Locus 10100

Sequence ID 3R_DroMel_CAF1
Location 27,057,335 – 27,057,551
Length 216
Max. P 0.994326
window16080 window16081 window16082

overview

Window 0

Location 27,057,335 – 27,057,452
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.44
Mean single sequence MFE -25.48
Consensus MFE -19.26
Energy contribution -19.58
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.76
SVM decision value 0.77
SVM RNA-class probability 0.845657
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27057335 117 - 27905053
GUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---UGUUUUCUAAAUUAAGGGAAAACUAAAAAAUAUGGUCAGGGUGGUGAAUUAAAUUACAAAAUCU
((((....((..(((((((((.....))))))((((((..(((((...(((..---..((..((......))..))..))).))))).))))))...)))..)).....))))....... ( -26.70)
>DroSec_CAF1 104575 112 - 1
GUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---GGUUUUCCAAAUUAAGGGAAAACUAAAAAAUAUAGUCAUGGUGGUGAA-----UUACAAAAUCU
((((((((((((.((((((((.....))))))))..))))))))........(---((((((((........)))))))))..........))))(((..((..-----...))..))). ( -26.40)
>DroSim_CAF1 107372 112 - 1
GUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---GGUUUUCCAAAUUAAGGGAAAACUAAAAAAUAUAGUCAGGGUGGUGAA-----UUACAAAAACU
((((.........((((((((.....))))))))((((....((((((((..(---((((((((........))))))))).....)))..))))).))))...-----))))....... ( -26.80)
>DroEre_CAF1 111863 103 - 1
GUAAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGUCGUGGUUUUCAAAAUUAGGGGAAAAUUAA-AAAUGUAAUCAGGGCGGU----------------UCU
...(((((((((.((((((((.....))))))))..)))))))))((((..(((.(((((..((...((((.......))))-...)).))))).))).))----------------)). ( -24.40)
>DroYak_CAF1 107903 115 - 1
GUAAAAACUUUGCCAACUUGCUUCUAGUAAGCUGACCAAAGUUUUGAAAAGGUCGUGGUUUUCAAAAUUAAGGGAAAAUUAGGAAAUAUAGUCAGGGCGGUGAA-----UUAAACAAUGU
........((..((..(((((.....))))).........(((((((.....((.((((((((..........)))))))).)).......)))))))))..))-----........... ( -23.10)
>consensus
GUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU___GGUUUUCAAAAUUAAGGGAAAACUAAAAAAUAUAGUCAGGGUGGUGAA_____UUACAAAAUCU
...(((((((((.((((((((.....))))))))..)))))))))...........((((((((........))))))))........................................ (-19.26 = -19.58 +   0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 27,057,375 – 27,057,492
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.85
Mean single sequence MFE -26.70
Consensus MFE -22.64
Energy contribution -23.32
Covariance contribution 0.68
Combinations/Pair 1.12
Mean z-score -2.27
Structure conservation index 0.85
SVM decision value 2.47
SVM RNA-class probability 0.994326
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27057375 117 - 27905053
UAAUAUUAAUAUCAGCCUAUAUGUCAUUUGUACUAUCUCUGUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---UGUUUUCUAAAUUAAGGGAAAACU
.............(((((((..........(((.......)))(((((((((.((((((((.....))))))))..)))))))))..))))))---)(((((((........))))))). ( -27.50)
>DroSec_CAF1 104610 117 - 1
UAAUAUUAACAUCAGCCUAUAUGCCAUUUGUACUAUCUCUGUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---GGUUUUCCAAAUUAAGGGAAAACU
..............((((((..........(((.......)))(((((((((.((((((((.....))))))))..)))))))))..))))))---((((((((........)))))))) ( -29.50)
>DroSim_CAF1 107407 117 - 1
UAAUAUUAACAUCAGCCUAUAUGCCAUUUCUUCUAUCUCUGUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU---GGUUUUCCAAAUUAAGGGAAAACU
..............((((((....(((.............)))(((((((((.((((((((.....))))))))..)))))))))..))))))---((((((((........)))))))) ( -28.62)
>DroEre_CAF1 111886 120 - 1
UAAUAUAAAAACCAGCCUAGAAACCAUUUGUACUAUCUCUGUAAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGUCGUGGUUUUCAAAAUUAGGGGAAAAUU
...........((..((((((((((((.....((((.((....(((((((((.((((((((.....))))))))..)))))))))))))))...))))))))......))))))...... ( -26.70)
>DroYak_CAF1 107938 120 - 1
UAAUAUUAACACCAGCCUAGAAACCAUUCGUACUAUCUCUGUAAAAACUUUGCCAACUUGCUUCUAGUAAGCUGACCAAAGUUUUGAAAAGGUCGUGGUUUUCAAAAUUAAGGGAAAAUU
.........(((..((((............(((.......)))(((((((((.((.(((((.....))))).))..)))))))))....)))).)))((((((..........)))))). ( -21.20)
>consensus
UAAUAUUAACAUCAGCCUAUAUGCCAUUUGUACUAUCUCUGUGAAAAUUUUGCCAACUUGCUUCUAGUAAGUUGACCAAAGUUUUGAAUAGGU___GGUUUUCAAAAUUAAGGGAAAACU
..............((((((..........(((.......)))(((((((((.((((((((.....))))))))..)))))))))..))))))....(((((((........))))))). (-22.64 = -23.32 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 27,057,452 – 27,057,551
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.04
Mean single sequence MFE -16.35
Consensus MFE -8.84
Energy contribution -9.24
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.18
Structure conservation index 0.54
SVM decision value 1.11
SVM RNA-class probability 0.916804
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27057452 99 - 27905053
AUUACUGGAGU---AAUUAUUUAUU-----UAUUACUAUUUUAGGUUCUUC-------------AAGUUCGCAAUUCCAGUAAUAUUAAUAUCAGCCUAUAUGUCAUUUGUACUAUCUCU
(((((((((((---...........-----....(((......))).....-------------.........))))))))))).................................... ( -12.15)
>DroSec_CAF1 104687 99 - 1
AUUACUGGACU---AAUUAUUCAUU-----UAUUACUAUUUUUGGUUCUCC-------------AAGUUCGCAUUUCCAGUAAUAUUAACAUCAGCCUAUAUGCCAUUUGUACUAUCUCU
(((((((((..---...........-----...........((((....))-------------))(....)...)))))))))....(((...((......))....)))......... ( -13.30)
>DroSim_CAF1 107484 99 - 1
AUUACUGGACU---AAUUAUUCAUU-----UAUUACUAUUUUUGGUUCUCC-------------AAGUUCGCAUUUCCAGUAAUAUUAACAUCAGCCUAUAUGCCAUUUCUUCUAUCUCU
(((((((((..---...........-----...........((((....))-------------))(....)...))))))))).................................... ( -12.40)
>DroEre_CAF1 111966 119 - 1
AUUACUGGAGUGCAACUUAUUUAUUACUUGUAAAACUAUUUUUGGUUCUUCCUUCA-CCACUCAAAGUUCGCUAUUCCAGUAAUAUAAAAACCAGCCUAGAAACCAUUUGUACUAUCUCU
((((((((((((((((((.(((((.....)))))........((((.........)-)))....))))).)).))))))))))).................................... ( -21.40)
>DroYak_CAF1 108018 120 - 1
AUUACUGGAUAGGAACUUCUUUAGUACUUAUAAAACUAUUUUUCGUUCUUCCUUAAGCUACUCAAAGUUCGCUAUUCCAGUAAUAUUAACACCAGCCUAGAAACCAUUCGUACUAUCUCU
((((((((((((((((((....((((((((...(((........)))......)))).))))..)))))).))).))))))))).................................... ( -22.50)
>consensus
AUUACUGGACU___AAUUAUUUAUU_____UAUUACUAUUUUUGGUUCUUC_____________AAGUUCGCAAUUCCAGUAAUAUUAACAUCAGCCUAUAUGCCAUUUGUACUAUCUCU
(((((((((.........................((((....))))....................(....)...))))))))).................................... ( -8.84 =  -9.24 +   0.40)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:48:54 2006