Locus 4479

Sequence ID 3R_DroMel_CAF1
Location 11,839,415 – 11,839,542
Length 127
Max. P 0.988022
window7322 window7323

overview

Window 2

Location 11,839,415 – 11,839,509
Length 94
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 72.33
Mean single sequence MFE -33.45
Consensus MFE -17.86
Energy contribution -19.53
Covariance contribution 1.67
Combinations/Pair 1.17
Mean z-score -2.30
Structure conservation index 0.53
SVM decision value 2.10
SVM RNA-class probability 0.988022
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11839415 94 + 27905053
-----UGCUCCUUAUCCCUGUCUCUAGCGUAUCCUUC------AUGGGCUUGGGGUUGGU--UUUGUGAAUGAAU------------GCCAACCCUUGGCUCAUCUGGGGGUACUUUUU
-----.(((................)))((((((((.------(((((((.(((((((((--(((......))).------------))))))))).)))))))..))))))))..... ( -34.89)
>DroSec_CAF1 19324 101 + 1
-----UGCUUCUUAUCCCUGUCUCUA-----UCCAUGAAGGAAAUGGGUUUGGGGUUGGU--UUUGUGAAUGAAUGAC------CCUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUU
-----.......(((((((.......-----(((.....))).((((((..(((((((((--...((.(.....).))------...)))))))))..))))))..)))))))...... ( -34.40)
>DroSim_CAF1 20814 106 + 1
-----UGCUCCUUAUCCCUGUCUCUAGCGUAUCCUUC------AUGGGCUUGGGGUUGGU--UUUGUGAAUGAAUGAGACGGCGUCUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUU
-----.(((................)))((((((((.------(((((((.((((((.((--((..(......)..))))(((....))))))))).)))))))..))))))))..... ( -37.09)
>DroEre_CAF1 23318 101 + 1
-----UGGUCCUUAUCCAUGCCCCUAGCGUAUCCUUU------UUGGAUUUGGGGUGGGU--U-UAUGAAUGAA----CCGGCGACUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUU
-----(((.......)))(((((((((((.((((...------..)))).))((((.(((--(-((....))))----))(((....))).)))).........)))))))))...... ( -35.50)
>DroYak_CAF1 23954 106 + 1
GGUCCUGGUCCUUAUCCCUGUCUCUAGCGUAUCCUUU------UAGGGUUUGGGGUGGGU--U-UAUGAAUGAA----CCGGCCGCUGCCAACCCCUGGCUCAUCUGGGGGUACUUUUU
(((..(((((..((((((...((((((.........)------)))))...))))))(((--(-((....))))----)))))))..))).(((((..(.....)..)))))....... ( -39.10)
>DroAna_CAF1 19060 80 + 1
-----U-------------GUCUCGAGCGUAUCCUUA------AGGGA--UGGAGUGAGUGCCUUAUGAAUGAA-------------GCCAACCCUUGUCCCUUUGGGGGUUACUUUUC
-----.-------------.........(((((((((------(((((--(((..((.((..(........)..-------------))))..))..))))).))))))).)))..... ( -19.70)
>consensus
_____UGCUCCUUAUCCCUGUCUCUAGCGUAUCCUUC______AUGGGUUUGGGGUGGGU__UUUAUGAAUGAA___________CUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUU
............................((((((((.......(((((((.(((((.(((...........................))).))))).)))))))..))))))))..... (-17.86 = -19.53 +   1.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,839,447 – 11,839,542
Length 95
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 76.94
Mean single sequence MFE -35.92
Consensus MFE -20.98
Energy contribution -21.81
Covariance contribution 0.84
Combinations/Pair 1.32
Mean z-score -1.66
Structure conservation index 0.58
SVM decision value 0.44
SVM RNA-class probability 0.736507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11839447 95 + 27905053
---AUGGGCUUGGGGUUGGU--UUUGUGAAUGAAU------------GCCAACCCUUGGCUCAUCUGGGGGUACUUUUUAUCCUGCCGGAAGUGUC-------CUUUCGACCAAUGGAA
---(((((((.(((((((((--(((......))).------------))))))))).))))))).((((((((.....)))))...((((((....-------)))))).)))...... ( -35.50)
>DroSec_CAF1 19354 104 + 1
GAAAUGGGUUUGGGGUUGGU--UUUGUGAAUGAAUGAC------CCUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUUACCCUGCCGGAAGUGUC-------CUUUCGACCAAUGGAA
...((((((..(((((((((--...((.(.....).))------...)))))))))..)))))).((((((((.....)))))...((((((....-------)))))).)))...... ( -37.20)
>DroSim_CAF1 20846 107 + 1
---AUGGGCUUGGGGUUGGU--UUUGUGAAUGAAUGAGACGGCGUCUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUUACCCUGCCGGAAGUGUC-------CUUUCGACCAAUGGAA
---(((((((.((((((.((--((..(......)..))))(((....))))))))).))))))).((((((((.....)))))...((((((....-------)))))).)))...... ( -40.30)
>DroEre_CAF1 23350 102 + 1
---UUGGAUUUGGGGUGGGU--U-UAUGAAUGAA----CCGGCGACUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUUGCCCUGCCGGAAGUCUC-------CGUUCGACCAAUGGAA
---........(((((.(((--(-((....))))----))(((....))).))))).((((..((((((((((.....)))))..)))))))))((-------((((.....)))))). ( -34.80)
>DroYak_CAF1 23991 102 + 1
---UAGGGUUUGGGGUGGGU--U-UAUGAAUGAA----CCGGCCGCUGCCAACCCCUGGCUCAUCUGGGGGUACUUUUUACCCUGCCGGAAGUGUC-------CUUUCGACCAAUGGAA
---..((((..(((((.(((--(-((....))))----))(((....))).)))))..))))...((((((((.....)))))...((((((....-------)))))).)))...... ( -38.70)
>DroAna_CAF1 19079 101 + 1
---AGGGA--UGGAGUGAGUGCCUUAUGAAUGAA-------------GCCAACCCUUGUCCCUUUGGGGGUUACUUUUCACUAGCCCGGAAGUGGCACUCGUACUACUGGCCAAUGAAA
---..((.--(((..((((((((...(((..(((-------------(..((((((((......)))))))).)))))))......(....).))))))))..)))....))....... ( -29.00)
>consensus
___AUGGGUUUGGGGUGGGU__UUUAUGAAUGAA___________CUGCCAACCCUUGGCUCAUCUGGGGGUACUUUUUACCCUGCCGGAAGUGUC_______CUUUCGACCAAUGGAA
....((((((.(((((.(((...........................))).))))).))))))..((((((((.....)))))...((((((...........)))))).)))...... (-20.98 = -21.81 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:23 2006