Locus 2465

Sequence ID 2L_DroMel_CAF1
Location 6,758,039 – 6,758,138
Length 99
Max. P 0.981253
window3953 window3954

overview

Window 3

Location 6,758,039 – 6,758,138
Length 99
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 67.29
Mean single sequence MFE -33.12
Consensus MFE -21.00
Energy contribution -20.68
Covariance contribution -0.32
Combinations/Pair 1.27
Mean z-score -1.38
Structure conservation index 0.63
SVM decision value 0.58
SVM RNA-class probability 0.789492
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6758039 99 + 22407834
AGUCGCUGC------AUUCU------A------AUCCAUUGUGGAGUUCAGUCUCAUGAACUCCUCGUUGAGCAACGCCAUAUUCGUGGAGUGCGUGUUGGCUCCCUGCUCGCCCAG
.......((------.....------.------.......(.((((((((......)))))))).)...(((((..((((....(((.....)))...))))....))))))).... ( -29.50)
>DroSec_CAF1 24768 79 + 1
--------------------------------------UUGUGGAGUUCAGUCUCCUGAACUCCUCGUUGAGCAGCGCCAUUUUCGAGGAGUGCGUGUUGGCUCCCUGCCCGCCCAG
--------------------------------------..(.(((((((((....))))))))).)..((.((((((((((((.....))))).)))))(((.....))).)).)). ( -29.30)
>DroSim_CAF1 25503 79 + 1
--------------------------------------UUGUGGAGUUCAGUCUCAUGAACUCCUCGUUGAGCAGCGCCAUUUUCGCGGAGUGCGUGUUGGCUCCCUGCCCGCCCAG
--------------------------------------..(.((((((((......)))))))).)((.(.((((.((((....((((.....)))).))))...))))).)).... ( -28.30)
>DroEre_CAF1 28346 84 + 1
---------------------------------GCCCGUGGUGGAGCUUAUCUUCAUGAACUCCUCGUUGAGCAGCGCCAUCUUCGUGGAGUGCGUGGUGCCUCCCAUGCCUCCAUG
---------------------------------......(((((.(((...(((.((((.....)))).))).))).)))))..(((((((.((((((......))))))))))))) ( -33.00)
>DroYak_CAF1 27154 117 + 1
AGUCGCUCCCCGUGGAGUUUAGCUUUAAGAACUCCUCGUCGUGGAGUUCAUCUGGAUGAACUCCCGGUUGAGCAGCGUCAUCUUGGAGGAGUGCAUGGUGCCUCCCUGCUCGCCCAG
....((...(((.((((((((.((....(((((((.......)))))))....)).)))))))))))..((((((..((......))((((.((.....)))))))))))))).... ( -45.50)
>consensus
____________________________________C_UUGUGGAGUUCAGUCUCAUGAACUCCUCGUUGAGCAGCGCCAUCUUCGAGGAGUGCGUGUUGGCUCCCUGCCCGCCCAG
..........................................(((((((((....))))))))).....(((((((((((.(((....))))).)))))).))).(((......))) (-21.00 = -20.68 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,758,039 – 6,758,138
Length 99
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 67.29
Mean single sequence MFE -32.44
Consensus MFE -22.60
Energy contribution -23.28
Covariance contribution 0.68
Combinations/Pair 1.19
Mean z-score -1.73
Structure conservation index 0.70
SVM decision value 1.88
SVM RNA-class probability 0.981253
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6758039 99 - 22407834
CUGGGCGAGCAGGGAGCCAACACGCACUCCACGAAUAUGGCGUUGCUCAACGAGGAGUUCAUGAGACUGAACUCCACAAUGGAU------U------AGAAU------GCAGCGACU
....((((((((...((((...((.......))....)))).)))))).....((((((((......)))))))).........------.------.....------...)).... ( -27.90)
>DroSec_CAF1 24768 79 - 1
CUGGGCGGGCAGGGAGCCAACACGCACUCCUCGAAAAUGGCGCUGCUCAACGAGGAGUUCAGGAGACUGAACUCCACAA--------------------------------------
.(((((((((.(((((..........)))))........)).)))))))....(((((((((....)))))))))....-------------------------------------- ( -34.60)
>DroSim_CAF1 25503 79 - 1
CUGGGCGGGCAGGGAGCCAACACGCACUCCGCGAAAAUGGCGCUGCUCAACGAGGAGUUCAUGAGACUGAACUCCACAA--------------------------------------
......((((((...((((...(((.....)))....)))).)))))).....((((((((......))))))))....-------------------------------------- ( -30.90)
>DroEre_CAF1 28346 84 - 1
CAUGGAGGCAUGGGAGGCACCACGCACUCCACGAAGAUGGCGCUGCUCAACGAGGAGUUCAUGAAGAUAAGCUCCACCACGGGC---------------------------------
..(((((((.(((......))).)).))))).............((((...(.((((((.((....)).)))))).)...))))--------------------------------- ( -24.40)
>DroYak_CAF1 27154 117 - 1
CUGGGCGAGCAGGGAGGCACCAUGCACUCCUCCAAGAUGACGCUGCUCAACCGGGAGUUCAUCCAGAUGAACUCCACGACGAGGAGUUCUUAAAGCUAAACUCCACGGGGAGCGACU
....((((((((((((((.....)).))))((......))..))))))..((((((((((((....))))))))).......((((((..........)))))).)))...)).... ( -44.40)
>consensus
CUGGGCGGGCAGGGAGCCAACACGCACUCCACGAAAAUGGCGCUGCUCAACGAGGAGUUCAUGAGACUGAACUCCACAA_G____________________________________
......((((((((((..........)))).((.......)))))))).....(((((((((....))))))))).......................................... (-22.60 = -23.28 +   0.68)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:34 2006