Locus 573

Sequence ID 2R_DroMel_CAF1
Location 2,956,679 – 2,956,799
Length 120
Max. P 0.999302
window1047 window1048

overview

Window 7

Location 2,956,679 – 2,956,799
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.67
Mean single sequence MFE -29.85
Consensus MFE -19.89
Energy contribution -22.32
Covariance contribution 2.44
Combinations/Pair 1.22
Mean z-score -2.26
Structure conservation index 0.67
SVM decision value 2.03
SVM RNA-class probability 0.986236
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2956679 120 + 20766785
AAUGGAUCAAUACGAGUACGAUUGGGGAGAUCCCAAGGAUCUCUUGAACUUAAAGCCAAAUCUGUGGCAUUCAUAGCUACUGUUAAGUAUCGGAGAUUAUUGGGACACUCCCGAAUAAAA
.......((((.((....))))))(((((.((((((.(((((((.((((((((..........(((((.......)))))..)))))).))))))))).))))))..)))))........ ( -37.80)
>DroSec_CAF1 4005 120 + 1
AAUGGAUCAAUACGAGUACGAUUAGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCGAAGACUGUGGCAUUCACAACUACAUUAAGGUCUCUGAGAUUAUUGGAACACUCCCGAGUAAAA
................(((.....(((((((.((((.((((((.....(((((.(...((..((((.....)))).)).).)))))......)))))).)))).)).)))))..)))... ( -27.90)
>DroSim_CAF1 4098 120 + 1
AAUGGAUCAAUACGAGUACGAUUGGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCAGAGUCUGUUGCAUUGAGAGCUACUUUUAAGUUUCUGAGAUUAUUGGAACACUCCCGAAUAAAA
.......((((.((....))))))(((((((.((((.((((((...(((((((((...((.((.((.....)).))))..)))))))))...)))))).)))).)).)))))........ ( -34.40)
>DroEre_CAF1 4264 92 + 1
AAUUGAUCAAUACGA-UACGAUUGGGGAGGACCCGAAAAUCUCUUUAACUUAAAGCAAA---------------------------GUCGCUGAGAUUUUGAGAACACUCCUGAAUAAAA
((((((((.....))-).))))).(((((....(.((((((((....((((......))---------------------------))....))))))))..)....)))))........ ( -19.30)
>consensus
AAUGGAUCAAUACGAGUACGAUUGGGGAGGUCCCGAAAAUCUCUUCAACUUAAAGCAAAGUCUGUGGCAUUCA_AGCUACUUUUAAGUCUCUGAGAUUAUUGGAACACUCCCGAAUAAAA
....................(((.(((((((.((((.((((((....(((((((.......(((((.....))))).....)))))))....)))))).)))).)).))))).))).... (-19.89 = -22.32 +   2.44) 

alignment

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secondary structure

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dotplot

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Window 8

Location 2,956,679 – 2,956,799
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.67
Mean single sequence MFE -31.05
Consensus MFE -20.58
Energy contribution -20.70
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -2.85
Structure conservation index 0.66
SVM decision value 3.50
SVM RNA-class probability 0.999302
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2956679 120 - 20766785
UUUUAUUCGGGAGUGUCCCAAUAAUCUCCGAUACUUAACAGUAGCUAUGAAUGCCACAGAUUUGGCUUUAAGUUCAAGAGAUCCUUGGGAUCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((((..(((((....((((((((.......))...((((......)))).))))))....)))))..))))))))))))((((((....)).))))....... ( -36.10)
>DroSec_CAF1 4005 120 - 1
UUUUACUCGGGAGUGUUCCAAUAAUCUCAGAGACCUUAAUGUAGUUGUGAAUGCCACAGUCUUCGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCUAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((...(((.((((.(((((((((.....))))).))..)).)))))))...))))))...))))))))))((((((....)).))))....... ( -32.20)
>DroSim_CAF1 4098 120 - 1
UUUUAUUCGGGAGUGUUCCAAUAAUCUCAGAAACUUAAAAGUAGCUCUCAAUGCAACAGACUCUGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((...((((((((.((((.(((.........)))..))))))))))))...))))))...))))))))))((((((....)).))))....... ( -36.00)
>DroEre_CAF1 4264 92 - 1
UUUUAUUCAGGAGUGUUCUCAAAAUCUCAGCGAC---------------------------UUUGCUUUAAGUUAAAGAGAUUUUCGGGUCCUCCCCAAUCGUA-UCGUAUUGAUCAAUU
.........((((.(..((.((((((((...(((---------------------------((......)))))...)))))))).))..))))).((((((..-.)).))))....... ( -19.90)
>consensus
UUUUAUUCGGGAGUGUUCCAAUAAUCUCAGAGACUUAAAAGUAGCU_UGAAUGCCACAGACUUUGCUUUAAGUUGAAGAGAUUUUCGGGACCUCCCCAAUCGUACUCGUAUUGAUCCAUU
........(((((.(((((...((((((............((.((.......)).))....((.((.....)).)).))))))...))))))))))((((((....)).))))....... (-20.58 = -20.70 +   0.12) 

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 09:41:56 2006