Locus 1269

Sequence ID 3R_DroMel_CAF1
Location 3,782,567 – 3,782,709
Length 142
Max. P 0.989182
window2072 window2073

overview

Window 2

Location 3,782,567 – 3,782,671
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.73
Mean single sequence MFE -26.90
Consensus MFE -15.92
Energy contribution -17.16
Covariance contribution 1.24
Combinations/Pair 1.11
Mean z-score -1.96
Structure conservation index 0.59
SVM decision value -0.02
SVM RNA-class probability 0.525826
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3782567 104 + 27905053
CAGAUGUUUAAAAAUCACUAAACGCAUUACACUGACUAUAACCUUAUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGUCGCAGUUUCCUACUGAUACUGGGGCA----------------
..(.((((((........)))))))................(((..(((((.(((.....))).))))).)))...(((.((((.((.....)).)))).))).---------------- ( -19.30)
>DroSec_CAF1 11994 115 + 1
CAGAUGUUUAAAAAUCACUAAAC-----ACACUGACCAUAACCUUGUGUUUUGGAAAUUAUCUUGAGCACAGGAAUGCCCCAGUUUCCUACUGAUACUGGGGCAAUUGACGACUGUUCUA
(((.((((((........)))))-----)..)))........(((((((((.(((.....))).)))))))))..(((((((((.((.....)).)))))))))................ ( -35.60)
>DroSim_CAF1 15708 117 + 1
CAGAUGUUUAAAAAUCACUAAACGCAUUACACUGACCAUAACCUUGUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGACCCAGUUUCCUACUGAUACUGGGGCAAUUG---ACUGUUCUA
(((..(((((........)))))((.................(((((((((.(((.....))).))))))))).....((((((.((.....)).)))))))).....---.)))..... ( -29.50)
>DroEre_CAF1 2340 117 + 1
CAGAUGUUUAAAAAGCACUAAUCGCAUUACACUGGCCAUAACCUUAUGUUUUGGAAAUUAUCUUGAGUACAGGAAAGGCCCAGUAUCCAACGGAUACUAGGGCAAUAA---AUUGUUCUA
.(((.(((((.......((..((.((..(((..((......))...)))..)))).....(((((....))))).))(((((((((((...))))))).))))..)))---))...))). ( -27.40)
>DroYak_CAF1 15718 114 + 1
CAGAUGUUUAAAAAGCACUAAUCGCA---CACUGACCAUAGCCUUAUGUUUUAGAAAAUAUCUUGAGUACAGGAAAGCCCCAGUAUCCAACUGAUACCAGGGCAAUAU---AUUGUUCUA
.((((((((.....((.......)).---..((((.((((....))))..)))).))))))))..((.((((....((((..(((((.....)))))..)))).....---.)))).)). ( -22.70)
>consensus
CAGAUGUUUAAAAAUCACUAAACGCAUUACACUGACCAUAACCUUAUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGCCCCAGUUUCCUACUGAUACUGGGGCAAUAG___ACUGUUCUA
(((.(((.....................)))))).(((.(((.....))).)))......(((((....)))))..((((((((.((.....)).))))))))................. (-15.92 = -17.16 +   1.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,782,607 – 3,782,709
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.49
Mean single sequence MFE -34.80
Consensus MFE -21.88
Energy contribution -24.00
Covariance contribution 2.12
Combinations/Pair 1.11
Mean z-score -2.79
Structure conservation index 0.63
SVM decision value 2.15
SVM RNA-class probability 0.989182
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3782607 102 + 27905053
ACCUUAUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGUCGCAGUUUCCUACUGAUACUGGGGCA------------------AUAUUGGCACUCAGCUAUUAUCGGUGGGAUAUGAUGGC
.(((..(((((.(((.....))).))))).)))...((((((...((((((((((((((((((.------------------......)).)))))....)))))))))))..)).)))) ( -32.90)
>DroSec_CAF1 12029 117 + 1
ACCUUGUGUUUUGGAAAUUAUCUUGAGCACAGGAAUGCCCCAGUUUCCUACUGAUACUGGGGCAAUUGACGACUGUUCUACAAUAUUGGCAUUCAGCUAUUAUCG---GGAUAUGAUGGC
..(((((((((.(((.....))).)))))))))..(((((((((.((.....)).))))))))).....((.(((((((...(((.((((.....)))).))).)---))))).).)).. ( -38.10)
>DroSim_CAF1 15748 114 + 1
ACCUUGUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGACCCAGUUUCCUACUGAUACUGGGGCAAUUG---ACUGUUCUACAAUAUUGGCAUUCAGCUAUUAUCG---GGAUAUGAUGGC
..(((((((((.(((.....))).))))))))).....((((((.((.....)).)))))).....((---(.((((..........)))).)))((((((((..---....)))))))) ( -31.00)
>DroEre_CAF1 2380 117 + 1
ACCUUAUGUUUUGGAAAUUAUCUUGAGUACAGGAAAGGCCCAGUAUCCAACGGAUACUAGGGCAAUAA---AUUGUUCUAGAAUAUUGGAACUCAGCCAUUAUCGGUGGAGUAUGAUGGC
.((..(((((((((((....(((((....)))))...(((((((((((...))))))).)))).....---....))))))))))).))......(((((((((......).)))))))) ( -40.40)
>DroYak_CAF1 15755 110 + 1
GCCUUAUGUUUUAGAAAAUAUCUUGAGUACAGGAAAGCCCCAGUAUCCAACUGAUACCAGGGCAAUAU---AUUGUUCUACAAUAUUG-------CCCAUUAUCGGUGGAGUAUGAUGGC
((((((((............(((((....)))))...........((((.((((((...(((((((((---..((.....))))))))-------)))..)))))))))).))))).))) ( -31.60)
>consensus
ACCUUAUGUUUUGGAAAUUAUCUUGAGCACAGGAAAGCCCCAGUUUCCUACUGAUACUGGGGCAAUAG___ACUGUUCUACAAUAUUGGCACUCAGCUAUUAUCGGUGGGAUAUGAUGGC
.((..(((((.(((((....(((((....)))))..((((((((.((.....)).))))))))............))))).))))).))......((((((((.........)))))))) (-21.88 = -24.00 +   2.12)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:13 2006