Locus 3067

Sequence ID 2R_DroMel_CAF1
Location 10,538,633 – 10,538,785
Length 152
Max. P 0.784379
window5057 window5058

overview

Window 7

Location 10,538,633 – 10,538,745
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.18
Mean single sequence MFE -30.70
Consensus MFE -21.70
Energy contribution -23.40
Covariance contribution 1.70
Combinations/Pair 1.14
Mean z-score -2.34
Structure conservation index 0.71
SVM decision value 0.57
SVM RNA-class probability 0.784379
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10538633 112 + 20766785
UUUUUGUUUUCUACAAACAUAUUCUGUUUUUAUGGCGCUGCG----UU----UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAAUUCAGCGCUGGAGAAUGCGAUUUCCAGCA
..(((((.....)))))((((.........))))((((((((----..----........))))))...............(((((....)))))))((((((((......)))))))). ( -29.30)
>DroSec_CAF1 31871 112 + 1
UUUUUGUUUUCUACAAACAUAUUCUGUUUUUACGGCGCUGCG----UU----UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCUGGAGAUUGCGAUUUCCAGCA
..(((((.....)))))........((((((((((..(((((----..----........)))))..))...(((.....))).)))))))).....(((((((((....))))))))). ( -33.70)
>DroSim_CAF1 28266 111 + 1
UUUUUGUUUUCUACAAACAUAUUCUGUUUUUACGGCGCUGCG----UU----UUU-UUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCCGGAGAAUGCGAUUUCCAGCA
.....((((((...(((((.....)))))...((((((((.(----((----(((-..(((((((....))))((.....))))).)))))).))))))))))))))((........)). ( -33.40)
>DroEre_CAF1 33585 104 + 1
UUUUUGUUUUCUACGAACAUAUUCUGUU-UUAUGGC---------------GCUUUUUUUCGCAGUACUUUGCACGUGAAGUGAGUGAAAACUCAGAGCCGUAGAAUGCGAUUUCCAGCA
...((((.(((((((((((.....))))-)...(((---------------(((((.....((((....))))....)))))((((....))))...))))))))).))))......... ( -28.60)
>DroYak_CAF1 32110 120 + 1
UUUUUGUUUUCUACAAACAUAUUCUGUUUUUAUGGUGCUGCUGCUGUUGCUGCUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGAGCCGGAGAAUGCGAUUUCCAGCA
..(((((.....)))))...............((..(.(((....((.(((((........)))))))...))))..))..(((((....)))))..((.(((((......))))).)). ( -28.50)
>consensus
UUUUUGUUUUCUACAAACAUAUUCUGUUUUUAUGGCGCUGCG____UU____UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCCGGAGAAUGCGAUUUCCAGCA
...((((.((((..(((((.....)))))...((((((.......................((((....))))........(((((....))))))))))).)))).))))......... (-21.70 = -23.40 +   1.70)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,538,673 – 10,538,785
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.78
Mean single sequence MFE -35.78
Consensus MFE -28.72
Energy contribution -30.34
Covariance contribution 1.62
Combinations/Pair 1.09
Mean z-score -1.56
Structure conservation index 0.80
SVM decision value 0.38
SVM RNA-class probability 0.712373
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10538673 112 + 20766785
CG----UU----UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAAUUCAGCGCUGGAGAAUGCGAUUUCCAGCAUGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUUGGCUUCUG
..----..----.........((((....))))..(((((((...((((((((((..((((((((......)))))))).)))))......(((....))))))))..)))))))..... ( -35.70)
>DroSec_CAF1 31911 112 + 1
CG----UU----UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCUGGAGAUUGCGAUUUCCAGCAUGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUCGCCUGCUG
..----..----.........((((...((..(((.(((..(((((....)))))..(((((((((....))))))))).))))))..)).((((....(((.....))))))))))).. ( -38.40)
>DroSim_CAF1 28306 111 + 1
CG----UU----UUU-UUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCCGGAGAAUGCGAUUUCCAGCAUGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUCGCCUGCUG
..----..----...-...(((((...(((((..(((....(((((....)))))))).)))))..)))))....((((((((((.((((.(((....))).))))..)))))..))))) ( -35.40)
>DroEre_CAF1 33620 109 + 1
-----------GCUUUUUUUCGCAGUACUUUGCACGUGAAGUGAGUGAAAACUCAGAGCCGUAGAAUGCGAUUUCCAGCACGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUCGCCAGCUG
-----------........(((((....(((((..((....(((((....)))))..)).))))).)))))....((((.(((((.((((.(((....))).))))..)))))...)))) ( -32.70)
>DroYak_CAF1 32150 120 + 1
CUGCUGUUGCUGCUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGAGCCGGAGAAUGCGAUUUCCAGCAUGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUCGUAUGCUG
.(((...((((((........))))))....))).......(((((....)))))..((.(((((......))))).))((((((.((((.(((....))).))))..))))))...... ( -36.70)
>consensus
CG____UU____UUUUUUUUCGCAGUACUUUGCACGUCAAGUGAGUGAAAACUCAGCGCCGGAGAAUGCGAUUUCCAGCAUGAGUGUGAAUGCGAAUGCGCUUUCAAAGCUCGCCUGCUG
...................(((((...((((((((.....))((((....))))...)).))))..)))))....((((((((((.((((.(((....))).))))..)))))..))))) (-28.72 = -30.34 +   1.62)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:36 2006