Locus 4501

Sequence ID X_DroMel_CAF1
Location 11,887,394 – 11,887,488
Length 94
Max. P 0.769179
window7404 window7405

overview

Window 4

Location 11,887,394 – 11,887,488
Length 94
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 80.07
Mean single sequence MFE -22.50
Consensus MFE -14.60
Energy contribution -14.22
Covariance contribution -0.38
Combinations/Pair 1.11
Mean z-score -1.89
Structure conservation index 0.65
SVM decision value 0.52
SVM RNA-class probability 0.769179
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11887394 94 + 22224390
CGAAGGGGAUUCCCCACCUCGGCCACGCCUU-CACUUCUUCCGCAAAGGACUUUCCCUUCGAUUCACUCGGAAAAAUCAUUAACUUAGCUACAUA
(((((((((...........(((...)))..-.......(((.....)))..))))))))).................................. ( -19.00)
>DroSec_CAF1 19299 92 + 1
CGAAGGGGAUUCCCCACCUCGGCCACGCCUU-CACUUUUUCCGCAGAGGACUUUCCUUUCCACUCACUCGGAAAAAUCAUUUGCGUAGCUACA--
....((((...)))).....(((.((((...-...((((((((.((.(((........))).))....))))))))......)))).)))...-- ( -25.30)
>DroEre_CAF1 20763 78 + 1
CGAAGGGGAUUCCCCACCUCGGCCACGCCUU-CACUUCUUCCGCAGAGGACUUUCC-----GCUCACUUGGAAAAAUCACU-G----------CG
.(((((((....))).....(((...)))..-..))))...(((((.((..(((((-----(......))))))..)).))-)----------)) ( -23.30)
>DroYak_CAF1 23392 90 + 1
CGAAGGGGAUUCCCCACCUCGGCCACGCCUUCCACUUCCUCCGCUGAGGACUUUCC-----ACACACCUGGAGAAAUCAUUUACGUUGCUACAUG
....((((...)))).....(((.(((.........(((((....))))).(((((-----(......)))))).........))).)))..... ( -22.40)
>consensus
CGAAGGGGAUUCCCCACCUCGGCCACGCCUU_CACUUCUUCCGCAGAGGACUUUCC_____ACUCACUCGGAAAAAUCAUUUACGUAGCUACAUG
.(((((((....))).....(((...))).....)))).(((.....))).(((((.............)))))..................... (-14.60 = -14.22 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,887,394 – 11,887,488
Length 94
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 80.07
Mean single sequence MFE -29.91
Consensus MFE -19.80
Energy contribution -21.17
Covariance contribution 1.37
Combinations/Pair 1.21
Mean z-score -1.69
Structure conservation index 0.66
SVM decision value 0.16
SVM RNA-class probability 0.614159
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11887394 94 - 22224390
UAUGUAGCUAAGUUAAUGAUUUUUCCGAGUGAAUCGAAGGGAAAGUCCUUUGCGGAAGAAGUG-AAGGCGUGGCCGAGGUGGGGAAUCCCCUUCG
......((((.(((.....((((((((.......(((((((....)))))))))))))))...-..))).))))(((((.(((....)))))))) ( -28.51)
>DroSec_CAF1 19299 92 - 1
--UGUAGCUACGCAAAUGAUUUUUCCGAGUGAGUGGAAAGGAAAGUCCUCUGCGGAAAAAGUG-AAGGCGUGGCCGAGGUGGGGAAUCCCCUUCG
--....(((((((......((((((((....((.(((........))).)).))))))))...-...)))))))(((((.(((....)))))))) ( -35.40)
>DroEre_CAF1 20763 78 - 1
CG----------C-AGUGAUUUUUCCAAGUGAGC-----GGAAAGUCCUCUGCGGAAGAAGUG-AAGGCGUGGCCGAGGUGGGGAAUCCCCUUCG
((----------(-((.(..((((((........-----))))))..).))))).........-..(((...)))((((.(((....))))))). ( -26.60)
>DroYak_CAF1 23392 90 - 1
CAUGUAGCAACGUAAAUGAUUUCUCCAGGUGUGU-----GGAAAGUCCUCAGCGGAGGAAGUGGAAGGCGUGGCCGAGGUGGGGAAUCCCCUUCG
......((.((((......(((((((.(.((...-----((.....)).)).)))))))).......)))).))(((((.(((....)))))))) ( -29.12)
>consensus
CAUGUAGCUACGCAAAUGAUUUUUCCAAGUGAGU_____GGAAAGUCCUCUGCGGAAGAAGUG_AAGGCGUGGCCGAGGUGGGGAAUCCCCUUCG
......(((((((......((((((((....((.....(((.....))))).)))))))).......)))))))(((((.(((....)))))))) (-19.80 = -21.17 +   1.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:43 2006