Locus 3804

Sequence ID 2L_DroMel_CAF1
Location 11,113,765 – 11,113,899
Length 134
Max. P 0.706455
window5999 window6000 window6001

overview

Window 9

Location 11,113,765 – 11,113,860
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 87.70
Mean single sequence MFE -22.12
Consensus MFE -17.18
Energy contribution -18.54
Covariance contribution 1.36
Combinations/Pair 1.11
Mean z-score -1.45
Structure conservation index 0.78
SVM decision value -0.04
SVM RNA-class probability 0.513176
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11113765 95 + 22407834
AAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUUAACGCAGGACUUAGGGGAAUCCUUAUAUGGAAAAACCCCAAUGUCGCCGCAACGAAAAUG
..............(((((..((((((((........))))))))...((((..(((......)))....))))...))).))............ ( -24.40)
>DroSec_CAF1 6674 94 + 1
AAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUU-ACGCAGGACUUAAGGGAAUCCUUAUAUGGAAAAACCCCAAUGUCGCUGUAGCGAAAUUG
..((((((((....(((((((((((((((......-.))))))))......))))))).))))))))......((((.((((....)))).)))) ( -26.70)
>DroSim_CAF1 6920 86 + 1
AAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUU-ACGCAG--------GGAAUCCUUAUAUGGAAAAACCCCAAUAUCGCCGUAACGAAAAUG
.(((((....((((((((((((...((((......-.))))(--------((..(((......)))....)))))).))).))))))..))))). ( -19.80)
>DroEre_CAF1 6803 92 + 1
GAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUU-AGGCAGGAUUUAAGGGAAUCCGUAUAAGGAAAA-C-CAAAUAUCGUCGUAACGAAAUUG
..................(((((..(((((.(((.-.....((((((....))))))......((....-)-)....))).)))))))))).... ( -16.30)
>DroYak_CAF1 6784 93 + 1
GAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUU-ACGCAGGACUUAAGGGAAUCCUUAUAAAGAAAA-CCCAAAUAUCGUCGUGACGAAAUUG
.............((((....((((((((......-.)))))))).(((((....))))).........-))))(((.((((....)))).))). ( -23.40)
>consensus
AAUUUUAUAUUUAUGGGAUUUGUUUUGCGGGGAUU_ACGCAGGACUUAAGGGAAUCCUUAUAUGGAAAAACCCCAAUAUCGCCGUAACGAAAUUG
..((((((((....(((((((((((((((........))))))))......))))))).))))))))...........((((....))))..... (-17.18 = -18.54 +   1.36)

alignment

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secondary structure

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Window 0

Location 11,113,765 – 11,113,860
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 87.70
Mean single sequence MFE -17.38
Consensus MFE -11.94
Energy contribution -12.58
Covariance contribution 0.64
Combinations/Pair 1.16
Mean z-score -2.18
Structure conservation index 0.69
SVM decision value 0.36
SVM RNA-class probability 0.706455
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11113765 95 - 22407834
CAUUUUCGUUGCGGCGACAUUGGGGUUUUUCCAUAUAAGGAUUCCCCUAAGUCCUGCGUUAAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUU
..........((((.(((...((((....(((......)))..))))...)))))))...................................... ( -20.80)
>DroSec_CAF1 6674 94 - 1
CAAUUUCGCUACAGCGACAUUGGGGUUUUUCCAUAUAAGGAUUCCCUUAAGUCCUGCGU-AAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUU
.....((((....))))...((((((((.......(((((....))))).((..((((.-......))))..))))))))))............. ( -22.50)
>DroSim_CAF1 6920 86 - 1
CAUUUUCGUUACGGCGAUAUUGGGGUUUUUCCAUAUAAGGAUUCC--------CUGCGU-AAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUU
.....((((....))))...((((((((.(((......)))....--------.((((.-......))))....))))))))............. ( -17.10)
>DroEre_CAF1 6803 92 - 1
CAAUUUCGUUACGACGAUAUUUG-G-UUUUCCUUAUACGGAUUCCCUUAAAUCCUGCCU-AAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUC
(((..((((....))))...)))-(-((((........(((((......))))).((..-.......)))))))..................... (  -9.40)
>DroYak_CAF1 6784 93 - 1
CAAUUUCGUCACGACGAUAUUUGGG-UUUUCUUUAUAAGGAUUCCCUUAAGUCCUGCGU-AAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUC
.(((.((((....)))).)))((((-.(((.....(((((....))))).((..((((.-......))))..))))).))))............. ( -17.10)
>consensus
CAAUUUCGUUACGGCGAUAUUGGGGUUUUUCCAUAUAAGGAUUCCCUUAAGUCCUGCGU_AAUCCCCGCAAAACAAAUCCCAUAAAUAUAAAAUU
.....((((....))))...((((((((.(((......))).............((((........))))....))))))))............. (-11.94 = -12.58 +   0.64)

alignment

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secondary structure

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Window 1

Location 11,113,781 – 11,113,899
Length 118
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 74.31
Mean single sequence MFE -20.72
Consensus MFE -10.56
Energy contribution -11.40
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -1.75
Structure conservation index 0.51
SVM decision value 0.22
SVM RNA-class probability 0.640520
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11113781 118 - 22407834
AUGCAAAAGAUUCUAGGAAAUGUCUGCUCAAUUCCUAUUCAUUUUCGUUGCGGCGACAUUGGGGUUUUUCCAUAUAAGGAUUCCCCUAAGUCCUGCGUUAAUCCCCGCAAAACAAAUC
.(((....((...((((((.((......)).)))))).)).........((((.(((...((((....(((......)))..))))...)))))))..........)))......... ( -31.70)
>DroSec_CAF1 6690 103 - 1
AUCCAUAAGAUUC--------------UCAAAUCCUAUUCAAUUUCGCUACAGCGACAUUGGGGUUUUUCCAUAUAAGGAUUCCCUUAAGUCCUGCGU-AAUCCCCGCAAAACAAAUC
.............--------------...((((((...((((.((((....)))).))))(((....))).....)))))).......((..((((.-......))))..))..... ( -20.60)
>DroSim_CAF1 6936 95 - 1
AUCCAAAAGAUUC--------------UCAAUUCCUAUUCAUUUUCGUUACGGCGAUAUUGGGGUUUUUCCAUAUAAGGAUUCC--------CUGCGU-AAUCCCCGCAAAACAAAUC
.............--------------............((...((((....))))...))(((....(((......)))..))--------)((((.-......))))......... ( -14.50)
>DroEre_CAF1 6819 112 - 1
AUCCA---GAUUCUAGGCAAUGUCUGCUUAAUUUCUAUUCAAUUUCGUUACGACGAUAUUUG-G-UUUUCCUUAUACGGAUUCCCUUAAAUCCUGCCU-AAUCCCCGCAAAACAAAUC
.....---(((..((((((...................((((..((((....))))...)))-)-............(((((......))))))))))-))))............... ( -17.10)
>DroYak_CAF1 6800 96 - 1
A---------UUCCACGCAAUGUCU-----------ACUCAAUUUCGUCACGACGAUAUUUGGG-UUUUCUUUAUAAGGAUUCCCUUAAGUCCUGCGU-AAUCCCCGCAAAACAAAUC
.---------....((((...(...-----------((((((..((((....))))...)))))-)...)......((((((......))))))))))-................... ( -19.70)
>consensus
AUCCA_AAGAUUC_A_G_AAUGUCU__UCAAUUCCUAUUCAAUUUCGUUACGGCGAUAUUGGGGUUUUUCCAUAUAAGGAUUCCCUUAAGUCCUGCGU_AAUCCCCGCAAAACAAAUC
.......................................((((.((((....)))).))))(((....(((......)))..)))........((((........))))......... (-10.56 = -11.40 +   0.84)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:54 2006