Locus 5516

Sequence ID 2R_DroMel_CAF1
Location 17,659,974 – 17,660,092
Length 118
Max. P 0.999599
window8833 window8834

overview

Window 3

Location 17,659,974 – 17,660,092
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.46
Mean single sequence MFE -26.83
Consensus MFE -24.28
Energy contribution -24.56
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.90
SVM decision value 3.77
SVM RNA-class probability 0.999599
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17659974 118 + 20766785
AUUUCUCUUGUUUUUUAAGCCAAAGAAAAAGUGAUUCAUGAUCUUUUUGGGUCAAGUUUACUGUUUUU--UGUUGGUUAUACUCUUCCGAUUGCCAUGAAUCAUUUGUAUCUUGGCCAAA
..................(((((.((..((((((((((((......(((((...(((..((((.....--...))))...)))..)))))....))))))))))))...))))))).... ( -28.40)
>DroSec_CAF1 13474 119 + 1
AUUUCUCUCGUUUUUUAAACCAAAAGAAAAGUGAUUCAUGAUCUUUUUGGGUCAAGUUUACUGUUUUUUUU-UUGGCUAUACUCUUCCGAUUGCCAUGAAUCAUUUGUAUCUUGGCCAAA
...................((((.....((((((((((((((((....)))))).................-.((((...............)))))))))))))).....))))..... ( -23.56)
>DroSim_CAF1 19440 120 + 1
AUUUCUCUUGUUUUUUAAGCCAAAAGAAAAGUGAUUCAUGAUCUUUUUGGGUCAAGUUUACUGUUUUUUUUGUUGGUUAUACUGUUCCGAUUGCCAUGAAUCAUUUGUAUCUUGGCCAAA
..................(((((.....((((((((((((......(((((...(((..((((..........))))...)))..)))))....)))))))))))).....))))).... ( -27.70)
>DroEre_CAF1 13774 110 + 1
AAU--------UUCUUAAGCCAAAAGAAAAGUGAUUCAUGAUCUUUUUGGGUCAAGUUUACUGUUUUU--UGUUGGUUAUACUCUUCCGAUUGCCAUGAAUCAUUUGUAUCUUGGCCAGA
...--------.......(((((.....((((((((((((......(((((...(((..((((.....--...))))...)))..)))))....)))))))))))).....))))).... ( -27.50)
>DroYak_CAF1 25249 118 + 1
AUUUUUCUUGUUUUUUAUGCCAAAAGAAAAGUGAUUCACGAUCUUUUUGGGUCAAGUUUACUGUUUUU--UGUUGGUUAUACUCUUCUGAUUGCCAUGAAUCACUUGUAUCUUGGCCAAA
..................(((((.....((((((((((.(((((....)))))...............--...((((.((.(......))).)))))))))))))).....))))).... ( -27.00)
>consensus
AUUUCUCUUGUUUUUUAAGCCAAAAGAAAAGUGAUUCAUGAUCUUUUUGGGUCAAGUUUACUGUUUUU__UGUUGGUUAUACUCUUCCGAUUGCCAUGAAUCAUUUGUAUCUUGGCCAAA
..................(((((.....((((((((((((......(((((...(((..((((..........))))...)))..)))))....)))))))))))).....))))).... (-24.28 = -24.56 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,659,974 – 17,660,092
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.46
Mean single sequence MFE -23.46
Consensus MFE -20.20
Energy contribution -20.28
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -2.87
Structure conservation index 0.86
SVM decision value 3.71
SVM RNA-class probability 0.999547
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17659974 118 - 20766785
UUUGGCCAAGAUACAAAUGAUUCAUGGCAAUCGGAAGAGUAUAACCAACA--AAAAACAGUAAACUUGACCCAAAAAGAUCAUGAAUCACUUUUUCUUUGGCUUAAAAAACAAGAGAAAU
...((((((((...((.((((((((((...((....))............--............(((........))).)))))))))).))..)).))))))................. ( -22.90)
>DroSec_CAF1 13474 119 - 1
UUUGGCCAAGAUACAAAUGAUUCAUGGCAAUCGGAAGAGUAUAGCCAA-AAAAAAAACAGUAAACUUGACCCAAAAAGAUCAUGAAUCACUUUUCUUUUGGUUUAAAAAACGAGAGAAAU
.................(((((((((((..((....)).....)))..-...............(((........)))...))))))))..(((((((((..........))))))))). ( -22.90)
>DroSim_CAF1 19440 120 - 1
UUUGGCCAAGAUACAAAUGAUUCAUGGCAAUCGGAACAGUAUAACCAACAAAAAAAACAGUAAACUUGACCCAAAAAGAUCAUGAAUCACUUUUCUUUUGGCUUAAAAAACAAGAGAAAU
...((((((((......((((((((((.....((..........))..................(((........))).))))))))))......))))))))................. ( -21.10)
>DroEre_CAF1 13774 110 - 1
UCUGGCCAAGAUACAAAUGAUUCAUGGCAAUCGGAAGAGUAUAACCAACA--AAAAACAGUAAACUUGACCCAAAAAGAUCAUGAAUCACUUUUCUUUUGGCUUAAGAA--------AUU
(((((((((((......((((((((((...((....))............--............(((........))).))))))))))......))))))))..))).--------... ( -25.00)
>DroYak_CAF1 25249 118 - 1
UUUGGCCAAGAUACAAGUGAUUCAUGGCAAUCAGAAGAGUAUAACCAACA--AAAAACAGUAAACUUGACCCAAAAAGAUCGUGAAUCACUUUUCUUUUGGCAUAAAAAACAAGAAAAAU
....(((((((.(.(((((((((((((...((....))............--............(((........))).))))))))))))).).))))))).................. ( -25.40)
>consensus
UUUGGCCAAGAUACAAAUGAUUCAUGGCAAUCGGAAGAGUAUAACCAACA__AAAAACAGUAAACUUGACCCAAAAAGAUCAUGAAUCACUUUUCUUUUGGCUUAAAAAACAAGAGAAAU
....(((((((......((((((((((...((....))..........................(((........))).))))))))))......))))))).................. (-20.20 = -20.28 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:24 2006