Locus 3459

Sequence ID 3R_DroMel_CAF1
Location 9,358,916 – 9,359,013
Length 97
Max. P 0.999010
window5550 window5551

overview

Window 0

Location 9,358,916 – 9,359,013
Length 97
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 94.76
Mean single sequence MFE -22.20
Consensus MFE -18.22
Energy contribution -18.66
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.81
Structure conservation index 0.82
SVM decision value 0.98
SVM RNA-class probability 0.894152
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9358916 97 + 27905053
AG-GAAUAAAGCCACCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUC-CGGAAUCCGGGAAAAAAACCGGACUCAUGUACUCAUGG-----
.(-(.......)).(((......(((((((.....................)))))))..-)))..(((((........)))))..((((....)))).----- ( -19.80)
>DroSec_CAF1 128600 96 + 1
AG-GAAUAAAGCCGCCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUC-CGGAAUCCGGGAAA-AACCCGGACUCAUGUACUCAUAG-----
.(-(.......))....(((...(((((((.....................)))))))..-..((.((((((...-..)))))).)).)))........----- ( -20.70)
>DroSim_CAF1 137454 103 + 1
AGGGAAUAAAGCCGCCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUCCCGGAAUCCGGGAAA-AACCCAGACUCAUGUACUCAUGGAAUCA
.(((...................(((((((.....................)))))))((((((...))))))..-..))).((.(((((....)))))..)). ( -24.70)
>DroEre_CAF1 128879 96 + 1
AG-GAAUAAAGCCGCCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUC-CGGAAUCCGGGAAA-AACCCGGACUCAUGUACUCGUGG-----
..-........((((..(((...(((((((.....................)))))))..-..((.((((((...-..)))))).)).)))....))))----- ( -24.30)
>DroYak_CAF1 129129 96 + 1
AG-GAAUAAAGCCGCCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUC-CGGAAUCCGGGAAA-AACCCGGACUCAUGUACUCAUGG-----
.(-(.......)).(((......(((((((.....................)))))))..-)))..((((((...-..))))))..((((....)))).----- ( -21.50)
>consensus
AG_GAAUAAAGCCGCCGACAAACGAUGCAUAAAUAAAUAAUACCUACAAACGUGCGUCUC_CGGAAUCCGGGAAA_AACCCGGACUCAUGUACUCAUGG_____
..............(((......(((((((.....................)))))))...)))..((((((......))))))..((((....))))...... (-18.22 = -18.66 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,358,916 – 9,359,013
Length 97
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 94.76
Mean single sequence MFE -28.98
Consensus MFE -27.34
Energy contribution -27.22
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -2.01
Structure conservation index 0.94
SVM decision value 3.33
SVM RNA-class probability 0.999010
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9358916 97 - 27905053
-----CCAUGAGUACAUGAGUCCGGUUUUUUUCCCGGAUUCCG-GAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGUGGCUUUAUUC-CU
-----((((........((((((((........))))))))..-..((((.(((..((((((((.....))))))))...))).)))).))))........-.. ( -25.40)
>DroSec_CAF1 128600 96 - 1
-----CUAUGAGUACAUGAGUCCGGGUU-UUUCCCGGAUUCCG-GAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGCGGCUUUAUUC-CU
-----....(((((...(((((((((..-...)))))))))((-..((((.(((..((((((((.....))))))))...))).))))..))....)))))-.. ( -30.20)
>DroSim_CAF1 137454 103 - 1
UGAUUCCAUGAGUACAUGAGUCUGGGUU-UUUCCCGGAUUCCGGGAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGCGGCUUUAUUCCCU
.(((((.(((....)))))))).(((..-..((((((...))))))((((.(((..((((((((.....))))))))...))).))))............))). ( -28.60)
>DroEre_CAF1 128879 96 - 1
-----CCACGAGUACAUGAGUCCGGGUU-UUUCCCGGAUUCCG-GAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGCGGCUUUAUUC-CU
-----....(((((...(((((((((..-...)))))))))((-..((((.(((..((((((((.....))))))))...))).))))..))....)))))-.. ( -30.50)
>DroYak_CAF1 129129 96 - 1
-----CCAUGAGUACAUGAGUCCGGGUU-UUUCCCGGAUUCCG-GAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGCGGCUUUAUUC-CU
-----....(((((...(((((((((..-...)))))))))((-..((((.(((..((((((((.....))))))))...))).))))..))....)))))-.. ( -30.20)
>consensus
_____CCAUGAGUACAUGAGUCCGGGUU_UUUCCCGGAUUCCG_GAGACGCACGUUUGUAGGUAUUAUUUAUUUAUGCAUCGUUUGUCGGCGGCUUUAUUC_CU
.........((((....(((((((((......)))))))))((...((((.(((..((((((((.....))))))))...))).))))..))))))........ (-27.34 = -27.22 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:01:31 2006