Locus 1183

Sequence ID 3R_DroMel_CAF1
Location 3,571,947 – 3,572,154
Length 207
Max. P 0.701982
window1935 window1936

overview

Window 5

Location 3,571,947 – 3,572,056
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 86.65
Mean single sequence MFE -23.20
Consensus MFE -17.64
Energy contribution -17.60
Covariance contribution -0.04
Combinations/Pair 1.13
Mean z-score -1.73
Structure conservation index 0.76
SVM decision value 0.35
SVM RNA-class probability 0.701982
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3571947 109 + 27905053
AUCGCACACACUUAACGAGCACUUAAGCGUCUUCGCUUGGAGCUGCUUAGCUCGAAAUAUUAUGUUUAAUUAAAUAUGAGCUCAUAAUCGAGUUCUCCCAUUAAAC-CUG
...............(((((...((((((.((((....)))).))))))))))).........(((((((.......((((((......))))))....)))))))-... ( -26.70)
>DroSec_CAF1 22907 109 + 1
AUCGCACACACUUAACGAGCACUUAAGCGUCUUCGCUCGGAGCUGCUUAGCUCGAAAUAUUAUGUUUAAUUAAAUAUGAGCUCAUAAUCGGGUUCCCCCAUUAAGC-CUG
...((..........(((((...((((((.((((....)))).))))))))))).....((((((((....))))))))))...((((.(((....)))))))...-... ( -27.00)
>DroSim_CAF1 23266 109 + 1
AUCGCACACACUUAACGAGCACUUAAGCGUCUUCGCUCGGAGCUGCUUAGCUCGAAAUAUUAUGUUUAAUUAAAUAUGAGCUCAUAAUCGGGUUCCUCCAUUAAGC-CUG
...((..........(((((...((((((.((((....)))).))))))))))).....((((((((....)))))))))).......((((((.........)))-))) ( -26.60)
>DroEre_CAF1 28306 108 + 1
AUCGCACACACUUAACUAGCACUUAAGCGUCUUCGCUCGGAGCUGCUUAGCUCUAAAUAUUAUGUUUAAUUAAAUAUGAGCUCAUAAUCGAGUUGC-CCAUUAAAC-CUG
...(((...((((.....((......))......((((((((((....)))))).......((((((....))))))))))........)))))))-.........-... ( -19.60)
>DroAna_CAF1 18565 95 + 1
-------ACACUUAACGAGCUCUUAAACGUCUCC----UGAGCUGUUUAGCUCUAAAUAUUACAUUUAAUUAAAUAUGAGCUCAUAAUCGCUU-CUCC---UAACCCCGG
-------.........((((((............----.(((((....)))))(((((.....))))).........))))))..........-....---......... ( -16.10)
>consensus
AUCGCACACACUUAACGAGCACUUAAGCGUCUUCGCUCGGAGCUGCUUAGCUCGAAAUAUUAUGUUUAAUUAAAUAUGAGCUCAUAAUCGAGUUCCCCCAUUAAAC_CUG
................((((..(((((((.((((....)))).))))))).........((((((((....))))))))))))........................... (-17.64 = -17.60 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,572,056 – 3,572,154
Length 98
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 88.14
Mean single sequence MFE -22.36
Consensus MFE -15.07
Energy contribution -15.35
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -2.22
Structure conservation index 0.67
SVM decision value 0.22
SVM RNA-class probability 0.638515
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3572056 98 + 27905053
CUGA-------CCAGCUGGCCUAUCU---GCCAUUUUAUAGCCACUUUAUCUGUUUAAUUAAAAGCCUGGCUUUUAAUUGAAAUCGCUCUGAUAUCUAAGCUGUCACA
.(((-------(.(((((((......---)))...(((.(((...........(((((((((((((...)))))))))))))...))).)))......)))))))).. ( -23.24)
>DroSec_CAF1 23016 98 + 1
CUGA-------CCAGCUGGCCUAUCU---GCCAUUUUAUAGCCACUUUAUCUGUUUAAUUAAAAGCCUGGCUUUUAAUUGAAAUCGCUCUGAUAUCUGAGCUGUCACA
.(((-------(.(((((((......---)))..........((...((((.((((((((((((((...))))))))))))....))...))))..)))))))))).. ( -23.40)
>DroSim_CAF1 23375 98 + 1
CUGA-------CCAGCUGGCCUAUCU---GCCAUUUUAUAGCCACUUUAUCUGUUUAAUUAAAAGCCUGGCUUUUAAUUGAAAUCGCUCUGAUAUCUGAGCUGUCACA
.(((-------(.(((((((......---)))..........((...((((.((((((((((((((...))))))))))))....))...))))..)))))))))).. ( -23.40)
>DroEre_CAF1 28414 98 + 1
CUGA-------CCAGCUUGCCUAUCU---CCCACUUUAUAGCCACUUUAUCUGUUUAAUUAAAAGGCUGGCUUUUAAUUGAAAUCGCUCUGAUAUCUGAGCUGUCACA
.(((-------(.((((((..((((.---....((....))............((((((((((((.....))))))))))))........))))..)))))))))).. ( -19.60)
>DroAna_CAF1 18660 108 + 1
CUUGUCAGCUGCCGGCUGGCUUUCCUCUAUCCAUUUCAUAGCCACCUUAUCUGCUUAAUUAAAUGGUUGGCCUUUAAUUGAAAUCGCUCCGAUAUCUGACCUGUCACA
...(((((.....((.(((((..................))))))).((((.(((((((((((.((....)))))))))))....))...)))).)))))........ ( -22.17)
>consensus
CUGA_______CCAGCUGGCCUAUCU___GCCAUUUUAUAGCCACUUUAUCUGUUUAAUUAAAAGCCUGGCUUUUAAUUGAAAUCGCUCUGAUAUCUGAGCUGUCACA
............((((((((....................)))....((((.(((((((((((((.....)))))))))))....))...))))....)))))..... (-15.07 = -15.35 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:01 2006