Locus 5417

Sequence ID 3R_DroMel_CAF1
Location 14,274,070 – 14,274,201
Length 131
Max. P 0.853991
window8814 window8815

overview

Window 4

Location 14,274,070 – 14,274,181
Length 111
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 79.64
Mean single sequence MFE -19.14
Consensus MFE -13.92
Energy contribution -13.70
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -1.68
Structure conservation index 0.73
SVM decision value 0.80
SVM RNA-class probability 0.853991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14274070 111 - 27905053
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAACCAACACACACACACA----CGUGCGAACGAAUGUGCAAAAAAAAAACAAGACUAA
(((...((((((......))))))......))).....((((((........)).))))..........((((..----(((....)))..)))).................... ( -19.50)
>DroPse_CAF1 57854 87 - 1
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAGGCAGC---------CA----C---------------CAAAAAGAAAAAGAGACGAA
(((...((((((......))))))......))).....(((((...............))))).---------..----.---------------.................... ( -14.56)
>DroSim_CAF1 44753 114 - 1
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAACCAACACACACAGACACACACGUGCAAACGUAUGUGC-AAAAAAAAACACGACUAA
(((...((((((......))))))......))).....((((((........)).))))............(.((((.((((....)))).)))))-.................. ( -22.50)
>DroEre_CAF1 55422 108 - 1
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAACCGAAACACGCACACA----CGUGCACACGUAUGUGCAAAA---AAACACGACUAA
(((...((((((......))))))......))).....((((((........)).)))).........(((((.(----(((....)))).)))))....---............ ( -26.20)
>DroYak_CAF1 50173 106 - 1
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAACCAAAACACACACAC--------GCAUACG-AUGUGCAAAAAAAAAACACGACUAA
(((...((((((......))))))......))).....((((((........)).))))...............--------((((...-..))))................... ( -17.50)
>DroPer_CAF1 58184 87 - 1
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAGGCAGC---------CA----C---------------CAAAAAGAAAAAGAGACGAA
(((...((((((......))))))......))).....(((((...............))))).---------..----.---------------.................... ( -14.56)
>consensus
GCUUAUGGGUCGUAAAGUUGACCUUCAAACAGCAACAUUUGCCGAAAAAAUACGAGCAACCAACACACACACACA____C__GCA_ACG_AUGUGCAAAAAAAAAACAAGACUAA
(((...((((((......))))))......))).....((((((........)).))))........................................................ (-13.92 = -13.70 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 14,274,106 – 14,274,201
Length 95
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 75.16
Mean single sequence MFE -17.49
Consensus MFE -11.02
Energy contribution -11.35
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.63
SVM decision value 0.52
SVM RNA-class probability 0.766506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14274106 95 - 27905053
----CA-AAAACACACA-------------UU-U-UUGGCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA-GCAACAUUUGCCGAAA---AAAUACGAGCAACCAACACACACACACA
----..-..........-------------..-.-((((.(((...((((((......))))))......)-)).....((((((...---.....)).))))))))............ ( -16.80)
>DroPse_CAF1 57875 103 - 1
ACAACA-CACACACACAUGAGCACAAUUUUUU-U-UUUGCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA-GCAACAUUUGCCGAAA---AAAUACGAGCAGGCAGC---------CA
......-........(((((((.(((......-.-.))).)))))))(((((......)))))........-.......(((((....---...........))))).---------.. ( -22.76)
>DroEre_CAF1 55455 95 - 1
----CG-AAAACACACA-------------UU-U-UUGGCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA-GCAACAUUUGCCGAAA---AAAUACGAGCAACCGAAACACGCACACA
----..-..........-------------.(-(-((((.(((...((((((......))))))......)-)).....((((((...---.....)).)))))))))).......... ( -18.30)
>DroWil_CAF1 55556 87 - 1
----CA-AAAACAUUUU-------------UUUU-UUUUUGCCUUUGGGUCGUA-AGUUGACCUUCAAACAAGCAACAUUUGCCGAAA---AAAUACGAACAUACACA---------CA
----..-.....(((((-------------(((.-...(((.....((((((..-...)))))).....)))(((.....))).))))---)))).............---------.. ( -11.80)
>DroAna_CAF1 45742 100 - 1
----CGCAAAACACACA-------------UU-UUUUUGCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA-GCAACAUUUGCCGAAAAAAAAAUACGAGCAACCAAAAAACACACUCA
----.((((((......-------------..-.))))))((((..((((((......)))))).....(.-(((.....))).)............)))).................. ( -17.00)
>DroPer_CAF1 58205 99 - 1
A------CACACACACAUGAGCACAAUUUUUUUU-UUUUCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA-GCAACAUUUGCCGAAA---AAAUACGAGCAGGCAGC---------CA
.------........(((((((............-.....)))))))(((((......)))))........-.......(((((....---...........))))).---------.. ( -18.29)
>consensus
____CA_AAAACACACA_____________UU_U_UUUGCGCUUAUGGGUCGUAAAGUUGACCUUCAAACA_GCAACAUUUGCCGAAA___AAAUACGAGCAACCAAA_________CA
........................................((((..((((((......))))))........(((.....)))..............)))).................. (-11.02 = -11.35 +   0.33)

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 11:54:09 2006