Locus 3364

Sequence ID 3L_DroMel_CAF1
Location 9,830,669 – 9,830,901
Length 232
Max. P 0.918934
window5256 window5257

overview

Window 6

Location 9,830,669 – 9,830,783
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.56
Mean single sequence MFE -38.17
Consensus MFE -32.26
Energy contribution -33.01
Covariance contribution 0.75
Combinations/Pair 1.14
Mean z-score -2.02
Structure conservation index 0.85
SVM decision value 1.12
SVM RNA-class probability 0.918934
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9830669 114 - 23771897
CGCCUAGCUUCGAAUUUUGUGGGCGGGGCAAAUGGAGGAGGAGGAGGA------AUCGAGUGGACAGCUGGAAACGGAAAAAAAGAAGAAAAGCCCUGUCUCCUCUUCUUCCCACGUCGG
.((((.(((((((...))).)))).))))..(((..((((((((((((------..(.((.((....(((....)))................)))))..))))))))))))..)))... ( -38.45)
>DroSec_CAF1 124638 110 - 1
CACCUAGCUCCGAAUUUUGUGGGCGGAGCAAAUGGAGGA---GGAGGA------AUCGAGUGGACAGCUGGAAACGGAAA-AUAGAAGAAAAGCCAUGUCUCCUCUUCUUCCCACGUCGG
..((..((((((..(.....)..))))))....((((((---((((((------.....((((....(((....)))...-............))))...))))))))))))......)) ( -38.91)
>DroSim_CAF1 127950 113 - 1
CACCUAGCUCCGAAUUUUGUGGGCGGAGCAAAUGGAGGAGGAGGAGGA------AUCGAGUGGACAGCUGGAAACGGAAA-AUAGAAGAAAAGCCAUGUCUCCUCUUCUUCCCACGUCGG
..((..((((((..(.....)..))))))....((((((((((((((.------.....((((....(((....)))...-............)))).))))))))))))))......)) ( -42.21)
>DroYak_CAF1 137891 119 - 1
CACCUAGCUCCAAAUUUCGUGGGAGGAGUAAAUGGAAGAGGAGGAGGAGGGAGGAUCGAGUGGACAGCUGAAAUAGGAAA-AUUGAAGAAAAGCCGUGUCGCCUCUUCUUCCCACGUUGG
..(((..((((...((((((...........))))))..)))).))).(((((((..(((..(((((((...........-..........)))..))))..))).)))))))....... ( -33.10)
>consensus
CACCUAGCUCCGAAUUUUGUGGGCGGAGCAAAUGGAGGAGGAGGAGGA______AUCGAGUGGACAGCUGGAAACGGAAA_AUAGAAGAAAAGCCAUGUCUCCUCUUCUUCCCACGUCGG
..((..((((((..(.....)..))))))....((((((((((((((........((..........(((....)))..........)).........))))))))))))))......)) (-32.26 = -33.01 +   0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,830,783 – 9,830,901
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.28
Mean single sequence MFE -25.55
Consensus MFE -21.55
Energy contribution -22.05
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.84
SVM decision value 1.07
SVM RNA-class probability 0.910318
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9830783 118 - 23771897
AAUAUGAGAAAAUAUGGGAGGAGUGGG--UUUAUAAACAGGCCCAAAAACCUGAAACCGAAACUCGUAGACCCAUUCAUACGAAUGGAAAUGCCACAAAAUACUAUAUUUAUAACAUCUG
.........((((((((...(((((((--(((((...((((........)))).....(.....))))))))))))).......(((.....))).......)))))))).......... ( -28.10)
>DroSec_CAF1 124748 118 - 1
AAUACAUGAAAAUAUGGGAGGGGUGGU--CUUAUAAACAGGCCCAAAAACCUGAAACCGAAACUCGUAAACCCAUUCAUACGAAUGGAUCUGCCACAAAAUACUAUAUUUAUAACAUCUG
.........((((((((.....(((((--........((((........))))..................((((((....))))))....)))))......)))))))).......... ( -25.00)
>DroSim_CAF1 128063 118 - 1
AAUACAUGAAAAUAUGGGAGGGGUGGG--UUCAUAAACAGGCCCAAAAACCUGAAACCGAAACUCGUAAACCCAUUCAUACGAAUGGAACUGCCACAAAAUACUAUAUUUAUAACAUCUG
.........((((((((.(((..((((--((........))))))....))).............(((...((((((....))))))...))).........)))))))).......... ( -24.50)
>DroYak_CAF1 138010 120 - 1
AAUACAUGAAAAUAUGGAAGGGGUGGGGUUUUAUAAACAGGCCCGAAAACCUGAAACCGAAACUCGUAAACCCAUUCAUACGCAUGGAACUGCCACAAAAUACUAUUUUUAUAACAUCUG
.....(((((((((..(((.((((.(((((((.....((((........)))).....)))))))....)))).)))....(((......)))..........)))))))))........ ( -24.60)
>consensus
AAUACAUGAAAAUAUGGGAGGGGUGGG__UUUAUAAACAGGCCCAAAAACCUGAAACCGAAACUCGUAAACCCAUUCAUACGAAUGGAACUGCCACAAAAUACUAUAUUUAUAACAUCUG
.........((((((((.....((((...........((((........))))..................((((((....)))))).....))))......)))))))).......... (-21.55 = -22.05 +   0.50)

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 10:56:17 2006