Locus 1456

Sequence ID X_DroMel_CAF1
Location 4,381,841 – 4,381,933
Length 92
Max. P 0.871440
window2324 window2325

overview

Window 4

Location 4,381,841 – 4,381,933
Length 92
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 78.34
Mean single sequence MFE -29.69
Consensus MFE -18.68
Energy contribution -18.90
Covariance contribution 0.22
Combinations/Pair 1.12
Mean z-score -1.30
Structure conservation index 0.63
SVM decision value -0.03
SVM RNA-class probability 0.516750
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4381841 92 + 22224390
GCU--------GCUCGCUUUCGUCUUGUUCGCUUUCGUGUC-CAU----CGC-UCACAUGGCGAAACUGAGCUGCAGAGCAUUGCGCAGCUCGUUGAGCACCAUGG
(.(--------((((..(((((((.(((..((.........-...----.))-..))).)))))))..(((((((..........)))))))...))))).).... ( -29.72)
>DroSec_CAF1 167007 76 + 1
CCU--------GC-------UGUCUCGCUCGGUUU--------------CGC-UCACAUGGCGAAACUGAGCUGCAGAGCAUUGCGCAGCUCGUUGAGCACCAUGG
(((--------(.-------((.((((((((((((--------------(((-(.....)))))))))))))....((((........))))...))))).)).)) ( -33.20)
>DroSim_CAF1 154502 76 + 1
CCU--------GC-------UGUCUCGCUCGGUUU--------------CGC-UCACAUGGCGAAACUGAGCUGCAGAGCAUUGCGCAGCUCGUUGAGCACCAUGG
(((--------(.-------((.((((((((((((--------------(((-(.....)))))))))))))....((((........))))...))))).)).)) ( -33.20)
>DroEre_CAF1 177850 85 + 1
GCU--------GC-------UGUCUCGCUUGCAUUCGUGUC-CAU----CGC-UCACAUGGCGAAACUGAGCUGCAGAGCAUUGCGCAGUUCGUUGAGCACCAUGG
((.--------((-------......))..))....(((..-...----)))-...(((((.(.(((.(((((((..........))))))))))...).))))). ( -24.00)
>DroYak_CAF1 170288 94 + 1
GCUGUGGAGUCGC-------UGUCUCGCUCACUUUUGUGUCCCAU----CGC-UUACAUGGCAAAACUGAGCUGCAGAGCAUUGCGCAACUCGUUGAGCACCAUGG
.((((((.((..(-------(((...(((((.(((((....((((----...-....))))))))).))))).)))).))..(((.(((....))).))))))))) ( -26.00)
>DroAna_CAF1 200575 90 + 1
UCU--------GC-------CAUCUCGCUUGCUUUCGCAUC-GCUGGCUCGCUUCACAUGGCGAAGCUGAGCUGCAGGGCAUUCCUCAGCUCGUUCAGCACCAUGG
...--------.(-------(((......(((....)))..-(((((((((((......)))).))).((((((.(((.....)))))))))...))))...)))) ( -32.00)
>consensus
GCU________GC_______UGUCUCGCUCGCUUUCGUGUC_CAU____CGC_UCACAUGGCGAAACUGAGCUGCAGAGCAUUGCGCAGCUCGUUGAGCACCAUGG
........................................................(((((.(.(((.(((((((..........))))))))))...).))))). (-18.68 = -18.90 +   0.22)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 4,381,841 – 4,381,933
Length 92
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 78.34
Mean single sequence MFE -30.97
Consensus MFE -20.09
Energy contribution -20.32
Covariance contribution 0.22
Combinations/Pair 1.11
Mean z-score -1.79
Structure conservation index 0.65
SVM decision value 0.87
SVM RNA-class probability 0.871440
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4381841 92 - 22224390
CCAUGGUGCUCAACGAGCUGCGCAAUGCUCUGCAGCUCAGUUUCGCCAUGUGA-GCG----AUG-GACACGAAAGCGAACAAGACGAAAGCGAGC--------AGC
....(.(((((...((((((((........))))))))..(((((.(.(((..-((.----.((-....))...))..))).).)))))..))))--------).) ( -31.50)
>DroSec_CAF1 167007 76 - 1
CCAUGGUGCUCAACGAGCUGCGCAAUGCUCUGCAGCUCAGUUUCGCCAUGUGA-GCG--------------AAACCGAGCGAGACA-------GC--------AGG
((.((.(((((...((((........))))....((((.((((((((....).-)))--------------)))).))))))).))-------.)--------))) ( -31.40)
>DroSim_CAF1 154502 76 - 1
CCAUGGUGCUCAACGAGCUGCGCAAUGCUCUGCAGCUCAGUUUCGCCAUGUGA-GCG--------------AAACCGAGCGAGACA-------GC--------AGG
((.((.(((((...((((........))))....((((.((((((((....).-)))--------------)))).))))))).))-------.)--------))) ( -31.40)
>DroEre_CAF1 177850 85 - 1
CCAUGGUGCUCAACGAACUGCGCAAUGCUCUGCAGCUCAGUUUCGCCAUGUGA-GCG----AUG-GACACGAAUGCAAGCGAGACA-------GC--------AGC
....(.((((....((.(((((........))))).)).(((((((..((((.-.((----...-....))..)))).))))))))-------))--------).) ( -23.30)
>DroYak_CAF1 170288 94 - 1
CCAUGGUGCUCAACGAGUUGCGCAAUGCUCUGCAGCUCAGUUUUGCCAUGUAA-GCG----AUGGGACACAAAAGUGAGCGAGACA-------GCGACUCCACAGC
.......(((....((((((((((......))).(((((.((((((((((...-.).----))))....))))).)))))......-------)))))))...))) ( -29.70)
>DroAna_CAF1 200575 90 - 1
CCAUGGUGCUGAACGAGCUGAGGAAUGCCCUGCAGCUCAGCUUCGCCAUGUGAAGCGAGCCAGC-GAUGCGAAAGCAAGCGAGAUG-------GC--------AGA
.(((((((..(...(((((((((.....))).))))))..)..)))))))........((((.(-(.(((....)))..))...))-------))--------... ( -38.50)
>consensus
CCAUGGUGCUCAACGAGCUGCGCAAUGCUCUGCAGCUCAGUUUCGCCAUGUGA_GCG____AUG_GACACGAAAGCGAGCGAGACA_______GC________AGC
.(((((((...(((((((((((........)))))))).))).)))))))........................................................ (-20.09 = -20.32 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:53 2006