Locus 5136

Sequence ID 2L_DroMel_CAF1
Location 14,584,251 – 14,584,345
Length 94
Max. P 0.946873
window8178 window8179

overview

Window 8

Location 14,584,251 – 14,584,345
Length 94
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 81.35
Mean single sequence MFE -27.39
Consensus MFE -19.32
Energy contribution -19.32
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -2.23
Structure conservation index 0.71
SVM decision value 1.37
SVM RNA-class probability 0.946873
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14584251 94 + 22407834
AUUUGCAGUGCGAUCUAAAGGAUUGCAAUGCAGAGAAAAAAAGCGGAAGGU----------CGGAAAUUGGAACUGACACCAGUUAAUUCAGCCAU-----GUUUCUCC
...((((.(((((((.....))))))).))))((((((.....(....)..----------.((.......(((((....))))).......))..-----.)))))). ( -28.14)
>DroSec_CAF1 125947 104 + 1
AUUUGCAGUGCGAUCUAAAGGAUUGCAAUGCAGAGAAAAAAAGUGGAAGGCCAAUCGUAACCGGAAAUGGAAGCUUAACCAAUUUAAUUCAGCCAU-----CUUUCUCC
...((((.(((((((.....))))))).))))(((((.......(((.(((...(((....)))...(((........)))..........))).)-----))))))). ( -25.41)
>DroSim_CAF1 103703 104 + 1
AUUUGCACUGCGAUCUAAAGGAUUGCAAUGCAGAGAAAAAAAGUGGAAGGCCAAUCGUAACCGGAAAUGGAAGCUUAAACAAUUUAAUUCAGCCAU-----GUUUCUCC
...((((.(((((((.....))))))).))))((((((....((((...((.....))..(((....)))......................))))-----.)))))). ( -25.00)
>DroYak_CAF1 107920 105 + 1
AUUUGCAGUGCGAUCUAAAGGAUUGCAGUGCAGUGGAAAAAAG-GGAAG--CCAUCGU-UCCGGAAAUUGGAACUGAACCCAGUUAAUUCAGCCAAUUCAGCUUAAUCC
..(((((.(((((((.....))))))).)))))(((((....(-(....--))....)-))))(((.((((..(((((.........)))))))))))).......... ( -31.00)
>consensus
AUUUGCAGUGCGAUCUAAAGGAUUGCAAUGCAGAGAAAAAAAGUGGAAGGCCAAUCGU_ACCGGAAAUGGAAACUGAAACAAGUUAAUUCAGCCAU_____CUUUCUCC
.((((((.(((((((.....))))))).))))))............................((.......(((((....))))).......))............... (-19.32 = -19.32 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 14,584,251 – 14,584,345
Length 94
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 81.35
Mean single sequence MFE -24.95
Consensus MFE -15.29
Energy contribution -17.10
Covariance contribution 1.81
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.61
SVM decision value -0.05
SVM RNA-class probability 0.505962
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14584251 94 - 22407834
GGAGAAAC-----AUGGCUGAAUUAACUGGUGUCAGUUCCAAUUUCCG----------ACCUUCCGCUUUUUUUCUCUGCAUUGCAAUCCUUUAGAUCGCACUGCAAAU
(((((((.-----..(((.(((..(((((....)))))..........----------...))).)))...)))))))(((.(((.(((.....))).))).))).... ( -21.06)
>DroSec_CAF1 125947 104 - 1
GGAGAAAG-----AUGGCUGAAUUAAAUUGGUUAAGCUUCCAUUUCCGGUUACGAUUGGCCUUCCACUUUUUUUCUCUGCAUUGCAAUCCUUUAGAUCGCACUGCAAAU
((((((((-----(.(((..(....((((((..............))))))....)..)))........)))))))))(((.(((.(((.....))).))).))).... ( -25.64)
>DroSim_CAF1 103703 104 - 1
GGAGAAAC-----AUGGCUGAAUUAAAUUGUUUAAGCUUCCAUUUCCGGUUACGAUUGGCCUUCCACUUUUUUUCUCUGCAUUGCAAUCCUUUAGAUCGCAGUGCAAAU
(((((...-----..((((((((......)))).))))....)))))(((((....)))))................((((((((.(((.....))).))))))))... ( -26.20)
>DroYak_CAF1 107920 105 - 1
GGAUUAAGCUGAAUUGGCUGAAUUAACUGGGUUCAGUUCCAAUUUCCGGA-ACGAUGG--CUUCC-CUUUUUUCCACUGCACUGCAAUCCUUUAGAUCGCACUGCAAAU
(((..(((..((((((((((((((.....)))))))..)))))))..(((-((....)--.))))-)))...)))..((((.(((.(((.....))).))).))))... ( -26.90)
>consensus
GGAGAAAC_____AUGGCUGAAUUAAAUGGGUUAAGCUCCAAUUUCCGGU_ACGAUUGGCCUUCCACUUUUUUUCUCUGCAUUGCAAUCCUUUAGAUCGCACUGCAAAU
(((((((........(((((((((.....)))))))))........((....))..............)))))))..((((.(((.(((.....))).))).))))... (-15.29 = -17.10 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:55 2006