Locus 1614

Sequence ID 2L_DroMel_CAF1
Location 4,342,219 – 4,342,338
Length 119
Max. P 0.999933
window2591 window2592

overview

Window 1

Location 4,342,219 – 4,342,338
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 76.54
Mean single sequence MFE -28.33
Consensus MFE -20.37
Energy contribution -21.70
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -3.42
Structure conservation index 0.72
SVM decision value 4.64
SVM RNA-class probability 0.999933
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4342219 119 + 22407834
AGUUUGAUAUAUAGGCACAGAUAAAUGAAGAUAAGGAGAUCAAGUUCCUUUAAGCCAGAUGAUUGUCUUAAAGAAAGAUGGUAUUUCAUUUAGUGGUGCCUAAAUCAAA-UGACUUUAAG
.(((((((...(((((((...(((((((((..((((((......))))))...........((..((((.....))))..)).)))))))))...))))))).))))))-)......... ( -34.10)
>DroSec_CAF1 11109 94 + 1
AGUUUGAUA--UAGGCACACA------------------------UCCCUUAAGCCAGAUGCUUGUCUUAAAGAAAGAUUAUAAAUCAUGUAGUAGUGCCUCAAUCAAAUUGACUUUAAA
((((((((.--.((((((((.------------------------......((((.....))))(((((.....))))).............)).))))))..))))))))......... ( -20.90)
>DroSim_CAF1 11731 118 + 1
AGUUUGAUG--UAGGCACACAUAAAUGAAGAUGAGAAGAUCAAGGUCCUUUAAGCCAGAUGAUUGUCUUAAAGAAAGAUUAAAUAUCAUGUAGUAGUGCCUAAAUCAAAUUGACUUUAAU
((((((((.--(((((((((...........(((((.(((((.(((.......)))...))))).)))))......(((.....))).....)).))))))).))))))))......... ( -30.00)
>consensus
AGUUUGAUA__UAGGCACACAUAAAUGAAGAU_AG_AGAUCAAG_UCCUUUAAGCCAGAUGAUUGUCUUAAAGAAAGAUUAUAUAUCAUGUAGUAGUGCCUAAAUCAAAUUGACUUUAAA
((((((((...(((((((.............................(((((((.(((....))).)))))))...(((.....)))........))))))).))))))))......... (-20.37 = -21.70 +   1.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,342,219 – 4,342,338
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.54
Mean single sequence MFE -26.73
Consensus MFE -21.19
Energy contribution -21.63
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -4.21
Structure conservation index 0.79
SVM decision value 4.61
SVM RNA-class probability 0.999928
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4342219 119 - 22407834
CUUAAAGUCA-UUUGAUUUAGGCACCACUAAAUGAAAUACCAUCUUUCUUUAAGACAAUCAUCUGGCUUAAAGGAACUUGAUCUCCUUAUCUUCAUUUAUCUGUGCCUAUAUAUCAAACU
..........-((((((.(((((((...((((((((........((((((((((.((......)).))))))))))...(((......)))))))))))...)))))))...)))))).. ( -30.20)
>DroSec_CAF1 11109 94 - 1
UUUAAAGUCAAUUUGAUUGAGGCACUACUACAUGAUUUAUAAUCUUUCUUUAAGACAAGCAUCUGGCUUAAGGGA------------------------UGUGUGCCUA--UAUCAAACU
...........((((((..((((((.((.....(((.....))).(((((((((.((......)).)))))))))------------------------.)))))))).--.)))))).. ( -22.40)
>DroSim_CAF1 11731 118 - 1
AUUAAAGUCAAUUUGAUUUAGGCACUACUACAUGAUAUUUAAUCUUUCUUUAAGACAAUCAUCUGGCUUAAAGGACCUUGAUCUUCUCAUCUUCAUUUAUGUGUGCCUA--CAUCAAACU
...........((((((.(((((((.((((.((((..........(((((((((.((......)).)))))))))...(((.....)))...)))).)).)))))))))--.)))))).. ( -27.60)
>consensus
AUUAAAGUCAAUUUGAUUUAGGCACUACUACAUGAUAUAUAAUCUUUCUUUAAGACAAUCAUCUGGCUUAAAGGA_CUUGAUCU_CU_AUCUUCAUUUAUGUGUGCCUA__UAUCAAACU
...........((((((.(((((((........(((.....))).(((((((((.((......)).)))))))))...........................)))))))...)))))).. (-21.19 = -21.63 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:43 2006