Locus 2109

Sequence ID 2L_DroMel_CAF1
Location 5,685,454 – 5,685,602
Length 148
Max. P 0.988394
window3401 window3402

overview

Window 1

Location 5,685,454 – 5,685,563
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.03
Mean single sequence MFE -29.52
Consensus MFE -22.09
Energy contribution -22.03
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -1.31
Structure conservation index 0.75
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5685454 109 - 22407834
GGAGCAAUUUAUGCUGCCUGCCCGACUCCUCGGGGGCAAUUGUCUGACUGCUCCUC---GCCUG--------GCUAGAACCUCCUCCUCCUCAAUUUCGCUCCUCCUCCUCUGGUCUUGU
((((((..(((.((((((..(((((....)))))))))...)).))).))))))..---((..(--------((((((...............................)))))))..)) ( -28.38)
>DroSec_CAF1 130822 99 - 1
GGAGCAAUUUAUGCUGCCUGCCCGACUCCUCGGGGGCAAUUGUCUGACUGCUCCUC---GCCUG--------GCUAGAACCUCCUCCUCCU----------CCUACUCCUCUGGUCUACU
((((((..(((.((((((..(((((....)))))))))...)).))).))))))..---....(--------((((((.............----------........))))))).... ( -28.20)
>DroEre_CAF1 133583 90 - 1
GGAGCAAUUUAUGCUGCUAGCCCGACUCCUCGGGGGCAAUUGUCUGACUGCUCCUC---GGAUG--------GCUGGAACCUC---------------GCUCCUC----UCCAGUCUUCC
((((((..(((.((((((..(((((....)))))))))...)).))).))))))..---(((.(--------((((((.....---------------.......----))))))).))) ( -33.10)
>DroYak_CAF1 132269 102 - 1
GGAGCAAUUUAUGCUGCCUGCCCGACUCCUCGGGGGCAAUUGUCUGACUGCUCCUCCUCGCCUGGAACCUCGCCUGGAACCUC---------------GCUCCUCC---UGCCGUCCUCC
((((((..(((.((((((..(((((....)))))))))...)).))).))))))(((..((..(....)..))..))).....---------------((......---.))........ ( -28.40)
>consensus
GGAGCAAUUUAUGCUGCCUGCCCGACUCCUCGGGGGCAAUUGUCUGACUGCUCCUC___GCCUG________GCUAGAACCUC_______________GCUCCUCC___UCCGGUCUUCC
((((((..(((.((((((..(((((....)))))))))...)).))).))))))..................((((((...............................))))))..... (-22.09 = -22.03 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,685,494 – 5,685,602
Length 108
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 93.42
Mean single sequence MFE -41.56
Consensus MFE -33.86
Energy contribution -34.02
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -2.42
Structure conservation index 0.81
SVM decision value 2.12
SVM RNA-class probability 0.988394
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5685494 108 + 22407834
GUUCUAGC--------CAGGC---GAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCAGGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAAGGAUAAGCAG
(((((.((--------(.(((---((((((((((.......((((((((((....)))))..))))).....))))))))(((.(....)..)))...))))).))).)))))...... ( -43.10)
>DroSec_CAF1 130852 108 + 1
GUUCUAGC--------CAGGC---GAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCAGGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAUGGAUAAGCAG
..((((((--------(.(((---((((((((((.......((((((((((....)))))..))))).....))))))))(((.(....)..)))...))))).))).))))....... ( -41.80)
>DroSim_CAF1 130313 108 + 1
GUUCUAGC--------CAGGC---GAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCAGGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAAGGAUAAGCAG
(((((.((--------(.(((---((((((((((.......((((((((((....)))))..))))).....))))))))(((.(....)..)))...))))).))).)))))...... ( -43.10)
>DroEre_CAF1 133604 108 + 1
GUUCCAGC--------CAUCC---GAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCUAGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAAGGAUAAGCAG
...((.((--------.((((---((((((((((.......((((.(((((....)))))...)))).....))))))))....(....)...)))))).)).))((........)).. ( -35.70)
>DroYak_CAF1 132291 119 + 1
GUUCCAGGCGAGGUUCCAGGCGAGGAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCAGGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAAGGAUAAGCAG
..(((.(((...(((((.........))))).)))......((((((((((....))))...(((((((.....)))((((((.(....)..)))))).)))))))))))))....... ( -44.10)
>consensus
GUUCUAGC________CAGGC___GAGGAGCAGUCAGACAAUUGCCCCCGAGGAGUCGGGCAGGCAGCAUAAAUUGCUCCGACACGAAAGAAGUUGGAUUGCCGGGCAAGGAUAAGCAG
(((((.....................))))).(((......((((((((((....))))...(((((((.....)))((((((.(....)..)))))).)))))))))).)))...... (-33.86 = -34.02 +   0.16)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:45 2006