Locus 2378

Sequence ID 2R_DroMel_CAF1
Location 8,612,819 – 8,612,958
Length 139
Max. P 0.636181
window3932 window3933

overview

Window 2

Location 8,612,819 – 8,612,919
Length 100
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 81.23
Mean single sequence MFE -26.97
Consensus MFE -16.82
Energy contribution -17.27
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.62
SVM decision value 0.21
SVM RNA-class probability 0.636181
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8612819 100 - 20766785
AAUUUAAGGAC-------------------GUCCUCUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUUGGAACUUGUCUAUACAUAAUUUCUCUACAUUGACUUACUAAUCUAUAAG
.......((((-------------------((((..((((....))))(((((....)))))........)))...)))))...................................... ( -17.90)
>DroSec_CAF1 15137 119 - 1
GAUUCAAGGACUACAACUCCUGCAAGAUGGGUCGUCAGCUGGAAUGCAGCGACAUCUGUUGCUCAUUUUAGGAACUCGUCCAUACAUAAUUUCUCUACAUUGACAUACUAAUGUAGAAU
.......((((.((.((.((........)))).))...((((((((.((((((....))))))))))))))......))))............(((((((((......))))))))).. ( -33.30)
>DroSim_CAF1 11372 119 - 1
GAUUUAAGGACUACAACUCCUGCAAAAUGGGUUCACUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUAGGAACUCGUCCAUACAUAAUUUCUCUACAUUGACAUACUAAUGUAUAAU
.......((((......(((((..((((((((((.(((((....))))).))........)))))))))))))....))))..............(((((((......))))))).... ( -29.70)
>consensus
GAUUUAAGGACUACAACUCCUGCAA_AUGGGUCCUCUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUAGGAACUCGUCCAUACAUAAUUUCUCUACAUUGACAUACUAAUGUAUAAU
.......((((..........................(((....)))((((((....))))))..............))))..............(((((((......))))))).... (-16.82 = -17.27 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,612,858 – 8,612,958
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.73
Mean single sequence MFE -25.65
Consensus MFE -10.01
Energy contribution -10.41
Covariance contribution 0.40
Combinations/Pair 1.27
Mean z-score -1.77
Structure conservation index 0.39
SVM decision value 0.21
SVM RNA-class probability 0.633383
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8612858 100 - 20766785
UACCAAACGCAGUUAAA-AAUUUAUUAACAAAAACUGUGAAAUUUAAGGAC-------------------GUCCUCUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUUGGAACUUGUC
..((((((((((((...-..............)))))))........(((.-------------------(((..(((((....))))).))).)))..........)))))........ ( -23.93)
>DroSec_CAF1 15176 119 - 1
UACCAAGCACAGUUAAA-AAUUUAUUAACAAAACCUUUGAGAUUCAAGGACUACAACUCCUGCAAGAUGGGUCGUCAGCUGGAAUGCAGCGACAUCUGUUGCUCAUUUUAGGAACUCGUC
......(((..(((((.-......))))).....(((((.....)))))...........)))..(((((((..((..((((((((.((((((....))))))))))))))))))))))) ( -29.30)
>DroSim_CAF1 11411 119 - 1
UGCCAAGCGCAGUUAAA-AAUUUAUUAACAAAAACUGUGAGAUUUAAGGACUACAACUCCUGCAAAAUGGGUUCACUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUAGGAACUCGUC
(((....(((((((...-..............))))))).......((((.......)))))))..((((((((.(((((....)))((((((....))))))......)))))))))). ( -30.73)
>DroEre_CAF1 13044 89 - 1
UUCCAAGCGCAGUUCAA-AAAUAAUUAACAGAAAUCGCGAGGUUUAAGGACC----------------------------AUG--GCAGCGCCAUCUGUUGCACAUUAUGGGAACUAGUA
......((..(((((..-..((((((((((((........((((....))))----------------------------.((--((...)))))))))))...)))))..))))).)). ( -21.80)
>DroYak_CAF1 8545 114 - 1
UACCAAACACUGUUAAAAAAAUUAUUAACCGAAAUCAUCAGAUUAAAGGUCC------CCUGCAAAUUGGGAUUUACACUAUGAAGCAGCGACAUCCGUUGCAUAUCUUUGGAACUAGUA
..(((((((..((((((..........(((..((((....))))...))).(------((........))).)))).))..))..((((((.....)))))).....)))))........ ( -22.50)
>consensus
UACCAAGCGCAGUUAAA_AAUUUAUUAACAAAAACUGUGAGAUUUAAGGACC______CCUGCAA__UGGGUCCUCUGCUGGAAAGCAGCGACAUCUGUUGCUCAUUUUAGGAACUAGUC
..((...(((((((..................)))))))..............................................((((((.....))))))........))........ (-10.01 = -10.41 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:32 2006