Locus 7918

Sequence ID 3L_DroMel_CAF1
Location 21,056,672 – 21,056,832
Length 160
Max. P 0.996644
window12913 window12914 window12915

overview

Window 3

Location 21,056,672 – 21,056,792
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -34.19
Consensus MFE -30.04
Energy contribution -30.56
Covariance contribution 0.52
Combinations/Pair 1.06
Mean z-score -1.63
Structure conservation index 0.88
SVM decision value 1.29
SVM RNA-class probability 0.940254
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056672 120 + 23771897
AGACGCUGCGUCAUCGGAUGGAAGAUCUGUUCAAAGUCCAAAGCGCCUUACUAUAAAUAGGCAAACAAUUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAG
.((((...)))).((((((((.....))))))((((((......((((..........)))).......(((((((((((((.(((.....))).))))))).))))))))))))..)). ( -31.90)
>DroSec_CAF1 111723 120 + 1
AGACGCUGCGUCAUCGGAUCGAAGAUCUGUUCAAAGUCCACAGCGCCUGACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAG
....((((.(....((((((...)))))).........).))))(((((........)))))......((((((((((((((.(((.....))).))))))).))))))).......... ( -34.02)
>DroSim_CAF1 17982 120 + 1
AGACGCUGCGUCAUCGGAUCGAAGAUCUGUUCAAAGUCCACAGCGCCUAACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAG
....((((.(....((((((...)))))).........).))))(((((........)))))......((((((((((((((.(((.....))).))))))).))))))).......... ( -34.82)
>DroEre_CAF1 34365 120 + 1
AGACGCUGCGUCAUCGGAUAGAAGAUCUGUUCAAAGUCCAAAGCGCCCAGCUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUCAGCG
...(((((.(((...((((((.....)))))).........(((.....))).......)))......((((((((((((((.(((.....))).))))))).))))))).....))))) ( -37.00)
>DroYak_CAF1 5173 119 + 1
AGACGCUGCGUCAUCGGAUCGAAGAUCUGUUCAAAGUCCAAAGCGCCUAGCUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGACUCU-UGCAGAUUUGUAGAUUUUCAGAG
.((((...))))...(((((..((((((((....((((....(((((((........)))))......((((.....))))......)).))))..-.))))))))...)))))...... ( -33.20)
>consensus
AGACGCUGCGUCAUCGGAUCGAAGAUCUGUUCAAAGUCCAAAGCGCCUAACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAG
.((((...))))...((((.(((......)))...)))).....(((((........)))))......((((((((((((((.(((.....))).))))))).))))))).......... (-30.04 = -30.56 +   0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,056,712 – 21,056,832
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.25
Mean single sequence MFE -35.40
Consensus MFE -32.60
Energy contribution -33.12
Covariance contribution 0.52
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.92
SVM decision value 1.93
SVM RNA-class probability 0.983122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056712 120 + 23771897
AAGCGCCUUACUAUAAAUAGGCAAACAAUUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
....(((...((((((((..((((....))))...(((((((.(((.....))).))))))))))))))).......(((....)))......))).(((((.((....))..))))).. ( -33.00)
>DroSec_CAF1 111763 120 + 1
CAGCGCCUGACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
.((((((((........)))))......((((((((((((((.(((.....))).))))))).))))))).......(((....))).......)))(((((.((....))..))))).. ( -35.50)
>DroSim_CAF1 18022 120 + 1
CAGCGCCUAACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
.((((((((........)))))......((((((((((((((.(((.....))).))))))).))))))).......(((....))).......)))(((((.((....))..))))).. ( -36.30)
>DroEre_CAF1 34405 120 + 1
AAGCGCCCAGCUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUCAGCGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
.(((...(((((.......(((......((((.....))))......)))((((((((((.((...........)).))))))))))......)))))...)))..((((......)))) ( -38.80)
>DroYak_CAF1 5213 119 + 1
AAGCGCCUAGCUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGACUCU-UGCAGAUUUGUAGAUUUUCAGAGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
.((((((((........)))))......((((((((((((((...........)).-))))).)))))))....((.(((....))).))....)))(((((.((....))..))))).. ( -33.40)
>consensus
AAGCGCCUAACUAUAAAUAGGCAAACAACUGCAGACUGCAGAAACUGGCCGAGUCUUUGCAGAUUUGUAGAUUUUAAGAGAAGACUCCGAUCCGGCUGCCAGCUGAAAGCAAUCUGGCUU
.((((((((........)))))......((((((((((((((.(((.....))).))))))).)))))))........................)))(((((.((....))..))))).. (-32.60 = -33.12 +   0.52)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,056,712 – 21,056,832
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -38.26
Consensus MFE -34.67
Energy contribution -35.31
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.07
Structure conservation index 0.91
SVM decision value 2.73
SVM RNA-class probability 0.996644
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21056712 120 - 23771897
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCUCUUAAAAUCUACAAAUCUGCAAAGACUCGGCCAGUUUCUGCAGUCUGCAAUUGUUUGCCUAUUUAUAGUAAGGCGCUU
((((((((((((....(((((((...((...))(((((((..(.................)..))))))).)))))))...)))))))).........((((..........)))))))) ( -35.63)
>DroSec_CAF1 111763 120 - 1
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCUCUUAAAAUCUACAAAUCUGCAAAGACUCGGCCAGUUUCUGCAGUCUGCAGUUGUUUGCCUAUUUAUAGUCAGGCGCUG
....((((((((....(((((((...((...))(((((((..(.................)..))))))).)))))))...))))))))((((.(((((.(((....))).))))))))) ( -36.63)
>DroSim_CAF1 18022 120 - 1
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCUCUUAAAAUCUACAAAUCUGCAAAGACUCGGCCAGUUUCUGCAGUCUGCAGUUGUUUGCCUAUUUAUAGUUAGGCGCUG
.(((((((((((....(((((((...((...))(((((((..(.................)..))))))).)))))))...)))))))).........(((((........)))))))). ( -38.53)
>DroEre_CAF1 34405 120 - 1
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCGCUGAAAAUCUACAAAUCUGCAAAGACUCGGCCAGUUUCUGCAGUCUGCAGUUGUUUGCCUAUUUAUAGCUGGGCGCUU
..((((((((((....(((((((...((...))(((((((.((.((...........)).)).))))))).)))))))...))))))).(((((((..........)))))))))).... ( -42.20)
>DroYak_CAF1 5213 119 - 1
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCUCUGAAAAUCUACAAAUCUGCA-AGAGUCGGCCAGUUUCUGCAGUCUGCAGUUGUUUGCCUAUUUAUAGCUAGGCGCUU
((((((((((((....(((((((....(((((((((....))))))...))).....((....-.))....)))))))...)))))))).........(((((........))))))))) ( -38.30)
>consensus
AAGCCAGAUUGCUUUCAGCUGGCAGCCGGAUCGGAGUCUUCUCUUAAAAUCUACAAAUCUGCAAAGACUCGGCCAGUUUCUGCAGUCUGCAGUUGUUUGCCUAUUUAUAGUUAGGCGCUU
.(((((((((((....(((((((...((...))(((((((..(.................)..))))))).)))))))...)))))))).........(((((........)))))))). (-34.67 = -35.31 +   0.64)

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 13:00:53 2006