Locus 1306

Sequence ID 2L_DroMel_CAF1
Location 3,441,243 – 3,441,353
Length 110
Max. P 0.963501
window2141 window2142

overview

Window 1

Location 3,441,243 – 3,441,353
Length 110
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 78.11
Mean single sequence MFE -28.09
Consensus MFE -18.95
Energy contribution -20.51
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -1.85
Structure conservation index 0.67
SVM decision value 0.91
SVM RNA-class probability 0.880017
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3441243 110 + 22407834
UUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCCGC--CAAGACCGUUACUCCCGUAUAAGAGUUCGCUGAGCUU--C
((((((((((((..((((.....)))).))))))(.((((....)))).).....((((((((((.......--................))))))))))..))))))...--. ( -33.00)
>DroAna_CAF1 34888 97 + 1
UC----UUGCUUUUAUCCUUAAUGGACUGUGCAUGU-------------CUUACCACUCUUAUACUCGUUGGUGCAUGACCGUUACGCUCGUAUAAGAGUUCGUUGAGCUUUGC
..----...........((((((((((.......))-------------).....((((((((((.(((((((.....))))..)))...)))))))))).)))))))...... ( -23.10)
>DroSim_CAF1 30364 110 + 1
UUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCCGC--CGAGACCGUUAUUCCCGUAUAAAAGUUCGCUGAGCUU--C
((((((((((((..((((.....)))).))))))(.((((....)))).).....(((.((((((.......--((....))........)))))).)))..))))))...--. ( -28.16)
>consensus
UUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCCGC__CAAGACCGUUACUCCCGUAUAAGAGUUCGCUGAGCUU__C
....((((((((...(((.....)))..))))))))((((....)))).(((((.((((((((((.........................))))))))))..)).)))...... (-18.95 = -20.51 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,441,243 – 3,441,353
Length 110
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 78.11
Mean single sequence MFE -30.60
Consensus MFE -22.70
Energy contribution -23.27
Covariance contribution 0.56
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.74
SVM decision value 1.55
SVM RNA-class probability 0.963501
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3441243 110 - 22407834
G--AAGCUCAGCGAACUCUUAUACGGGAGUAACGGUCUUG--GCGGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAA
.--..(((..((..(((((......)))))...(((((((--.(.((..........)).)))))))))))))..(((.((((((..((((.....))))...))))))))).. ( -35.10)
>DroAna_CAF1 34888 97 - 1
GCAAAGCUCAACGAACUCUUAUACGAGCGUAACGGUCAUGCACCAACGAGUAUAAGAGUGGUAAG-------------ACAUGCACAGUCCAUUAAGGAUAAAAGCAA----GA
(((...((..((..((((((((((...(((...(((.....))).))).)))))))))).)).))-------------...)))...((((.....))))........----.. ( -24.50)
>DroSim_CAF1 30364 110 - 1
G--AAGCUCAGCGAACUUUUAUACGGGAAUAACGGUCUCG--GCGGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAA
.--....((((((.((((((((((.(......).(((...--..)))..))))))))))..)....((((....))))..(((((..((((.....))))...)))))))))). ( -32.20)
>consensus
G__AAGCUCAGCGAACUCUUAUACGGGAGUAACGGUCUUG__GCGGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAA
..........((..(((((((((((.......).(((.......)))..)))))))))).))....((((....)))).((((((..((((.....))))...))))))..... (-22.70 = -23.27 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:17 2006