Locus 5486

Sequence ID 2R_DroMel_CAF1
Location 17,646,147 – 17,646,256
Length 109
Max. P 0.571670
window8751 window8752

overview

Window 1

Location 17,646,147 – 17,646,256
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 81.38
Mean single sequence MFE -24.41
Consensus MFE -16.57
Energy contribution -16.57
Covariance contribution 0.01
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.525466
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17646147 109 + 20766785
-AUAUCAUACUCAUAUGUAUGUGUGCAAAUGAUAUA----------UCUGUCAGUUGUCCAUCAUUGGCUAAGAUCAAAUCCGAAUCUAAGCCAUUUCGAGUUGAACAAACCCAAUCGCA
-...(((.((((......(((((..(((.(((((..----------..))))).)))..)).)))(((((.(((((......).)))).)))))....)))))))............... ( -24.40)
>DroSim_CAF1 5673 109 + 1
-AUAUCAUACUCAUAU----GUGUGCAAAUGAUAUAGAAGACUGGCUCUGUCAGCUGUCUAUCAAUGGCUAAGAUC------GAAUCUAAGCCAUUUCGAGUUGAACAAACCCAAUCGCA
-(((((((...(((..----..)))...)))))))....((.(((...((((((((.......(((((((.((((.------..)))).)))))))...))))).)))...))).))... ( -25.20)
>DroYak_CAF1 11003 110 + 1
UAUAUCAUUCACAUAU----GCAUGCAAAUGGUAUGGAAGACUGGUACUGUCAGCUGUCCAUCAUUGGCUAAGAUC------GAAACUAAGCCAUUUCGAGUUGAACAAACCCAAUCGCA
(((((((((..(((..----..)))..)))))))))...((.(((...((((((((.........(((((.((...------....)).))))).....))))).)))...))).))... ( -23.64)
>consensus
_AUAUCAUACUCAUAU____GUGUGCAAAUGAUAUAGAAGACUGG_UCUGUCAGCUGUCCAUCAUUGGCUAAGAUC______GAAUCUAAGCCAUUUCGAGUUGAACAAACCCAAUCGCA
.(((((((...(((((....)))))...))))))).............((((((((.........(((((.((((.........)))).))))).....))))).)))............ (-16.57 = -16.57 +   0.01)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 17,646,147 – 17,646,256
Length 109
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.38
Mean single sequence MFE -28.50
Consensus MFE -19.28
Energy contribution -21.17
Covariance contribution 1.89
Combinations/Pair 1.06
Mean z-score -1.68
Structure conservation index 0.68
SVM decision value 0.08
SVM RNA-class probability 0.571670
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17646147 109 - 20766785
UGCGAUUGGGUUUGUUCAACUCGAAAUGGCUUAGAUUCGGAUUUGAUCUUAGCCAAUGAUGGACAACUGACAGA----------UAUAUCAUUUGCACACAUACAUAUGAGUAUGAUAU-
(((((.(((..(((((((..(((...(((((.(((((.......))))).))))).))))))))))(.....).----------....))).)))))..(((((......)))))....- ( -25.00)
>DroSim_CAF1 5673 109 - 1
UGCGAUUGGGUUUGUUCAACUCGAAAUGGCUUAGAUUC------GAUCUUAGCCAUUGAUAGACAGCUGACAGAGCCAGUCUUCUAUAUCAUUUGCACAC----AUAUGAGUAUGAUAU-
...((((((.((((((....((..(((((((.((((..------.)))).)))))))....)).....)))))).))))))....(((((((...((...----...))...)))))))- ( -31.60)
>DroYak_CAF1 11003 110 - 1
UGCGAUUGGGUUUGUUCAACUCGAAAUGGCUUAGUUUC------GAUCUUAGCCAAUGAUGGACAGCUGACAGUACCAGUCUUCCAUACCAUUUGCAUGC----AUAUGUGAAUGAUAUA
.....(((((((.....)))))))..(((((.((....------...)).)))))...(((((..((((.......))))..)))))..((((..(((..----..)))..))))..... ( -28.90)
>consensus
UGCGAUUGGGUUUGUUCAACUCGAAAUGGCUUAGAUUC______GAUCUUAGCCAAUGAUGGACAGCUGACAGA_CCAGUCUUCUAUAUCAUUUGCACAC____AUAUGAGUAUGAUAU_
((((((((((((.....)))))))..(((((.(((((.......))))).)))))...(((((..((((.......))))..))))).....)))))....................... (-19.28 = -21.17 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:04 2006