Locus 3479

Sequence ID X_DroMel_CAF1
Location 9,337,252 – 9,337,371
Length 119
Max. P 0.939303
window5689 window5690

overview

Window 9

Location 9,337,252 – 9,337,371
Length 119
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 86.34
Mean single sequence MFE -23.58
Consensus MFE -18.42
Energy contribution -18.55
Covariance contribution 0.13
Combinations/Pair 1.08
Mean z-score -2.27
Structure conservation index 0.78
SVM decision value 1.28
SVM RNA-class probability 0.939303
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9337252 119 + 22224390
UCUCCACUCCACCAAAACAAAAAAAAAAAACCCAAGCCGCAUGAAACUCUCCUGUUCCUUGGAAAAACAAACAAGAGCUCUGUUUAAUUUCGGUACGACCAAACGCUUGGGCGCUAUGA
..............................(((((((......((((.(((.((((...((......)))))).)))....))))......((.....))....)))))))........ ( -19.60)
>DroSec_CAF1 117588 107 + 1
---------CAAAAAAACAAAA-AAAAAACCCCAAGCCGAAUGGAACUCUCCUGUUCCUUGGAAAAACAAACAAGAGCUCUGUUUAAUUUCGGUACGACCAAACGCUUGGG--CUAUGA
---------.............-.......(((((((.(((((((.((((..((((...((......)))))))))).)))))))......((.....))....)))))))--...... ( -24.00)
>DroEre_CAF1 126459 108 + 1
---------CAAAAAAAAGAAAAAACAAACCCCAAGCCGAAUGGAACUCUCCUGUUCCUUGGAAAAAUAAACAAGAGCUCUGUUUAAAUUCGGUACCAGCAAAUGCUUGGG--CUAUGA
---------................((...(((((((((((((((((......))))).........((((((.(....))))))).)))))))....((....)))))))--...)). ( -25.80)
>DroYak_CAF1 120104 108 + 1
---------CAAAAAAAAAAAAAGAGAGACCCCAAACCGAAUGGAACUCUCCUGUUCCUUGGAAAAACAAACAAGAGCUCUGUUUAAUUUCGGUGCGACCAAACGCUUGGG--UUAUGA
---------..................(((((...((((((.(((((......)))))..........(((((.(....))))))...))))))(((......)))..)))--)).... ( -24.90)
>consensus
_________CAAAAAAAAAAAAAAAAAAACCCCAAGCCGAAUGGAACUCUCCUGUUCCUUGGAAAAACAAACAAGAGCUCUGUUUAAUUUCGGUACGACCAAACGCUUGGG__CUAUGA
..............................(((((((((((..((((.(((.((((..((.....))..)))).)))....))))...))))((........)))))))))........ (-18.42 = -18.55 +   0.13)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,337,252 – 9,337,371
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 86.34
Mean single sequence MFE -29.60
Consensus MFE -26.60
Energy contribution -26.73
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.73
Structure conservation index 0.90
SVM decision value 0.82
SVM RNA-class probability 0.858422
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9337252 119 - 22224390
UCAUAGCGCCCAAGCGUUUGGUCGUACCGAAAUUAAACAGAGCUCUUGUUUGUUUUUCCAAGGAACAGGAGAGUUUCAUGCGGCUUGGGUUUUUUUUUUUUGUUUUGGUGGAGUGGAGA
.......((((((((.(((((.....)))))((.((((....(((((((((.((.....)).))))))))).)))).))...))))))))......((((..(((.....)))..)))) ( -31.80)
>DroSec_CAF1 117588 107 - 1
UCAUAG--CCCAAGCGUUUGGUCGUACCGAAAUUAAACAGAGCUCUUGUUUGUUUUUCCAAGGAACAGGAGAGUUCCAUUCGGCUUGGGGUUUUUU-UUUUGUUUUUUUG---------
......--(((((((.(((((.....)))))........((((((((..(((((((.....)))))))))))))))......))))))).......-.............--------- ( -30.60)
>DroEre_CAF1 126459 108 - 1
UCAUAG--CCCAAGCAUUUGCUGGUACCGAAUUUAAACAGAGCUCUUGUUUAUUUUUCCAAGGAACAGGAGAGUUCCAUUCGGCUUGGGGUUUGUUUUUUCUUUUUUUUG---------
.((.(.--(((((((......(((....(((..(((((((.....)))))))..)))))).(((((......))))).....))))))).).))................--------- ( -27.50)
>DroYak_CAF1 120104 108 - 1
UCAUAA--CCCAAGCGUUUGGUCGCACCGAAAUUAAACAGAGCUCUUGUUUGUUUUUCCAAGGAACAGGAGAGUUCCAUUCGGUUUGGGGUCUCUCUUUUUUUUUUUUUG---------
......--(((((((.(((((.....)))))........((((((((..(((((((.....)))))))))))))))......))))))).....................--------- ( -28.50)
>consensus
UCAUAG__CCCAAGCGUUUGGUCGUACCGAAAUUAAACAGAGCUCUUGUUUGUUUUUCCAAGGAACAGGAGAGUUCCAUUCGGCUUGGGGUUUUUUUUUUUGUUUUUUUG_________
........(((((((.(((((.....)))))........((((((((..(((((((.....)))))))))))))))......))))))).............................. (-26.60 = -26.73 +   0.12)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:21 2006