Locus 1876

Sequence ID 3L_DroMel_CAF1
Location 5,241,340 – 5,241,471
Length 131
Max. P 0.889534
window2922 window2923

overview

Window 2

Location 5,241,340 – 5,241,431
Length 91
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 82.09
Mean single sequence MFE -22.57
Consensus MFE -15.34
Energy contribution -16.34
Covariance contribution 1.00
Combinations/Pair 1.09
Mean z-score -2.15
Structure conservation index 0.68
SVM decision value 0.94
SVM RNA-class probability 0.886887
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5241340 91 - 23771897
AAUUGACGCUUUUGCGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAAUCU-------------------ACAUUCGAA
.((..((((....))))..)).(((((((((((((......)))))))))))))...((((.....))))............-------------------......... ( -23.70)
>DroSec_CAF1 105670 110 - 1
AAUUGACGCUUUUACGUUGGUAACAUUGGUCGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAAUCUAAAAUGAUUAUAAAGUUAUACAUUCGAA
..((((.((((((((....)))((((((((..(((......)))..))))))))))))).........(((.(((((((((......)))))...)))).)))..)))). ( -21.10)
>DroSim_CAF1 101734 110 - 1
AAUUGACGCUUUUGCGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAAUCUAAAAUGAUUAUAAAGUUAUACAUUCGAA
.((..((((....))))..)).(((((((((((((......)))))))))))))..............(((.(((((((((......)))))...)))).)))....... ( -27.70)
>DroEre_CAF1 108765 102 - 1
AAUUGACGCAUUUACUUUGGUAACACUGAUUGAGCCAUUUUGCUUAAUUAAUGUAAUGCUUGCACAAAGUACAAUUUAAUCUAAAAGGAUUAUAAAGUAAUA--------
...........((((((((...(((.(((((((((......))))))))).)))..(((((.....))))).....((((((....))))))))))))))..-------- ( -21.40)
>DroYak_CAF1 108134 110 - 1
AAUUGACGCAUUUACGUUGGUAAACUUGAUUGCGUCGUUUUGCCUAAUUUAUGUAAAGCUUUCACAAAGUACCAUUUAAUCGAAAAUUAUUAUCAAGUUAUACAUUGGAA
....((((((.(((.(((....))).))).))))))(((((((.........))))))).(((.(((.(((..((((.................))))..))).)))))) ( -18.93)
>consensus
AAUUGACGCUUUUACGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAAUCUAAAAUGAUUAUAAAGUUAUACAUUCGAA
.((..(((......)))..)).(((((((((((((......)))))))))))))...((((.....))))........................................ (-15.34 = -16.34 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,241,352 – 5,241,471
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 85.06
Mean single sequence MFE -28.72
Consensus MFE -18.22
Energy contribution -19.04
Covariance contribution 0.82
Combinations/Pair 1.14
Mean z-score -2.73
Structure conservation index 0.63
SVM decision value 0.96
SVM RNA-class probability 0.889534
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5241352 119 - 23771897
UUUUGUUUUGGUGUUUUGGCAAAGUUUUGAGCACUUAUUCAAUUGACGCUUUUGCGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAA
..........((((((((..((((((((.............((..((((....))))..)).(((((((((((((......)))))))))))))))))))))..))))))))....... ( -34.60)
>DroSec_CAF1 105701 117 - 1
UUUUGUUUUCGUA--CUGGCAAAGUUUUGGGCACUUAUUCAAUUGACGCUUUUACGUUGGUAACAUUGGUCGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAA
..........(((--((.(.((((((((.............((..(((......)))..)).((((((((..(((......)))..)))))))))))))))))....)))))....... ( -27.40)
>DroSim_CAF1 101765 117 - 1
UUUUGUUUUCGUA--CUGGCAAAGUUUUGGGCACUUAUUCAAUUGACGCUUUUGCGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAA
..........(((--((.(.((((((((.............((..((((....))))..)).(((((((((((((......))))))))))))))))))))))....)))))....... ( -34.20)
>DroEre_CAF1 108788 117 - 1
UUUUGUUUUCGCA--UUGGCAAAGUUUUUGGCAGUUAUUCAAUUGACGCAUUUACUUUGGUAACACUGAUUGAGCCAUUUUGCUUAAUUAAUGUAAUGCUUGCACAAAGUACAAUUUAA
((((((.(..(((--((..((((((.....((.((((......))))))....))))))...(((.(((((((((......))))))))).))))))))..).)))))).......... ( -27.90)
>DroYak_CAF1 108165 101 - 1
UUUUGUUU------------------UUCGGCAGUUAUUAAAUUGACGCAUUUACGUUGGUAAACUUGAUUGCGUCGUUUUGCCUAAUUUAUGUAAAGCUUUCACAAAGUACCAUUUAA
((((((..------------------..................((((((.(((.(((....))).))).))))))(((((((.........)))))))....)))))).......... ( -19.50)
>consensus
UUUUGUUUUCGUA__CUGGCAAAGUUUUGGGCACUUAUUCAAUUGACGCUUUUACGUUGGUAACAUUGGUUGAGCCAUUUUGCUUAAUUAAUGUAAAGCUUUCACAAAGUACAAUUUAA
((((((....((......)).........(((.........((..(((......)))..)).(((((((((((((......)))))))))))))...)))...)))))).......... (-18.22 = -19.04 +   0.82)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:53 2006