Locus 1424

Sequence ID X_DroMel_CAF1
Location 4,300,920 – 4,301,024
Length 104
Max. P 0.999978
window2271 window2272

overview

Window 1

Location 4,300,920 – 4,301,024
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.77
Mean single sequence MFE -23.88
Consensus MFE -22.54
Energy contribution -22.38
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -3.53
Structure conservation index 0.94
SVM decision value 5.18
SVM RNA-class probability 0.999978
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4300920 104 + 22224390
CCCUUGCGCGAC-------UUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAA-AUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGUACUUGCCACCUC--------
......(((((.-------(((....))).....((((((((((.........-.))))))))))..))))).(((.(((((((......))))))).)))...........-------- ( -23.60)
>DroSec_CAF1 87319 113 + 1
CCCUUGCGCGAC-------UUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAACAUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGNNNNNNNNNNNNNNNNNNNNN
......(((((.-------(((....))).....((((((((((...........))))))))))..))))).....(((((((......)))))))....................... ( -22.40)
>DroSim_CAF1 80932 104 + 1
CCCUUGCGCGAC-------UUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAA-AUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGUACUUGCCACCUC--------
......(((((.-------(((....))).....((((((((((.........-.))))))))))..))))).(((.(((((((......))))))).)))...........-------- ( -23.60)
>DroEre_CAF1 94356 111 + 1
CCCCUGCGCGACUUCAGACUUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAA-AUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGUACUUGCCACCUC--------
......(((((.((((((.....)))))).....((((((((((.........-.))))))))))..))))).(((.(((((((......))))))).)))...........-------- ( -25.90)
>DroYak_CAF1 89117 104 + 1
CCCUUGCGCAAC-------UUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAA-AUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGUACUUGCCACCUC--------
......(((((.-------(((....))).....((((((((((.........-.))))))))))..))))).(((.(((((((......))))))).)))...........-------- ( -23.90)
>consensus
CCCUUGCGCGAC_______UUCAUUUGAAUAUUAAAAAAUUCCAAAACACAAA_AUGGAAUUUUUAUUUGCGAUAUUUUGUCGCACCUCAGCGACAACGUACUUGCCACCUC________
......(((((........(((....))).....((((((((((...........))))))))))..))))).....(((((((......)))))))....................... (-22.54 = -22.38 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,300,920 – 4,301,024
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.77
Mean single sequence MFE -27.46
Consensus MFE -23.70
Energy contribution -25.14
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -1.91
Structure conservation index 0.86
SVM decision value 1.60
SVM RNA-class probability 0.967033
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4300920 104 - 22224390
--------GAGGUGGCAAGUACGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAU-UUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAA-------GUCGCGCAAGGG
--------..((((((((.....))))))))...(((((((..............((((((((((.-.........)))))))))).....(((....)))-------)))))))..... ( -29.30)
>DroSec_CAF1 87319 113 - 1
NNNNNNNNNNNNNNNNNNNNNCGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAUGUUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAA-------GUCGCGCAAGGG
.............................((...(((((((..............((((((((((...........)))))))))).....(((....)))-------)))))))..)). ( -22.20)
>DroSim_CAF1 80932 104 - 1
--------GAGGUGGCAAGUACGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAU-UUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAA-------GUCGCGCAAGGG
--------..((((((((.....))))))))...(((((((..............((((((((((.-.........)))))))))).....(((....)))-------)))))))..... ( -29.30)
>DroEre_CAF1 94356 111 - 1
--------GAGGUGGCAAGUACGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAU-UUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAAGUCUGAAGUCGCGCAGGGG
--------..((((((((.....))))))))...(((((((..............((((((((((.-.........)))))))))).....(((....))).......)))))))..... ( -29.30)
>DroYak_CAF1 89117 104 - 1
--------GAGGUGGCAAGUACGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAU-UUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAA-------GUUGCGCAAGGG
--------..((((((((.....))))))))...(((((((..............((((((((((.-.........)))))))))).....(((....)))-------)))))))..... ( -27.20)
>consensus
________GAGGUGGCAAGUACGUUGUCGCUGAGGUGCGACAAAAUAUCGCAAAUAAAAAUUCCAU_UUUGUGUUUUGGAAUUUUUUAAUAUUCAAAUGAA_______GUCGCGCAAGGG
..........((((((((.....))))))))...(((((((..............((((((((((...........)))))))))).....(((....))).......)))))))..... (-23.70 = -25.14 +   1.44)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:07 2006