Locus 3128

Sequence ID 3L_DroMel_CAF1
Location 9,117,611 – 9,117,707
Length 96
Max. P 0.853712
window4877 window4878

overview

Window 7

Location 9,117,611 – 9,117,707
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.04
Mean single sequence MFE -28.17
Consensus MFE -22.43
Energy contribution -23.27
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.80
SVM decision value 0.29
SVM RNA-class probability 0.669601
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9117611 96 + 23771897
GGUAUGGCACAAAUAAUUGUUACCGCUGCAACCCCCAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGCGAGAGCGAUGCACAGCCA------------------------
(((.((((((.....((((.(((((((.(((((.....))))).)).))))).))))....(((((((.......)).))))).).))).))))).------------------------ ( -28.90)
>DroVir_CAF1 5604 90 + 1
GGUAUGGCACAAAUAAUUGUUACCGCUGCAACCCCAAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGAGAAAGGGACAAU------------------------------
....((((((((....)))).((((((.(((((.....))))).)).)))))))).....((((((((.......)).))))))......------------------------------ ( -25.00)
>DroGri_CAF1 4761 93 + 1
GGUAUGGCACAAAUAAUUGUUACCGCUGCAACCCCAAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGAGAGAGCGACAAU---UCA------------------------
......((.......((((.(((((((.(((((.....))))).)).))))).))))...(((((((........)))))))))......---...------------------------ ( -26.90)
>DroWil_CAF1 6221 96 + 1
GGUAUGGCACAAAUAAUAGUUACCGCUGCAACCCCAAUGGUUGAAGACGGUGCAGAUAAAUCUUUCCCACCAGUAGGAGAGAAGGAGGAACAGCAA------------------------
......((..........((.((((((.(((((.....))))).)).)))))).......(((((((........)))))))..........))..------------------------ ( -24.30)
>DroMoj_CAF1 4842 93 + 1
GGUAUGGCACAAAUAAUUGUUACCGCUGCAACCCCAAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGAGAGAGCGACAAU---ACA------------------------
.((((.((.......((((.(((((((.(((((.....))))).)).))))).))))...(((((((........)))))))))....))---)).------------------------ ( -28.60)
>DroAna_CAF1 5821 120 + 1
GGUAUGGCACAAAUAAUAGUUACCGCUGCAACCCCCAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGAGAGAGCGAUUCCCAGUCCGAUAAGGACACGGAUACGGAUAAG
((.((.((..........(.(((((((.(((((.....))))).)).))))).)......(((((((........))))))))).)).))..((((.....)))).((....))...... ( -35.30)
>consensus
GGUAUGGCACAAAUAAUUGUUACCGCUGCAACCCCAAUGGUUGAAGACGGUGCCGAUAAAUCUUUCCCACCAGUAGGAGAGAGCGACAAU___CCA________________________
....((((((((....)))).((((((.(((((.....))))).)).)))))))).....(((((((........)))))))...................................... (-22.43 = -23.27 +   0.83)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,117,611 – 9,117,707
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.04
Mean single sequence MFE -30.80
Consensus MFE -25.42
Energy contribution -25.78
Covariance contribution 0.36
Combinations/Pair 1.07
Mean z-score -2.08
Structure conservation index 0.83
SVM decision value 0.80
SVM RNA-class probability 0.853712
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9117611 96 - 23771897
------------------------UGGCUGUGCAUCGCUCUCGCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUGGGGGUUGCAGCGGUAACAAUUAUUUGUGCCAUACC
------------------------..((((((.(((..(((((((....)))))))..))).)).))))((((.((.(((((.....))))).)))))).((((....))))........ ( -33.00)
>DroVir_CAF1 5604 90 - 1
------------------------------AUUGUCCCUUUCUCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUUGGGGUUGCAGCGGUAACAAUUAUUUGUGCCAUACC
------------------------------.......((((((((.....).))))))).......(((((((.((.(((((.....))))).)))))).((((....)))))))..... ( -27.30)
>DroGri_CAF1 4761 93 - 1
------------------------UGA---AUUGUCGCUCUCUCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUUGGGGUUGCAGCGGUAACAAUUAUUUGUGCCAUACC
------------------------.((---...(((..((((.((....)).))))..)))...))(((((((.((.(((((.....))))).)))))).((((....)))))))..... ( -30.60)
>DroWil_CAF1 6221 96 - 1
------------------------UUGCUGUUCCUCCUUCUCUCCUACUGGUGGGAAAGAUUUAUCUGCACCGUCUUCAACCAUUGGGGUUGCAGCGGUAACUAUUAUUUGUGCCAUACC
------------------------..(((((..(((((((((.((....)).)))))(((....)))..................))))..)))))((((.(........)))))..... ( -25.90)
>DroMoj_CAF1 4842 93 - 1
------------------------UGU---AUUGUCGCUCUCUCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUUGGGGUUGCAGCGGUAACAAUUAUUUGUGCCAUACC
------------------------.((---((.(((..((((.((....)).))))..))).....(((((((.((.(((((.....))))).)))))).((((....))))))))))). ( -29.70)
>DroAna_CAF1 5821 120 - 1
CUUAUCCGUAUCCGUGUCCUUAUCGGACUGGGAAUCGCUCUCUCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUGGGGGUUGCAGCGGUAACUAUUAUUUGUGCCAUACC
.......(((((((.((((.....)))))))(((((..((((.((....)).))))..)))))...(((((((.((.(((((.....))))).)))))).((........))))))))). ( -38.30)
>consensus
________________________UGA___AUUGUCGCUCUCUCCUACUGGUGGGAAAGAUUUAUCGGCACCGUCUUCAACCAUUGGGGUUGCAGCGGUAACAAUUAUUUGUGCCAUACC
.................................(((..((((.((....)).))))..))).....(((((((.((.(((((.....))))).)))))).((((....)))))))..... (-25.42 = -25.78 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:14 2006