Locus 6420

Sequence ID 2L_DroMel_CAF1
Location 18,046,110 – 18,046,202
Length 92
Max. P 0.918187
window10245 window10246

overview

Window 5

Location 18,046,110 – 18,046,202
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 76.57
Mean single sequence MFE -25.97
Consensus MFE -15.64
Energy contribution -15.50
Covariance contribution -0.14
Combinations/Pair 1.07
Mean z-score -1.92
Structure conservation index 0.60
SVM decision value 1.12
SVM RNA-class probability 0.918187
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18046110 92 + 22407834
CACAAUGCAUAAGGUGCCUACUAUGAGCCGGCAACUGUCAAGUUGCCG-------GCUGCCAGACAACUCUUUCUUUGCUUUCCUCCAUCGCA-GCCCGU----
............(((((........(((((((((((....))))))))-------)))((.(((........)))..))...........)))-.))...---- ( -27.00)
>DroPse_CAF1 353958 79 + 1
CACACUGCAUAAGGUGCCGACGAUGAGCCGGCAACUUGACAGUUGCUG-------CCAGCCAGACAACUCUUUUC---------CCCCUCGUCGG---------
..((((......))))(((((((((.((.(((((((....))))))))-------)))...(((....)))....---------....)))))))--------- ( -23.10)
>DroSec_CAF1 262311 82 + 1
CACAAUGCAUAAGGUGCCUACUAUGAGCCGGCAACUGUCAAGUUGCCG-------GCUGCCAGACAACUCUUUCUUUG--------CAUCGCA-GCCC------
......((....(((((........(((((((((((....))))))))-------)))...(((....)))......)--------))))...-))..------ ( -27.80)
>DroSim_CAF1 262602 90 + 1
CACAAUGCAUAAGGUGCCUACUAUGAGCCGGCAACUGUCAAGUUGCCG-------GCUGCCAGACAACUCUUUCUUUGCUUUCCUCCAUCGCA-GCCC------
............(((((........(((((((((((....))))))))-------)))((.(((........)))..))...........)))-.)).------ ( -27.00)
>DroEre_CAF1 255526 70 + 1
CACAAUGCAUAAGGUGCCGACUAUGAGCCGGCAACUGUCAAGUUGCCG-------CUUGCCAGACAACUCUUUCCUU---------------------------
......((((...)))).......((((.(((((((....))))))))-------)))...................--------------------------- ( -17.10)
>DroYak_CAF1 271751 103 + 1
CACAAUGCAUAAGGUGCCGACUAUGAGCCGGCAACUGUCAAGUUGCCGGUUGCCGGUUGCCAGACAACUCUUUCUUUGCGUUUCUCCAUCGCA-GCCAGCAGCC
.....(((....(((..........(((((((((((....))))))))))))))((((((.(((.(((.(.......).)))))).....)))-))).)))... ( -33.80)
>consensus
CACAAUGCAUAAGGUGCCGACUAUGAGCCGGCAACUGUCAAGUUGCCG_______GCUGCCAGACAACUCUUUCUUUG______UCCAUCGCA_GCCC______
............((((((......).))((((((((....))))))))..........)))........................................... (-15.64 = -15.50 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,046,110 – 18,046,202
Length 92
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 76.57
Mean single sequence MFE -31.42
Consensus MFE -15.95
Energy contribution -16.12
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.05
Structure conservation index 0.51
SVM decision value 0.72
SVM RNA-class probability 0.832669
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18046110 92 - 22407834
----ACGGGC-UGCGAUGGAGGAAAGCAAAGAAAGAGUUGUCUGGCAGC-------CGGCAACUUGACAGUUGCCGGCUCAUAGUAGGCACCUUAUGCAUUGUG
----......-.((((((((((..(((.........)))(((((..(((-------((((((((....))))))))))).....))))).))))...)))))). ( -30.90)
>DroPse_CAF1 353958 79 - 1
---------CCGACGAGGGG---------GAAAAGAGUUGUCUGGCUGG-------CAGCAACUGUCAAGUUGCCGGCUCAUCGUCGGCACCUUAUGCAGUGUG
---------.(((((((((.---------((......)).)))((((((-------((((.........))))))))))..))))))((((........)))). ( -28.70)
>DroSec_CAF1 262311 82 - 1
------GGGC-UGCGAUG--------CAAAGAAAGAGUUGUCUGGCAGC-------CGGCAACUUGACAGUUGCCGGCUCAUAGUAGGCACCUUAUGCAUUGUG
------....-.((((((--------((....(((.((.(((((..(((-------((((((((....))))))))))).....)))))))))).)))))))). ( -34.30)
>DroSim_CAF1 262602 90 - 1
------GGGC-UGCGAUGGAGGAAAGCAAAGAAAGAGUUGUCUGGCAGC-------CGGCAACUUGACAGUUGCCGGCUCAUAGUAGGCACCUUAUGCAUUGUG
------....-.((((((((((..(((.........)))(((((..(((-------((((((((....))))))))))).....))))).))))...)))))). ( -30.90)
>DroEre_CAF1 255526 70 - 1
---------------------------AAGGAAAGAGUUGUCUGGCAAG-------CGGCAACUUGACAGUUGCCGGCUCAUAGUCGGCACCUUAUGCAUUGUG
---------------------------((((...((((((((.......-------.))))))))......(((((((.....))))))))))).......... ( -23.90)
>DroYak_CAF1 271751 103 - 1
GGCUGCUGGC-UGCGAUGGAGAAACGCAAAGAAAGAGUUGUCUGGCAACCGGCAACCGGCAACUUGACAGUUGCCGGCUCAUAGUCGGCACCUUAUGCAUUGUG
((.(((((((-((((.........))).......((((((((.(....).)))))(((((((((....))))))))))))..))))))))))............ ( -39.80)
>consensus
______GGGC_UGCGAUGGA______CAAAGAAAGAGUUGUCUGGCAGC_______CGGCAACUUGACAGUUGCCGGCUCAUAGUAGGCACCUUAUGCAUUGUG
..................................(((.((((..............((((((((....))))))))((.....)).)))).))).......... (-15.95 = -16.12 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:35 2006