Locus 4839

Sequence ID 3L_DroMel_CAF1
Location 13,570,295 – 13,570,385
Length 90
Max. P 0.838661
window7633 window7634

overview

Window 3

Location 13,570,295 – 13,570,385
Length 90
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 76.41
Mean single sequence MFE -17.42
Consensus MFE -9.63
Energy contribution -9.67
Covariance contribution 0.04
Combinations/Pair 1.33
Mean z-score -1.94
Structure conservation index 0.55
SVM decision value 0.74
SVM RNA-class probability 0.838661
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13570295 90 + 23771897
CAGCUUAAGGAUUGCUUUAGCUCAAACAAAUACGAAUAAGUUCUUCGAUUAAGAAGGAUAUAACCGUUAUAUAGGAUAUUUCCUCAU-----AAA
.((((.(((.....))).)))).........(((..((.(((((((......))))))).))..)))..(((((((....)))).))-----).. ( -16.90)
>DroSec_CAF1 51840 90 + 1
CAGCUUAAGAAUGGCUUAAACUCAAACAAAUACGAAUAAGUUCUUCGAUUAAGAAGGAUAUAUCCGUUAUAUAGGAUAUUUCCUCAU-----AAA
...((((.(((..(((((...((..........)).)))))..)))...)))).((((.((((((........)))))).))))...-----... ( -18.00)
>DroSim_CAF1 38010 90 + 1
CAGCUUAAGAAUGGCUUAAACUCAAACAAAUACGAAUAAGUUCUUCGAUUAAGAAGGAUAUAUCCGUUAUAUAGGAUAUUUCCUCAU-----AAA
...((((.(((..(((((...((..........)).)))))..)))...)))).((((.((((((........)))))).))))...-----... ( -18.00)
>DroEre_CAF1 53013 70 + 1
CAGCUUGUUGAAUGCCUA--------------------AGUUCAUCGAUUAAGAAAGAUAUAUCCGUUAUUUAGGAUAUAUCCUCGA-----AUA
....(((.(((((.....--------------------.))))).)))....((..(((((((((........))))))))).))..-----... ( -15.90)
>DroYak_CAF1 54419 95 + 1
CAGUUUGUUGUUUGCUUAAACUCAAACAAAUAUGAAGAAGUUCAUCGAUUGAGAAGGAUAUAUCUAUUAUAUUGGAUAUUUUCUCGUGUACUAUA
..(((((..((((....)))).)))))..((((((.(((((((.((......)).))))(((((((......))))))).)))))))))...... ( -18.30)
>consensus
CAGCUUAAGGAUUGCUUAAACUCAAACAAAUACGAAUAAGUUCUUCGAUUAAGAAGGAUAUAUCCGUUAUAUAGGAUAUUUCCUCAU_____AAA
...((((.(((..((((....................))))..)))...)))).((((.((((((........)))))).))))........... ( -9.63 =  -9.67 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,570,295 – 13,570,385
Length 90
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 76.41
Mean single sequence MFE -16.78
Consensus MFE -9.14
Energy contribution -11.54
Covariance contribution 2.40
Combinations/Pair 1.16
Mean z-score -1.69
Structure conservation index 0.54
SVM decision value -0.04
SVM RNA-class probability 0.511075
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13570295 90 - 23771897
UUU-----AUGAGGAAAUAUCCUAUAUAACGGUUAUAUCCUUCUUAAUCGAAGAACUUAUUCGUAUUUGUUUGAGCUAAAGCAAUCCUUAAGCUG
...-----.((((((.............(((..((....((((......))))....))..)))..((((((......))))))))))))..... ( -15.40)
>DroSec_CAF1 51840 90 - 1
UUU-----AUGAGGAAAUAUCCUAUAUAACGGAUAUAUCCUUCUUAAUCGAAGAACUUAUUCGUAUUUGUUUGAGUUUAAGCCAUUCUUAAGCUG
..(-----(((((((.((((((........)))))).)))(((((.....))))).....)))))........((((((((.....)))))))). ( -20.40)
>DroSim_CAF1 38010 90 - 1
UUU-----AUGAGGAAAUAUCCUAUAUAACGGAUAUAUCCUUCUUAAUCGAAGAACUUAUUCGUAUUUGUUUGAGUUUAAGCCAUUCUUAAGCUG
..(-----(((((((.((((((........)))))).)))(((((.....))))).....)))))........((((((((.....)))))))). ( -20.40)
>DroEre_CAF1 53013 70 - 1
UAU-----UCGAGGAUAUAUCCUAAAUAACGGAUAUAUCUUUCUUAAUCGAUGAACU--------------------UAGGCAUUCAACAAGCUG
...-----((((((((((((((........)))))))))).......))))......--------------------..(((.........))). ( -14.91)
>DroYak_CAF1 54419 95 - 1
UAUAGUACACGAGAAAAUAUCCAAUAUAAUAGAUAUAUCCUUCUCAAUCGAUGAACUUCUUCAUAUUUGUUUGAGUUUAAGCAAACAACAAACUG
..((((....(((((.(((((..........)))))....))))).....(((((....)))))..(((((((........)))))))...)))) ( -12.80)
>consensus
UUU_____AUGAGGAAAUAUCCUAUAUAACGGAUAUAUCCUUCUUAAUCGAAGAACUUAUUCGUAUUUGUUUGAGUUUAAGCAAUCCUUAAGCUG
..........(((((.((((((........)))))).)))))...............................((((((((.....)))))))). ( -9.14 = -11.54 +   2.40)

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 11:34:52 2006