Locus 849

Sequence ID 3R_DroMel_CAF1
Location 2,884,886 – 2,885,045
Length 159
Max. P 0.924691
window1350 window1351 window1352

overview

Window 0

Location 2,884,886 – 2,885,005
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 93.00
Mean single sequence MFE -27.23
Consensus MFE -24.59
Energy contribution -24.70
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.61
Structure conservation index 0.90
SVM decision value -0.05
SVM RNA-class probability 0.506589
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2884886 119 + 27905053
AUUAAGUUCUUUUGGAUCUAAGAGUUUCGUGGGAGACGAUAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUAAACUUGUAUAGUUUUGGGGGCAGG
.....(((.(((..((((...(((.((..(.(....).)..))...)))((((((((......))))))))))))..))).)))..((((....(((((.....)))))....)))).. ( -28.10)
>DroSec_CAF1 6558 111 + 1
AUUAAGUUCUUUUGGA--------UUUCUUGGGAGACGAAAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUGAACUUGUAUAGUUUUGGGGGCAGG
..(((((((..((((.--------..(((..((....(((....)))((((((((((......))))))))))))..)))........))))..))))))).................. ( -24.50)
>DroSim_CAF1 5336 119 + 1
AUUAAGUUCUUUUGGAUCCAAGAGUUUCUUGGGAGACGAUAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUGAACUUGUAAAGUUUUGGGGGCAGG
..(((((((..((((.((((((.....)))))).........(((((((((((((((......))))))))))...))))).......))))..))))))).................. ( -29.10)
>consensus
AUUAAGUUCUUUUGGAUC_AAGAGUUUCUUGGGAGACGAUAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUGAACUUGUAUAGUUUUGGGGGCAGG
.....(((.(((..((.......(((((....)))))..........((((((((((......))))))))))))..))).)))..((((....(((((.....)))))....)))).. (-24.59 = -24.70 +   0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,884,886 – 2,885,005
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 93.00
Mean single sequence MFE -15.94
Consensus MFE -13.19
Energy contribution -12.97
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.35
Structure conservation index 0.83
SVM decision value 0.40
SVM RNA-class probability 0.721963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2884886 119 - 27905053
CCUGCCCCCAAAACUAUACAAGUUUAACUGACAUUAUUAUCUCAGAUCAUCAGAUCAAAAUCAAUCUAAUGAGAAAUUUAUCGUCUCCCACGAAACUCUUAGAUCCAAAAGAACUUAAU
...................((((((...................((((....)))).......((((((.(((.......((((.....))))..)))))))))......))))))... ( -13.90)
>DroSec_CAF1 6558 111 - 1
CCUGCCCCCAAAACUAUACAAGUUCAACUGACAUUAUUAUCUCAGAUCAUCAGAUCAAAAUCAAUCUAAUGAGAAAUUUUUCGUCUCCCAAGAAA--------UCCAAAAGAACUUAAU
...................((((((..((((.((....)).)))).((((.((((........)))).)))).......................--------.......))))))... ( -13.80)
>DroSim_CAF1 5336 119 - 1
CCUGCCCCCAAAACUUUACAAGUUCAACUGACAUUAUUAUCUCAGAUCAUCAGAUCAAAAUCAAUCUAAUGAGAAAUUUAUCGUCUCCCAAGAAACUCUUGGAUCCAAAAGAACUUAAU
...................((((((....(((..((...(((((((((....)))).............)))))....))..)))..(((((.....)))))........))))))... ( -20.11)
>consensus
CCUGCCCCCAAAACUAUACAAGUUCAACUGACAUUAUUAUCUCAGAUCAUCAGAUCAAAAUCAAUCUAAUGAGAAAUUUAUCGUCUCCCAAGAAACUCUU_GAUCCAAAAGAACUUAAU
...................((((((..((((.((....)).)))).((((.((((........)))).))))......................................))))))... (-13.19 = -12.97 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,884,925 – 2,885,045
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.72
Mean single sequence MFE -29.27
Consensus MFE -25.34
Energy contribution -25.65
Covariance contribution 0.31
Combinations/Pair 1.19
Mean z-score -1.98
Structure conservation index 0.87
SVM decision value 1.16
SVM RNA-class probability 0.924691
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2884925 120 + 27905053
UAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUAAACUUGUAUAGUUUUGGGGGCAGGUUAGAUCUCAGAUUCAGUUUAGAUCCUGAUUCCACAGACA
........((((((((((......))))))))))((((((((.....((((....(((((.....)))))....))))......)))))))).((((........))))........... ( -31.50)
>DroSec_CAF1 6589 120 + 1
AAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUGAACUUGUAUAGUUUUGGGGGCAGGUUAGAUCUCAGAUUCAGUUUAGAUCCUGAUUCCACAGACA
........((((((((((......))))))))))((((((((.....((((....(((((.....)))))....))))......)))))))).((((........))))........... ( -31.90)
>DroSim_CAF1 5375 120 + 1
UAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUGAACUUGUAAAGUUUUGGGGGCAGGUUAGAUCUCAGAUUCAGUUUAGAUUCUGAUUCCACAGACA
((((((..((((((((((......))))))))))((((((((.....((((....(((((.....)))))....))))......))))))))...))))))...((((......)))).. ( -32.30)
>DroEre_CAF1 6612 120 + 1
UAAAUUUCUUAUUAGAUUUAUUUUAAACAUGUUAUCUGAGAUAAUAAUGUCAGUAAAACUUGUAAAAUUUUGGAAACGGGGUACAUCUCGGAUUCAGUUCAGGUCCUGAUUCCACAGACG
(((((((......)))))))......(((.(((..((((.((....)).))))...))).)))...((((((....)))))).......(((.((((........)))).)))....... ( -21.40)
>consensus
UAAAUUUCUCAUUAGAUUGAUUUUGAUCUGAUGAUCUGAGAUAAUAAUGUCAGUUAAACUUGUAAAGUUUUGGGGGCAGGUUAGAUCUCAGAUUCAGUUUAGAUCCUGAUUCCACAGACA
........((((((((((......))))))))))((((((((.....((((....(((((.....)))))....))))......)))))))).((((........))))........... (-25.34 = -25.65 +   0.31)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:42 2006