Locus 1391

Sequence ID 2R_DroMel_CAF1
Location 5,378,429 – 5,378,569
Length 140
Max. P 0.653231
window2386 window2387

overview

Window 6

Location 5,378,429 – 5,378,549
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.55
Mean single sequence MFE -27.84
Consensus MFE -22.72
Energy contribution -23.72
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.44
Structure conservation index 0.82
SVM decision value 0.25
SVM RNA-class probability 0.653231
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5378429 120 - 20766785
UGUUUUUCUUGUUUAUAUCCCGUGAAUAAAGCACUUUGAAGGCAUCAAUUAAGGAACGUGUUCAAGCUUUUGUAAGCUUGUUUAUUCGUUGAUUAGAACGCUACAAUUUGAAGUGACUAG
........((((((((.....))))))))(((((((..(((((.((((((((.((..(((..(((((((....)))))))..))))).)))))).))..)))....))..))))).)).. ( -28.80)
>DroSec_CAF1 912 119 - 1
-AUAUUUCUUGUUUAUAUUCGGUGAAUAAAGCACUUUGAAGGCAUCAAUUAAGGAACGUGUUCAAGCUUUUGCAAGCUUGUUUAUUCGUUGAUUAGAACGCUACAAUUUGAAGUGACUAG
-.......((((((((.....))))))))(((((((..(((((.((((((((.((..(((..(((((((....)))))))..))))).)))))).))..)))....))..))))).)).. ( -28.40)
>DroSim_CAF1 1100 119 - 1
-AUAUUUCUUGUUUAUAUUCGGUGAAUAAAGCACUUUGAAGGCAUCAAUUAAGGAACGUGUUCAAGCUUUUGCAAGCUUGUUUAUUCGUUGAUUAGAACGCUACAAUUUGAAGUGACUAG
-.......((((((((.....))))))))(((((((..(((((.((((((((.((..(((..(((((((....)))))))..))))).)))))).))..)))....))..))))).)).. ( -28.40)
>DroEre_CAF1 1106 118 - 1
-UUAUUUCUAGCUUAUAUUCGGCGAAUAAAGCACUUUGAAGGCAUCAGUUAAGGAACGUGUUCAAGCU-UUGCAAGCUUGUUUAUUCGUUGUAUAGAACGCUACAAUUUGAAGUGACUAG
-(((((((((((...(((.(((((((((((((((..(((.....)))(((....))))))).((((((-.....))))))))))))))))).)))....))))......))))))).... ( -28.00)
>DroYak_CAF1 1107 114 - 1
-ACAUAU-----UUAUAUUCGGCGAAUAAAGCACUUUGAUGGCAUCAAUUAAGGAACGUGUUCAAGCUUUUGCAAGCUUGUUUAUUCGUUGUUUAGAACGCUACAAUUUGAAGUGACUAG
-......-----...((..(((((((((((...(((((((.......)))))))........(((((((....))))))))))))))))))..))...((((.(.....).))))..... ( -25.60)
>consensus
_AUAUUUCUUGUUUAUAUUCGGUGAAUAAAGCACUUUGAAGGCAUCAAUUAAGGAACGUGUUCAAGCUUUUGCAAGCUUGUUUAUUCGUUGAUUAGAACGCUACAAUUUGAAGUGACUAG
.............................(((((((..(((((.((((((((.((..(((..(((((((....)))))))..))))).)))))).))..)))....))..))))).)).. (-22.72 = -23.72 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,378,469 – 5,378,569
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.47
Mean single sequence MFE -18.42
Consensus MFE -10.34
Energy contribution -10.38
Covariance contribution 0.04
Combinations/Pair 1.06
Mean z-score -1.64
Structure conservation index 0.56
SVM decision value -0.01
SVM RNA-class probability 0.529875
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5378469 100 + 20766785
CAAGCUUACAAAAGCUUGAACACGUUCCUUAAUUGAUGCCUUCAAAGUGCUUUAUUCACGGGAUAUAAACAAGAAAAACACAAUUAUUA-CUAAAUUA-------------------UGU
(((((((....))))))).....(((((....((((.....)))).(((.......)))))))).........................-........-------------------... ( -14.70)
>DroSec_CAF1 952 96 + 1
CAAGCUUGCAAAAGCUUGAACACGUUCCUUAAUUGAUGCCUUCAAAGUGCUUUAUUCACCGAAUAUAAACAAGAAAUAU-CAAUUGAAAGCGAAAU-A----------------------
(((((((....)))))))....((((..((((((((((..(((...((....(((((...)))))...))..))).)))-))))))).))))....-.---------------------- ( -21.80)
>DroSim_CAF1 1140 96 + 1
CAAGCUUGCAAAAGCUUGAACACGUUCCUUAAUUGAUGCCUUCAAAGUGCUUUAUUCACCGAAUAUAAACAAGAAAUAU-CAAUUGAAAGCGAAAU-A----------------------
(((((((....)))))))....((((..((((((((((..(((...((....(((((...)))))...))..))).)))-))))))).))))....-.---------------------- ( -21.80)
>DroEre_CAF1 1146 116 + 1
CAAGCUUGCAA-AGCUUGAACACGUUCCUUAACUGAUGCCUUCAAAGUGCUUUAUUCGCCGAAUAUAAGCUAGAAAUAA-CUAUUUAAAGUAAAAA-C-ACACCCACUUCACAUUUAUCC
((((((.....-))))))................((((......(((((((((((((...))))).))))........(-((......))).....-.-......))))......)))). ( -13.30)
>DroYak_CAF1 1147 113 + 1
CAAGCUUGCAAAAGCUUGAACACGUUCCUUAAUUGAUGCCAUCAAAGUGCUUUAUUCGCCGAAUAUAA-----AUAUGU-CUAUUAAAAGCGUAAA-UGGCACACACUUGAUAUUUGUCU
(((((((....)))))))................((((..(((((.(((((.....(((.....(((.-----......-.))).....)))....-.)))))....)))))...)))). ( -20.50)
>consensus
CAAGCUUGCAAAAGCUUGAACACGUUCCUUAAUUGAUGCCUUCAAAGUGCUUUAUUCACCGAAUAUAAACAAGAAAUAU_CAAUUAAAAGCGAAAU_A___________________U__
(((((((....))))))).....((((......(((.(((......).)).)))......))))........................................................ (-10.34 = -10.38 +   0.04)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:42 2006