Locus 1332

Sequence ID 3R_DroMel_CAF1
Location 3,927,072 – 3,927,178
Length 106
Max. P 0.999190
window2177 window2178

overview

Window 7

Location 3,927,072 – 3,927,178
Length 106
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 66.47
Mean single sequence MFE -18.65
Consensus MFE -8.32
Energy contribution -9.07
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 0.45
SVM decision value 1.53
SVM RNA-class probability 0.961504
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3927072 106 + 27905053
AUAAUCGUUUU-----UAUAUUCACAUUGACCUUUGUAGCC-AGCCGCUACAAAGUGGUAUAUAGUCGUUAGACAAUUUUAAGUUAUAAAUCCAUUUCUUUGUUAACACACC--------
......(..((-----((((..........((((((((((.-....))))))))).).......(((....)))..........))))))..)...................-------- ( -18.10)
>DroSec_CAF1 1917 107 + 1
AUAAUCAUUUG-----CAUAUUCACAUUGACCUUUGUAGCCCAUCCGCUACAAAGUAAUAUAUAGUCGUUAGACAAUUAUAAAUUAUAAACCCAUUUCUUUGUUAACACACC--------
...........-----.......(((..((.(((((((((......)))))))))...((((..(((....)))...))))...............))..))).........-------- ( -16.70)
>DroSim_CAF1 1951 107 + 1
AUAAUCAUUUG-----CAUAUUCACAUUGACCUUUGUAAAC-AGUCACUACAAAGUGGUAUAUAGU-------CAAUUAUAAAUUAUAAACCCAUUUCUUUGUUAACACACUUGUUAACA
...........-----...............(((((((...-......))))))).(((.((((((-------.........)))))).)))........((((((((....)))))))) ( -14.60)
>DroEre_CAF1 1915 90 + 1
AUUACCAUAUGGGUAUUAUAUUUACAUAGACCUUUGUAGCU-AAGCGCCACAAAGUGCUAUGUGAUUGUUAUUCAGUAAUAAAUUACU-------------------GC----------A
..((((.....))))..(((.((((((((..((((((.((.-....)).))))))..)))))))).)))....((((((....)))))-------------------).----------. ( -25.20)
>consensus
AUAAUCAUUUG_____CAUAUUCACAUUGACCUUUGUAGCC_AGCCGCUACAAAGUGGUAUAUAGUCGUUAGACAAUUAUAAAUUAUAAACCCAUUUCUUUGUUAACACACC________
...............................(((((((((......)))))))))................................................................. ( -8.32 =  -9.07 +   0.75)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,927,072 – 3,927,178
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 66.47
Mean single sequence MFE -23.88
Consensus MFE -12.94
Energy contribution -13.00
Covariance contribution 0.06
Combinations/Pair 1.26
Mean z-score -2.58
Structure conservation index 0.54
SVM decision value 3.42
SVM RNA-class probability 0.999190
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3927072 106 - 27905053
--------GGUGUGUUAACAAAGAAAUGGAUUUAUAACUUAAAAUUGUCUAACGACUAUAUACCACUUUGUAGCGGCU-GGCUACAAAGGUCAAUGUGAAUAUA-----AAAACGAUUAU
--------..((((((.(((..((..(((.((((.....))))...(((....)))......)))(((((((((....-.))))))))).))..))).))))))-----........... ( -23.40)
>DroSec_CAF1 1917 107 - 1
--------GGUGUGUUAACAAAGAAAUGGGUUUAUAAUUUAUAAUUGUCUAACGACUAUAUAUUACUUUGUAGCGGAUGGGCUACAAAGGUCAAUGUGAAUAUG-----CAAAUGAUUAU
--------.(((((((.(((..((..........((((.((((...(((....))))))).))))(((((((((......))))))))).))..))).))))))-----).......... ( -25.00)
>DroSim_CAF1 1951 107 - 1
UGUUAACAAGUGUGUUAACAAAGAAAUGGGUUUAUAAUUUAUAAUUG-------ACUAUAUACCACUUUGUAGUGACU-GUUUACAAAGGUCAAUGUGAAUAUG-----CAAAUGAUUAU
((((((((....))))))))........(((.((((.((.......)-------).)))).))).((((((((.....-..))))))))((((.(((......)-----))..))))... ( -19.60)
>DroEre_CAF1 1915 90 - 1
U----------GC-------------------AGUAAUUUAUUACUGAAUAACAAUCACAUAGCACUUUGUGGCGCUU-AGCUACAAAGGUCUAUGUAAAUAUAAUACCCAUAUGGUAAU
.----------.(-------------------(((((....))))))..........((((((..(((((((((....-.)))))))))..))))))........((((.....)))).. ( -27.50)
>consensus
________GGUGUGUUAACAAAGAAAUGGGUUUAUAAUUUAUAAUUGUCUAACGACUAUAUACCACUUUGUAGCGGCU_GGCUACAAAGGUCAAUGUGAAUAUA_____CAAAUGAUUAU
........................................(((((((((....)))(((((....(((((((((......)))))))))....)))))................)))))) (-12.94 = -13.00 +   0.06)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:57 2006