Locus 1702

Sequence ID 2L_DroMel_CAF1
Location 4,652,134 – 4,652,290
Length 156
Max. P 0.939512
window2729 window2730

overview

Window 9

Location 4,652,134 – 4,652,250
Length 116
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 88.94
Mean single sequence MFE -23.25
Consensus MFE -17.58
Energy contribution -18.32
Covariance contribution 0.75
Combinations/Pair 1.16
Mean z-score -2.00
Structure conservation index 0.76
SVM decision value 0.66
SVM RNA-class probability 0.813438
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4652134 116 - 22407834
GCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGGAAAUACAGUUUAGCACAUAAAUCAAGACUUGUACUCACGGUCUUGCCAUCAAAGUUAUGA
..((((((...(((((((((.(((.((((........))))))).)))))))))((.......(((((.....)))))(((((((((....)).))))))))).......)))))) ( -27.10)
>DroSec_CAF1 88439 116 - 1
GCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUGGCACAUAAAUCAAGGCUUGUACUCACGGUCUUGCCAUCAAAGUUAUGA
..((((((...(((((((((.(((.((((........))))))).)))))))))............(((((.........(((((((....)).))))))))))......)))))) ( -26.60)
>DroSim_CAF1 80025 116 - 1
GCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUUUCACAUAAAUCAAGGCUUGUACUCACGGUCUUGCCAUCAAAGUUAUGA
..((((((...(((((((((.(((.((((........))))))).)))))))))(((((......)))))........(((((((((....)).))))))).........)))))) ( -27.00)
>DroEre_CAF1 91816 111 - 1
ACUCGUAAACAUUUUAUAUAUGCCCUGAAAACUUCUAUUCACGCCAACAUAA-----AAUACAGCAUAGCAAAUAAAUCAAGAAUAGUACUCACAGUUCUGCCAUCAAAGUUGUGG
..........(((((((....((..((((........)))).))....))))-----)))....((((((..........(((((.((....)).))))).........)))))). ( -12.31)
>consensus
GCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUAGCACAUAAAUCAAGACUUGUACUCACGGUCUUGCCAUCAAAGUUAUGA
..((((((...(((((((((.(((.((((........))))))).)))))))))........................(((((((.((....))))))))).........)))))) (-17.58 = -18.32 +   0.75)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,652,170 – 4,652,290
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.78
Mean single sequence MFE -22.73
Consensus MFE -18.42
Energy contribution -20.68
Covariance contribution 2.25
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.81
SVM decision value 1.30
SVM RNA-class probability 0.939512
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4652170 120 - 22407834
CUCGACUAAGAACAUUCAGAUUUAGAUGUUUUCCUUAUAGGCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGGAAAUACAGUUUAGCACAUAAAUCA
..................((((((..(((........((((((.(((....(((((((((.(((.((((........))))))).))))))))).....))))))))))))..)))))). ( -26.40)
>DroSec_CAF1 88475 120 - 1
CUCAGCUAAGAACAUUCAGAUUUAGAUGUUUUCCUUAUAGGCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUGGCACAUAAAUCA
....((((((((((((........)))))))).......((((.(((....(((((((((.(((.((((........))))))).))))))))).....))))))))))).......... ( -26.60)
>DroSim_CAF1 80061 120 - 1
CUCAGCUAAGAACUUUUAGAUUUAGAUGUUUUCCUUAUUGGCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUUUCACAUAAAUCA
..................((((((.(((....((.....))..))).....(((((((((.(((.((((........))))))).)))))))))(((((......)))))...)))))). ( -22.90)
>DroEre_CAF1 91852 112 - 1
CUUAGCUA---ACUAUCAGAUUUAGAUGUUUUCUUUAUGGACUCGUAAACAUUUUAUAUAUGCCCUGAAAACUUCUAUUCACGCCAACAUAA-----AAUACAGCAUAGCAAAUAAAUCA
....((((---.......((..((((.((((((((((((....))))))(((.......)))....)))))).)))).))..((........-----......)).)))).......... ( -15.04)
>consensus
CUCAGCUAAGAACAUUCAGAUUUAGAUGUUUUCCUUAUAGGCUCGUAAAUAUUUUAUGUACGCCCUGAAAACUUCUAUUCAGGCCUACAUAAAAGAAAAUACAGUUUAGCACAUAAAUCA
..................((((((..(((........((((((.(((....(((((((((.(((.((((........))))))).))))))))).....))))))))))))..)))))). (-18.42 = -20.68 +   2.25)

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 10:08:56 2006