Locus 1857

Sequence ID 3R_DroMel_CAF1
Location 5,328,288 – 5,328,427
Length 139
Max. P 0.951797
window3053 window3054

overview

Window 3

Location 5,328,288 – 5,328,389
Length 101
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.96
Mean single sequence MFE -33.17
Consensus MFE -18.47
Energy contribution -18.59
Covariance contribution 0.12
Combinations/Pair 1.16
Mean z-score -1.95
Structure conservation index 0.56
SVM decision value 1.42
SVM RNA-class probability 0.951797
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5328288 101 - 27905053
UGCUCCACCGCGCUCUCUUCGUUCGCUCUUCGCGUAUCUGCGAGCUACUCGAACU--------------CUGCGAGCUAAACGAAUCGGAAUCGCCAAAGGUU-----CAGUUGUUCGAC
.((......))((((.(...(((((...((((((....)))))).....))))).--------------..).))))....(((((..(((((......))))-----)....))))).. ( -27.10)
>DroSim_CAF1 33826 91 - 1
--------CGCGCUCUCCUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGAAC----------------UGCGAGUGAAACGAAUCCGAAUCGCCAACGGUU-----CAGUUGUUCGAC
--------..........((((((((..((((.(((((.....))))).)))).----------------.))))))))..((((((.((((((....)))))-----).)..))))).. ( -34.00)
>DroYak_CAF1 33635 111 - 1
-------CUGCG--CUCUUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGUACUGCCGGAUACUCGAACUGCGAGCGAAACAGAAACAACUCGCCGAUGGUUCACUUCAGUUGUUUGAC
-------(((..--...(((((((((..((((.(((((((((((...)))))......)))))).))))..))))))))).)))((((((((....((....)).....))))))))... ( -38.40)
>consensus
_______CCGCGCUCUCUUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGAACU______________CUGCGAGCGAAACGAAUCCGAAUCGCCAAAGGUU_____CAGUUGUUCGAC
..................((((((((..((((.(((((.....))))).))))..................))))))))(((((.........(((...))).........))))).... (-18.47 = -18.59 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Window 4

Location 5,328,323 – 5,328,427
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.25
Mean single sequence MFE -33.94
Consensus MFE -19.36
Energy contribution -20.15
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.57
SVM decision value 0.88
SVM RNA-class probability 0.872542
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5328323 104 - 27905053
UAAGGAAACAUUGUGU--GCCAAGUGCUAAGAGAGAGAGCUGCUCCACCGCGCUCUCUUCGUUCGCUCUUCGCGUAUCUGCGAGCUACUCGAACU--------------CUGCGAGCUAA
...(....)...((.(--((..(((.....((((((((((.((......)))))))))..((((((.............))))))..)))..)))--------------..))).))... ( -31.02)
>DroSim_CAF1 33861 91 - 1
UAAGGAAACAUUGUGU--GCCAACUGCUAAGAGAGAG-----------CGCGCUCUCCUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGAAC----------------UGCGAGUGAA
...(....)...((((--((...((......))...)-----------))))).....((((((((..((((.(((((.....))))).)))).----------------.)))))))). ( -34.40)
>DroYak_CAF1 33675 108 - 1
UAAGGAAAUAUUAUAUUGGCCAACUGCUAAGAGAGAA----------CUGCG--CUCUUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGUACUGCCGGAUACUCGAACUGCGAGCGAA
...............(((((.....))))).((((..----------.....--))))((((((((..((((.(((((((((((...)))))......)))))).))))..)))))))). ( -36.40)
>consensus
UAAGGAAACAUUGUGU__GCCAACUGCUAAGAGAGAG__________CCGCGCUCUCUUCGCUCGCUCUUCGCGUAUCUGCGAGAUACUCGAACU______________CUGCGAGCGAA
...((..((.....))...)).........(((((.................))))).((((((((..((((.(((((.....))))).))))..................)))))))). (-19.36 = -20.15 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:14 2006