Locus 8366

Sequence ID X_DroMel_CAF1
Location 20,776,843 – 20,777,048
Length 205
Max. P 0.915840
window13739 window13740 window13741

overview

Window 9

Location 20,776,843 – 20,776,941
Length 98
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.58
Mean single sequence MFE -28.63
Consensus MFE -24.35
Energy contribution -24.13
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.85
SVM decision value 1.10
SVM RNA-class probability 0.915840
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20776843 98 + 22224390
UGGCAUAUUCGUUUAUAUUGCCAAGAUACAUA----------------------AAUUAGAACAUGUUUCAAUAAUGUGAGCAUGACAGGGUGUUGCGGUCUGUGCGUGCGUGUGUCAAU
((((((((......))).))))).(((((((.----------------------........((((((.....)))))).((((((((((.((...)).))))).))))))))))))... ( -29.70)
>DroSec_CAF1 105479 116 + 1
UGGCAUAUUCGUUUAUAUUGCCAAGAUACAUAUAUGUAUAUAUUUCAAUUUAAAAAUCAGAACAUGUUUCAACAAUGUGAGCAUGACAGGGUGUUGCGUUCUGUGG----GUGUGUCAAU
((((((((((((((((((((.....(((((....)))))....................(((.....)))..))))))))))...((((..((...))..))))))----)))))))).. ( -29.20)
>DroSim_CAF1 40955 116 + 1
UGGCAUAUUCGUUUAUGUUGCCAAGAUACAUAUAUGUAUAUAUUUCAAUUUAAAAAUCAGAACAUGUUUCAACAAUGUGAGCAUGACAGGGUGUUGCGGUCUGUGG----GUGUGUCAAU
((((((((((((((((((((.....(((((....)))))....................(((.....)))..))))))))))...(((((.((...)).)))))))----)))))))).. ( -27.00)
>consensus
UGGCAUAUUCGUUUAUAUUGCCAAGAUACAUAUAUGUAUAUAUUUCAAUUUAAAAAUCAGAACAUGUUUCAACAAUGUGAGCAUGACAGGGUGUUGCGGUCUGUGG____GUGUGUCAAU
((((((((......))).))))).(((((((...............................(((((((((....)).)))))))((((..((...))..))))......)))))))... (-24.35 = -24.13 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,776,901 – 20,777,021
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.76
Mean single sequence MFE -25.83
Consensus MFE -21.38
Energy contribution -22.27
Covariance contribution 0.89
Combinations/Pair 1.04
Mean z-score -2.07
Structure conservation index 0.83
SVM decision value 0.34
SVM RNA-class probability 0.697224
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20776901 120 - 22224390
CGUACAGCCACACGGCAAUAAAAAAUAUAGAAAAUUGGAAUUCAACAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUCAUUGACACACGCACGCACAGACCGCAACACCCUGUCAUGC
......(((....))).............................((((((((....)).(((...(..(((.((((....)))).)))..)...)))...............)))))). ( -23.00)
>DroSec_CAF1 105559 116 - 1
CGUACAGUCGCAAGAAUAUACAAAAUAUAAAUAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUCAUUGACACAC----CCACAGAACGCAACACCCUGUCAUGC
.(((...((....))...))).......................(((((((((....)).......(..(((.((((....)))).))).----.).................))))))) ( -21.10)
>DroSim_CAF1 41035 116 - 1
CGUACAGUCGCAAGACUAUACAAAAUACAGAAAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUGUGUUUCAAUUCAUUGACACAC----CCACAGACCGCAACACCCUGUCAUGC
.(((.((((....)))).)))......(((....))).......(((((((((....)).(((...(((((((..........)))))))----.)))...............))))))) ( -33.40)
>consensus
CGUACAGUCGCAAGACUAUACAAAAUAUAGAAAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUCAUUGACACAC____CCACAGACCGCAACACCCUGUCAUGC
.(((.((((....)))).))).......................(((((((((....)).(((......(((.((((....)))).)))......)))...............))))))) (-21.38 = -22.27 +   0.89)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,776,941 – 20,777,048
Length 107
Sequences 3
Columns 107
Reading direction reverse
Mean pairwise identity 88.16
Mean single sequence MFE -21.70
Consensus MFE -20.10
Energy contribution -20.00
Covariance contribution -0.10
Combinations/Pair 1.13
Mean z-score -1.55
Structure conservation index 0.93
SVM decision value 0.48
SVM RNA-class probability 0.752590
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20776941 107 - 22224390
UUGAGUUAGUCAUUCCCAUUAGUAUUUCGUACAGCCACACGGCAAUAAAAAAUAUAGAAAAUUGGAAUUCAACAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUC
....(((.(..(((((.(((.((((((..((..(((....)))..))..))))))....))).))))).)))).(((.((((((.........)))))).))).... ( -19.70)
>DroSec_CAF1 105595 107 - 1
UAGAGUUAUUCACCACCAUUAGUAUUUCGUACAGUCGCAAGAAUAUACAAAAUAUAAAUAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUC
..(((((.....(((..(((.((((((.(((...((....))...))).)))))).)))...)))..........((.((((((.........)))))).))))))) ( -20.10)
>DroSim_CAF1 41071 107 - 1
UAGAGUUAUUCACCACCAUUAGUAUUUCGUACAGUCGCAAGACUAUACAAAAUACAGAAAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUGUGUUUCAAUUC
..(((((.....(((...((.((((((.(((.((((....)))).))).)))))).))....)))..........((.((((((.........)))))).))))))) ( -25.30)
>consensus
UAGAGUUAUUCACCACCAUUAGUAUUUCGUACAGUCGCAAGACUAUACAAAAUAUAGAAAACUGGAAUUAAGCAUGACGCAUACGCAGUGAAAGUAUGUUUCAAUUC
..(((((........(((((.((((((.(((.((((....)))).))).)))))).))....)))..........((.((((((.........)))))).))))))) (-20.10 = -20.00 +  -0.10)

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 13:02:12 2006