Locus 5707

Sequence ID 3R_DroMel_CAF1
Location 14,932,183 – 14,932,336
Length 153
Max. P 0.746330
window9338 window9339

overview

Window 8

Location 14,932,183 – 14,932,299
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.14
Mean single sequence MFE -25.48
Consensus MFE -19.82
Energy contribution -20.30
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -1.72
Structure conservation index 0.78
SVM decision value 0.46
SVM RNA-class probability 0.746330
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14932183 116 - 27905053
GAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAAAAAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAGUCCCGUCCC----AGUCGAAUGCAAAAAAAAAAAAAAAAA
..((((........(((..((((..((((((...........))........((((((......))))))..........))))...))----)).)))))))................. ( -25.40)
>DroSec_CAF1 62102 105 - 1
CAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA-AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAGUCCCGUCCC----AGUCGAAUGAAAAAA----------AA
............(((((.((((((.((((((......-....))........((((((......))))))...............))))----.)))))))))))...----------.. ( -25.40)
>DroSim_CAF1 60797 106 - 1
CAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA-AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAGUCCCGUCCC----AGUCGAAUGCAAAAA---------AAA
..((((........(((..((((..((((((......-....))........((((((......))))))..........))))...))----)).))))))).....---------... ( -25.50)
>DroEre_CAF1 58655 104 - 1
GAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAA--AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGAUAAUGAAGUCCCGUCCC----AGUCAAAUGCAAAAAAA----------
................((((((((.(((((((....--...(((........)))..)))))...((((.(((......))))))).))----.)))))).)).......---------- ( -26.10)
>DroYak_CAF1 65653 113 - 1
GAGCAUAAAACGCUUCGCUUUGGCGGAGAGCAUAAA--AAAGGCACACAAAAUCCGUUGUUCAAAGCGGCGAUAAUGAAGUCCCAUGCCAUGAAGUCAAAUGCAAAAAAAAA-----AAA
..((((.....((((((((((.....))))).....--...((((........(((((......))))).(((......)))...))))..)))))...)))).........-----... ( -25.00)
>consensus
GAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA_AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAGUCCCGUCCC____AGUCGAAUGCAAAAAAA_______AAA
..((((..(((((..(((((((((.....))..........(((........)))......)))))))))))).(((......))).............))))................. (-19.82 = -20.30 +   0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,932,219 – 14,932,336
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -33.67
Consensus MFE -29.36
Energy contribution -29.76
Covariance contribution 0.40
Combinations/Pair 1.08
Mean z-score -1.29
Structure conservation index 0.87
SVM decision value 0.32
SVM RNA-class probability 0.689245
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14932219 117 - 27905053
---UUGCUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGGAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAAAAAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAG
---..((((((.((((((........((.((((.((((.(((((.......))))))))))))).))..............(((........)))))))))...)))))).......... ( -31.00)
>DroSec_CAF1 62128 119 - 1
CUGCUGUUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGCAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA-AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAG
.((((((.((((....((((.......))))...)))).))))))...(((((..(((((((((.....))......-...(((........)))......))))))))))))....... ( -35.60)
>DroSim_CAF1 60824 119 - 1
CUGCUGUUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGCAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA-AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAG
.((((((.((((....((((.......))))...)))).))))))...(((((..(((((((((.....))......-...(((........)))......))))))))))))....... ( -35.60)
>DroEre_CAF1 58681 116 - 1
--GCUGCUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGGAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAA--AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGAUAAUGAAG
--((((((....((((((........((.((((.((((.(((((.......))))))))))))).)).........--...(((........)))))))))...)))))).......... ( -34.50)
>DroYak_CAF1 65688 116 - 1
--GCUGCUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGGAGCAUAAAACGCUUCGCUUUGGCGGAGAGCAUAAA--AAAGGCACACAAAAUCCGUUGUUCAAAGCGGCGAUAAUGAAG
--((((((....((((((........(((((.....))))).((........((((((....))))))........--....))...........))))))...)))))).......... ( -31.65)
>consensus
__GCUGCUGUUCGAUAGCUGUACAAACCGGUCAAGAGCCGGAGCAUAAAACGUUUCGCUUUGGCAGGGAGCAUAAAA_AAAGGCGCACAAAAGCCGUUGUUCAAAGCGGCGUUAAUGAAG
..((((((....((((((..........(.((....((((((((............))))))))...)).)..........(((........)))))))))...)))))).......... (-29.36 = -29.76 +   0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:26 2006