Locus 4748

Sequence ID 3L_DroMel_CAF1
Location 13,349,398 – 13,349,495
Length 97
Max. P 0.666385
window7474 window7475

overview

Window 4

Location 13,349,398 – 13,349,495
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.57
Mean single sequence MFE -31.92
Consensus MFE -22.49
Energy contribution -23.72
Covariance contribution 1.23
Combinations/Pair 1.24
Mean z-score -1.47
Structure conservation index 0.70
SVM decision value 0.16
SVM RNA-class probability 0.614093
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13349398 97 + 23771897
AAGGUCCUUCUGCAAGGAUCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG-----------------------CAUUACUUUGACUGCAGCAUGAUGCAGAGGUGGUCGGCACU
.((((((((....))))))))((.(((((((..((((((.......)))))).(((-----------------------(((((..(((....)))..))))))))))))))).)).... ( -31.60)
>DroSec_CAF1 20969 97 + 1
AAGGUCCUUCCGCAAGGAUCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG-----------------------CAUUACUUUGACUGCAGCAUGAUGCAGAGGUGGUCGGCGCU
.((((((((....))))))))((.(((((((..((((((.......)))))).(((-----------------------(((((..(((....)))..))))))))))))))).)).... ( -31.60)
>DroSim_CAF1 20789 97 + 1
AAGGUCCUUCCGCAAGGAUCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG-----------------------CAUUACUUUGACUGCAGCAUGAUGCAGAGGUGGCCGGCGCU
..((((..(((....)))......(((......((((((.......)))))).(((-----------------------(((((..(((....)))..)))))))).)))))))...... ( -29.00)
>DroEre_CAF1 21316 95 + 1
AAGGUCCUUCCGCAAGGACCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG-----------------------CAUUACUUUGACUGCAGCAUGAUGCAGAGCCAGUCGGGC--
.((((((((....))))))))............(((..(((((((((((...))))-----------------------)..........(((((......)))))))))))..))).-- ( -34.20)
>DroYak_CAF1 22077 97 + 1
AAGGUCCUUCCGCAAGGAUCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG-----------------------CAUUACUUUGACUGCAGCAUGGUGCAGAGGUGGUCGGUGUU
.((((((((....))))))))((.(((((((..((((((.......)))))).(((-----------------------(((((..(((....)))..))))))))))))))).)).... ( -31.30)
>DroAna_CAF1 19971 113 + 1
AGGGUCUUUCCACAGGGAUCUCCAGCCAUAAACUUCCAUUGGUUGCAAUGGGAUUGGAAUCCCCUUUCACCCGGGGAGGCAUUACUUUGACUACAGCAU---CCAGAGGA-CUCGGU---
.((((((((......((....)).(((......((((((((....))))))))......(((((........))))))))...................---...)))))-)))...--- ( -33.80)
>consensus
AAGGUCCUUCCGCAAGGAUCUCCAACCAUUUACCCCAUUUGGCUGCAAUGGGAUUG_______________________CAUUACUUUGACUGCAGCAUGAUGCAGAGGUGGUCGGCGCU
.((((((((....))))))))((.(((((((..((((.(((....)))))))......................................(((((......)))))))))))).)).... (-22.49 = -23.72 +   1.23)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 13,349,398 – 13,349,495
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.57
Mean single sequence MFE -32.42
Consensus MFE -21.68
Energy contribution -23.38
Covariance contribution 1.70
Combinations/Pair 1.15
Mean z-score -1.72
Structure conservation index 0.67
SVM decision value 0.28
SVM RNA-class probability 0.666385
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13349398 97 - 23771897
AGUGCCGACCACCUCUGCAUCAUGCUGCAGUCAAAGUAAUG-----------------------CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGAUCCUUGCAGAAGGACCUU
....(((((((....(((((..((((........)))))))-----------------------))((((((((.......))))))))...)))))))((.(((((....))))).)). ( -31.70)
>DroSec_CAF1 20969 97 - 1
AGCGCCGACCACCUCUGCAUCAUGCUGCAGUCAAAGUAAUG-----------------------CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGAUCCUUGCGGAAGGACCUU
....(((((((....(((((..((((........)))))))-----------------------))((((((((.......))))))))...)))))))((.(((((....))))).)). ( -31.70)
>DroSim_CAF1 20789 97 - 1
AGCGCCGGCCACCUCUGCAUCAUGCUGCAGUCAAAGUAAUG-----------------------CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGAUCCUUGCGGAAGGACCUU
....(((((((....(((((..((((........)))))))-----------------------))((((((((.......))))))))...)))))))((.(((((....))))).)). ( -31.20)
>DroEre_CAF1 21316 95 - 1
--GCCCGACUGGCUCUGCAUCAUGCUGCAGUCAAAGUAAUG-----------------------CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGGUCCUUGCGGAAGGACCUU
--.((((..((((((((((......))))).....((((((-----------------------......)))))))))))..))))...........(((((((((....))))))))) ( -35.80)
>DroYak_CAF1 22077 97 - 1
AACACCGACCACCUCUGCACCAUGCUGCAGUCAAAGUAAUG-----------------------CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGAUCCUUGCGGAAGGACCUU
....(((((((....((((...((((........)))).))-----------------------))((((((((.......))))))))...)))))))((.(((((....))))).)). ( -30.60)
>DroAna_CAF1 19971 113 - 1
---ACCGAG-UCCUCUGG---AUGCUGUAGUCAAAGUAAUGCCUCCCCGGGUGAAAGGGGAUUCCAAUCCCAUUGCAACCAAUGGAAGUUUAUGGCUGGAGAUCCCUGUGGAAAGACCCU
---..(...-(((.(.((---((.((.((((((..........(((((........)))))........((((((....)))))).......)))))).))))))..).)))..)..... ( -33.50)
>consensus
AGCGCCGACCACCUCUGCAUCAUGCUGCAGUCAAAGUAAUG_______________________CAAUCCCAUUGCAGCCAAAUGGGGUAAAUGGUUGGAGAUCCUUGCGGAAGGACCUU
....(((((((...(((((......)))))....................................((((((((.......))))))))...)))))))((.(((((....))))).)). (-21.68 = -23.38 +   1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:32:12 2006