Locus 959

Sequence ID 3L_DroMel_CAF1
Location 2,857,565 – 2,857,661
Length 96
Max. P 0.786906
window1473 window1474

overview

Window 3

Location 2,857,565 – 2,857,661
Length 96
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 84.07
Mean single sequence MFE -25.86
Consensus MFE -21.57
Energy contribution -21.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.83
SVM decision value 0.57
SVM RNA-class probability 0.786906
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2857565 96 + 23771897
-------CUUGAGUCUGCUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUGCAAUUUGCGUGCUGCAAUUGCCCCG-UCCCCGGCCCU
-------........(((.((((...(((((((..((((((................)))))).)))))))....)))).)))...(((...-.....)))... ( -26.99)
>DroPse_CAF1 121939 98 + 1
UCUGCCACUCGUUUUCCAUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUACAAUUUGCGUGCUGCAAUUGCUGUG-U-----GCCCU
...................((((((.(((((((.(((.(((....((((.(((......))))))).....)))))).)))))))....)))-)-----))... ( -27.70)
>DroSec_CAF1 102306 95 + 1
-------CUUGAGUCUUCUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUGCAAUUUGCGUGCUGCAAUUGCCCCG-UCCC-UGCCCU
-------.....((((((((((......))))))).)))......((((.(((......)))))))((((((.((.....))))))))....-....-...... ( -24.00)
>DroEre_CAF1 105975 90 + 1
-------CUUGAGUAUGCUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUGCAAUUUGCGUGCUGCAAUUGCCCCUGCCC-------U
-------.....((((((.((((...(((((((..((((((................)))))).)))))))....)))).)))..)))........-------. ( -24.49)
>DroYak_CAF1 107591 96 + 1
-------CUUGAGUGUGCUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUGCAAUUUGCGUGCUGCAAUUGCCCCUGCCCC-AGCCCU
-------........(((.((((...(((((((..((((((................)))))).)))))))....)))).)))..............-...... ( -24.29)
>DroPer_CAF1 122891 98 + 1
UCUGCCACUCGUUUUCCAUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUACAAUUUGCGUGCUGCAAUUGCUGUG-U-----GCCCU
...................((((((.(((((((.(((.(((....((((.(((......))))))).....)))))).)))))))....)))-)-----))... ( -27.70)
>consensus
_______CUUGAGUCUGCUGCACAUUGUUGCAGAACGACAAUUAAAGUCUGAUUAUUUUGUCGACUGCAAUUUGCGUGCUGCAAUUGCCCCG_UCC___GCCCU
...................(((....(((((((.(((.(((....((((.(((......))))))).....)))))).))))))))))................ (-21.57 = -21.57 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,857,565 – 2,857,661
Length 96
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 84.07
Mean single sequence MFE -26.87
Consensus MFE -20.72
Energy contribution -20.50
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.97
Structure conservation index 0.77
SVM decision value 0.30
SVM RNA-class probability 0.677609
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2857565 96 - 23771897
AGGGCCGGGGA-CGGGGCAAUUGCAGCACGCAAAUUGCAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAGCAGACUCAAG-------
.((((((....-))).....((((.(((((....((((((.((((((..(((.......))).))))))..))))))...))))).)))).)))...------- ( -32.30)
>DroPse_CAF1 121939 98 - 1
AGGGC-----A-CACAGCAAUUGCAGCACGCAAAUUGUAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAUGGAAAACGAGUGGCAGA
...((-----.-(((.((....)).(((((....((((((.((((((..(((.......))).))))))..))))))...)))))...........)))))... ( -25.50)
>DroSec_CAF1 102306 95 - 1
AGGGCA-GGGA-CGGGGCAAUUGCAGCACGCAAAUUGCAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAGAAGACUCAAG-------
.((((.-..((-(...((((((((.....)).)))))).)))(((((..(((.......))).))))).(((((((......)))))))).)))...------- ( -25.30)
>DroEre_CAF1 105975 90 - 1
A-------GGGCAGGGGCAAUUGCAGCACGCAAAUUGCAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAGCAUACUCAAG-------
.-------.....(((.....(((.(((((....((((((.((((((..(((.......))).))))))..))))))...))))).)))..)))...------- ( -25.20)
>DroYak_CAF1 107591 96 - 1
AGGGCU-GGGGCAGGGGCAAUUGCAGCACGCAAAUUGCAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAGCACACUCAAG-------
.(((.(-(..((....((....)).(((((....((((((.((((((..(((.......))).))))))..))))))...))))).)).)))))...------- ( -27.40)
>DroPer_CAF1 122891 98 - 1
AGGGC-----A-CACAGCAAUUGCAGCACGCAAAUUGUAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAUGGAAAACGAGUGGCAGA
...((-----.-(((.((....)).(((((....((((((.((((((..(((.......))).))))))..))))))...)))))...........)))))... ( -25.50)
>consensus
AGGGC___GGA_CGGGGCAAUUGCAGCACGCAAAUUGCAGUCGACAAAAUAAUCAGACUUUAAUUGUCGUUCUGCAACAAUGUGCAGCAAACUCAAG_______
................((....)).(((((....((((((.((((((..(((.......))).))))))..))))))...)))))................... (-20.72 = -20.50 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:23 2006