Locus 166

Sequence ID 3R_DroMel_CAF1
Location 823,523 – 823,643
Length 120
Max. P 0.998666
window275 window276

overview

Window 5

Location 823,523 – 823,643
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.49
Mean single sequence MFE -25.48
Consensus MFE -23.10
Energy contribution -23.54
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.13
Structure conservation index 0.91
SVM decision value 3.18
SVM RNA-class probability 0.998666
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 823523 120 + 27905053
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAAUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUCUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUGG
......(((....)))(((...((((((((((((...(((.....)))((.(((....)))..))....................))))))))))))....)))................ ( -27.10)
>DroSec_CAF1 5885 120 + 1
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGCUUUGAUAUCUCGCUGGAAAAAACCUCUGGCUUAAAUUUAUAUUUUG
......(((....)))((((..((((((((((((..((((.....))))....((((..((...........))..)))).....))))))))))))...))))................ ( -27.40)
>DroSim_CAF1 3062 120 + 1
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAAUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGCUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
......(((....)))(((...((((((((((((..((((.....))))....((((..((...........))..)))).....))))))))))))....)))................ ( -27.40)
>DroEre_CAF1 6492 118 + 1
UUUUUUCCCAUUUCAGGUUAUUGUU--UUCCAGCCACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
......(((.....(((((....((--(((((((...(((......((((.(((....((......))...))).))))...))))))))))))))))).)))................. ( -23.40)
>DroYak_CAF1 6180 117 + 1
UUUUUUU-CAUUUGGGGUAAUGGUUU-UUUCAGCUACGAGUCGUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAUAUUUAUAUUUU-
.......-..((((((((.....(((-(((((((..((((.....))))....((((.((...........))...)))).....))))))))))))))))))................- ( -22.10)
>consensus
UUUUUUCCCAUUUGGGGUUAUUGUUUUUUCCAGCUACGAGUCUUUUUCGGUACGUCAUCGUUUCCUUGUUUCGUUUUGAUAUCUCGCUGGAAAAAACCUCGGGCUUAAAUUUAUAUUUUG
.........(((((((.(....((((((((((((..((((.....))))....((((.((...........))...)))).....))))))))))))....).))))))).......... (-23.10 = -23.54 +   0.44) 

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 823,523 – 823,643
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.49
Mean single sequence MFE -25.76
Consensus MFE -20.70
Energy contribution -21.50
Covariance contribution 0.80
Combinations/Pair 1.08
Mean z-score -3.34
Structure conservation index 0.80
SVM decision value 2.79
SVM RNA-class probability 0.997034
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 823523 120 - 27905053
CCAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAGAACGAAACAAGGAAACGAUGACGUACCGAAAAAGAUUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...(((((.(..(....).....((...)).....).))))).))))))))))))......(((....)))...... ( -27.70)
>DroSec_CAF1 5885 120 - 1
CAAAAUAUAAAUUUAAGCCAGAGGUUUUUUCCAGCGAGAUAUCAAAGCGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...((((.....(....).....((...))........)))).))))))))))))......(((....)))...... ( -26.70)
>DroSim_CAF1 3062 120 - 1
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAGCGAAACAAGGAAACGAUGACGUACCGAAAAAGAUUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...(((((.(..(....).....((...)).....).))))).))))))))))))......(((....)))...... ( -28.00)
>DroEre_CAF1 6492 118 - 1
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUGGCUGGAA--AACAAUAACCUGAAAUGGGAAAAAA
.................((((((((((((((((((...........(((......(....).....))).((((.......))).))))))))--))....)))))....))))...... ( -25.30)
>DroYak_CAF1 6180 117 - 1
-AAAAUAUAAAUAUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAACGACUCGUAGCUGAAA-AAACCAUUACCCCAAAUG-AAAAAAA
-.....................(((((((((.(((((....))...((((.....(....).....(((.......)))..)))).)))))))-))))).............-....... ( -21.10)
>consensus
CAAAAUAUAAAUUUAAGCCCGAGGUUUUUUCCAGCGAGAUAUCAAAACGAAACAAGGAAACGAUGACGUACCGAAAAAGACUCGUAGCUGGAAAAAACAAUAACCCCAAAUGGGAAAAAA
.......................((((((((((((((....))...((((.....(....).....((...))........)))).)))))))))))).....(((.....)))...... (-20.70 = -21.50 +   0.80) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:32 2006