCCGGAUUUUGGUUUAAGUACGAAAAGGAAAAGGCGAUGGGUGCGAGUGGUGAGUGGU
.((((...((...(((((.(((((((((..((((....))))..)))))..((((.((......)).))))......))))))))).))...))))....... ( -30.80)
>DroSec_CAF1 64331 101 + 1
AGCCGAGGGUUUUCCCAUAUGCCCGGAUCCGGAUUUGGAUCCCAGUUCGGAUUUUGGUUUAAGUACCAAAAGGAAAAGGCGAUGGGUGC--GUGGUGAGUGGU
.((((...((...(((((.((((.(((((((....)))))))...(((...(((((((......))))))).)))..))))))))).))--.))))....... ( -34.30)
>DroSim_CAF1 65059 101 + 1
AGCCGAGGGUUUUCCCAUAUGCCCGGAUCCGGAUUUGGAUCCCGGUUCGGAUUUUGGUUUAAGUACCAAAAGGAAAAGGAAAAGGGUGC--GUGGUGAGUGGU
.((((......(((((((..(((((((((((....)))))))(..(((...(((((((......))))))).)))..).....))))..--)))).))))))) ( -34.00)
>DroYak_CAF1 67195 81 + 1
AGCCGGAGGAUUUCCCAUAUGCCCGUAUACGGAUUGGGAACCGUGUCCGGAUUUUGGUUUAAGUACCAAAAUGCUAAAGGA----------------------
..(((((.(..((((((.....(((....)))..))))))...).)))))((((((((......)))))))).........---------------------- ( -28.20)
>consensus
AGCCGAGGGUUUUCCCAUAUGCCCGGAUACGGAUUUGGAUCCCGGUCCGGAUUUUGGUUUAAGUACCAAAAGGAAAAGGCAAUGGGUGC__GUGGUGAGUGGU
.((((...((...(((......(((((((.((((....)))).))))))).(((((((......)))))))............))).))...))))....... (-17.85 = -20.98 +   3.12)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 13,515,873 – 13,515,976
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 78.27
Mean single sequence MFE -25.85
Consensus MFE -16.76
Energy contribution -17.82
Covariance contribution 1.06
Combinations/Pair 1.18
Mean z-score -3.05
Structure conservation index 0.65
SVM decision value 3.36
SVM RNA-class probability 0.999077
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13515873 103 - 20766785
ACCACUCACCACUCGCACCCAUCGCCUUUUCCUUUUCGUACUUAAACCAAAAUCCGGACCAGGAUCCAAAUCCGUAUCCGGGCAUAUGGGAAAACCGUCGGUU
..................((..((..((((((((((.((......)).))))((((((...((((....))))...)))))).....))))))..))..)).. ( -21.50)
>DroSec_CAF1 64331 101 - 1
ACCACUCACCAC--GCACCCAUCGCCUUUUCCUUUUGGUACUUAAACCAAAAUCCGAACUGGGAUCCAAAUCCGGAUCCGGGCAUAUGGGAAAACCCUCGGCU
............--...(((((.((((.....(((((((......))))))).........((((((......))))))))))..)))))............. ( -28.40)
>DroSim_CAF1 65059 101 - 1
ACCACUCACCAC--GCACCCUUUUCCUUUUCCUUUUGGUACUUAAACCAAAAUCCGAACCGGGAUCCAAAUCCGGAUCCGGGCAUAUGGGAAAACCCUCGGCU
............--..................(((((((......))))))).((((.((.((((((......)))))).)).....(((....))))))).. ( -27.50)
>DroYak_CAF1 67195 81 - 1
----------------------UCCUUUAGCAUUUUGGUACUUAAACCAAAAUCCGGACACGGUUCCCAAUCCGUAUACGGGCAUAUGGGAAAUCCUCCGGCU
----------------------......(((((((((((......)))))))).((((.....((((((.((((....))))....))))))....))))))) ( -26.00)
>consensus
ACCACUCACCAC__GCACCCAUCGCCUUUUCCUUUUGGUACUUAAACCAAAAUCCGAACCGGGAUCCAAAUCCGGAUCCGGGCAUAUGGGAAAACCCUCGGCU
................................(((((((......))))))).((((.((.((((((......)))))).)).....(((....))))))).. (-16.76 = -17.82 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:05 2006