Locus 3547

Sequence ID 2L_DroMel_CAF1
Location 10,342,578 – 10,342,686
Length 108
Max. P 0.982915
window5600 window5601

overview

Window 0

Location 10,342,578 – 10,342,686
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 79.12
Mean single sequence MFE -28.02
Consensus MFE -15.20
Energy contribution -15.48
Covariance contribution 0.28
Combinations/Pair 1.23
Mean z-score -2.63
Structure conservation index 0.54
SVM decision value 1.93
SVM RNA-class probability 0.982915
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342578 108 + 22407834
UUUUCUGAUUUAAUCAAAGUCAGCUGAUAUCAGCUGAUCUUUGCCUU-AAAAACUGAU----AUGGAAUCUCCUAUCUGGAAUACUAGGAAUAUCGAUAAGUGUUGAAGUGCC
.((((((.(((((.((((((((((((....))))))).)))))..))-)))..(.(((----(.((.....)))))).)......))))))..(((((....)))))...... ( -25.90)
>DroSec_CAF1 4180 109 + 1
CUUUCUUAUUUAAGCGAAGUCAGCUGAUAUCAGCUGAUCUUUGCCCUUAAACACUGAU----AUGGAAUCUCCCAUCUGGAAUACCAGGAAUAUCGAUAAGUAUUAAAGUGCC
((((..((((((.(((((((((((((....))))))).))))))..........((((----((((......)).(((((....))))).)))))).))))))..)))).... ( -33.60)
>DroSim_CAF1 2420 107 + 1
CUUUCUUAUUUUAGCAAAGUCAGCUGAUAUCAGCUGAUCUUUGCCUUAAA--ACUGAU----AUGGAAUCUCCCAUCUGGAAUACCAGGAAUAUCGAUAGGUAUUAAAGUGCC
.............(((((((((((((....))))))).))))))......--..((((----((((......)).(((((....))))).))))))...(((((....))))) ( -32.70)
>DroEre_CAF1 4253 91 + 1
UUUUCCGAUUUUAAAGUAGUCAGCUGAGAUCAGCUGAUCU----------------------AUGGAAUCUCCCUUCUGUAGUUCUAUGAAUAUCGAUAAGUGUUCAAGUGCC
......(((((((.((..((((((((....))))))))))----------------------.)))))))...........((.((.(((((((......))))))))).)). ( -23.50)
>DroYak_CAF1 3058 108 + 1
UGUUCUGAUUUUACCCAAGUCAGCUGAGAUCAGCUGAUCUUUGC-----AAAACUGAUAUGGAUGGAAUCUCCCUUCUGAAGUGCUAAGAAUAUCGAUAAGUGUUCAAGUGUC
......(((((((.(((.((((((.((((((....)))))).))-----.....)))).))).)))))))...........(..((..((((((......)))))).))..). ( -24.40)
>consensus
UUUUCUGAUUUUAGCAAAGUCAGCUGAUAUCAGCUGAUCUUUGCC_U_AAA_ACUGAU____AUGGAAUCUCCCAUCUGGAAUACUAGGAAUAUCGAUAAGUGUUAAAGUGCC
..............((((((((((((....))))))).))))).....................((.....))...((..((((((.............))))))..)).... (-15.20 = -15.48 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,342,578 – 10,342,686
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 79.12
Mean single sequence MFE -25.88
Consensus MFE -15.15
Energy contribution -15.43
Covariance contribution 0.28
Combinations/Pair 1.12
Mean z-score -2.17
Structure conservation index 0.59
SVM decision value 1.06
SVM RNA-class probability 0.907980
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10342578 108 - 22407834
GGCACUUCAACACUUAUCGAUAUUCCUAGUAUUCCAGAUAGGAGAUUCCAU----AUCAGUUUUU-AAGGCAAAGAUCAGCUGAUAUCAGCUGACUUUGAUUAAAUCAGAAAA
.....((((((.(((((((((((.....)))))...)))))).(((.....----))).)))(((-((..(((((.(((((((....)))))))))))).)))))...))).. ( -25.60)
>DroSec_CAF1 4180 109 - 1
GGCACUUUAAUACUUAUCGAUAUUCCUGGUAUUCCAGAUGGGAGAUUCCAU----AUCAGUGUUUAAGGGCAAAGAUCAGCUGAUAUCAGCUGACUUCGCUUAAAUAAGAAAG
....(((.((((((....(((((..((((....))))...((.....))))----))))))))).)))(((.(((.(((((((....)))))))))).)))............ ( -30.50)
>DroSim_CAF1 2420 107 - 1
GGCACUUUAAUACCUAUCGAUAUUCCUGGUAUUCCAGAUGGGAGAUUCCAU----AUCAGU--UUUAAGGCAAAGAUCAGCUGAUAUCAGCUGACUUUGCUAAAAUAAGAAAG
.............((.(((((((..((((....))))...((.....))))----))).((--(((..(((((((.(((((((....)))))))))))))))))))..)).)) ( -31.30)
>DroEre_CAF1 4253 91 - 1
GGCACUUGAACACUUAUCGAUAUUCAUAGAACUACAGAAGGGAGAUUCCAU----------------------AGAUCAGCUGAUCUCAGCUGACUACUUUAAAAUCGGAAAA
................(((((...................((.....)).(----------------------((.(((((((....)))))))))).......))))).... ( -18.20)
>DroYak_CAF1 3058 108 - 1
GACACUUGAACACUUAUCGAUAUUCUUAGCACUUCAGAAGGGAGAUUCCAUCCAUAUCAGUUUU-----GCAAAGAUCAGCUGAUCUCAGCUGACUUGGGUAAAAUCAGAACA
.....((((.........((((((((.........)))).(((.......))).))))..((((-----((.(((.(((((((....))))))))))..)))))))))).... ( -23.80)
>consensus
GGCACUUGAACACUUAUCGAUAUUCCUAGUAUUCCAGAUGGGAGAUUCCAU____AUCAGU_UUU_A_GGCAAAGAUCAGCUGAUAUCAGCUGACUUCGCUAAAAUCAGAAAA
............((((((..................))))))..............................(((.(((((((....))))))))))................ (-15.15 = -15.43 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:09 2006