Locus 1139

Sequence ID 3R_DroMel_CAF1
Location 3,402,270 – 3,402,430
Length 160
Max. P 0.987101
window1872 window1873

overview

Window 2

Location 3,402,270 – 3,402,390
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -39.23
Consensus MFE -36.69
Energy contribution -37.03
Covariance contribution 0.34
Combinations/Pair 1.08
Mean z-score -1.83
Structure conservation index 0.94
SVM decision value 0.50
SVM RNA-class probability 0.759025
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3402270 120 + 27905053
GGUCUCCCUGUACUAUUAAAUGGCUUGUGCGAGAGGUGUCAGAUUCCCCAUCCGAUAACCCAUUGCUAGGAGCAGGUUGCUCCGAUAAGUUAGGGCCACCUGUGCGGUCUACCACGAAUU
(((....((((((.......((((((((((((..((((((.(((.....))).))).)))..))))..(((((.....))))).))))))))((....)).))))))...)))....... ( -37.10)
>DroSec_CAF1 423 120 + 1
GGUUUCUGUGUACUAUUAAAUGGCUUGUGCGAGAGGUGUCAGAUUCCCCAUUUGAUAACCCAUUGCUAGGAGCAGGUUGCUCCAAUAAGUUAGGACCACCUGAGUGGUCUCCCACGAAUU
...(((.(((..........((((((((((((..((((((((((.....))))))).)))..))))..(((((.....))))).))))))))(((((((....)))))))..)))))).. ( -40.30)
>DroSim_CAF1 11203 120 + 1
GGUUUCUGUGUACUAUUAAAUGGCUUGUGCGAGAGGUGUCAGAUUUCCCAUUUGAUAACCCAUUGCUAGGAGCAGGUUGCUCCAAUAAGUUAGGACCACCUGAGUGGUCUCCCACGAAUU
...(((.(((..........((((((((((((..((((((((((.....))))))).)))..))))..(((((.....))))).))))))))(((((((....)))))))..)))))).. ( -40.30)
>consensus
GGUUUCUGUGUACUAUUAAAUGGCUUGUGCGAGAGGUGUCAGAUUCCCCAUUUGAUAACCCAUUGCUAGGAGCAGGUUGCUCCAAUAAGUUAGGACCACCUGAGUGGUCUCCCACGAAUU
......((((..........((((((((((((..((((((((((.....))))))).)))..))))..(((((.....))))).))))))))(((((((....)))))))..)))).... (-36.69 = -37.03 +   0.34) 

alignment

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secondary structure

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dotplot

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Window 3

Location 3,402,310 – 3,402,430
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.31
Mean single sequence MFE -35.58
Consensus MFE -19.96
Energy contribution -21.32
Covariance contribution 1.36
Combinations/Pair 1.21
Mean z-score -2.40
Structure conservation index 0.56
SVM decision value 2.07
SVM RNA-class probability 0.987101
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3402310 120 - 27905053
UCCGACAGAGCACUUGACCAGCACCCUUGGUUUAUUUCUUAAUUCGUGGUAGACCGCACAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGGUUAUCGGAUGGGGAAUCU
......(((......((((((.....))))))...((((..((((((((....))))...((((((((...((....(((((.....))))).))....))))))))))))..))))))) ( -35.60)
>DroSec_CAF1 463 120 - 1
UCCGACAGAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGGAAUCU
(((..((((.((((((((((((...)))))...............((((....))))))))))).)).((((((((((((((.....)))))....))))))))).....)).))).... ( -40.60)
>DroSim_CAF1 11243 120 - 1
UCCGACAGAGCACUUGACCAGGACCCUUGGCUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGAAAUCU
(((....((.((((((((((((...)))))...............((((....))))))))))).)).((((((((((((((.....)))))....))))))))).......)))..... ( -40.20)
>DroEre_CAF1 9450 103 - 1
UCCGACAGAGAACUUGACCAGUGCCCUUGGUUGACUUCUUAAUUCGUGGGAGACCA---------------CUUAUCGCAGGAACCUCCUCCUUGCAAUGGCUUAUCAAAUUUGGAAU--
(((((..(((((.(..(((((.....)))))..).))))).....((((....)))---------------).....((((((......))).)))...............)))))..-- ( -30.70)
>DroYak_CAF1 14683 100 - 1
UCCG-------------------CCUUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUGG-GCUUCCCCAACUUAUCAGAAGAAUCUCCUCCUUCCAAUGAGUUAUCAAAUGUGGAACCU
((((-------------------(.((((((..............((((....)))).((-(....)))(((((((..((((.........))))..))))))))))))).))))).... ( -30.80)
>consensus
UCCGACAGAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGGAAUCU
(((............((((((.....))))))(((((..((((((((((....))))....................(((((.....))))).......))))))..))))).))).... (-19.96 = -21.32 +   1.36) 

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 10:02:03 2006