Locus 9050

Sequence ID 3R_DroMel_CAF1
Location 24,203,629 – 24,203,852
Length 223
Max. P 0.995175
window14493 window14494

overview

Window 3

Location 24,203,629 – 24,203,738
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 87.36
Mean single sequence MFE -27.42
Consensus MFE -22.54
Energy contribution -22.06
Covariance contribution -0.48
Combinations/Pair 1.17
Mean z-score -2.69
Structure conservation index 0.82
SVM decision value 2.55
SVM RNA-class probability 0.995175
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24203629 109 + 27905053
UUCUCCGUUGGGUAUCACCCAAUAGUCCCUAGUUUUUAUCCCUCUUUAUUCGUUUUGUGUGUCAAAUGGCAUACAAUGGCUUACUCACAUGUGAGUCCGUUUUUACUGU
......((((((.....))))))......((((.......................(((((((....)))))))((((((((((......))))).)))))...)))). ( -26.80)
>DroSec_CAF1 26375 103 + 1
------GUUGGGUAUCAACCAAUAGUCCCUAGUUUUUACCCCUCUUUACUCGUUUUGUGUGUCAAAUGGCACACAAUGGCUUACUCACAUGUGAGUCCGUUUUUACUGU
------(..(((((..(((............)))..)))))..)...........((((((((....))))))))(((((((((......))))).))))......... ( -27.00)
>DroSim_CAF1 30246 103 + 1
------GUUGGGUAUCCACCAAUAGUCCCUAGUUUUUACCCCUCUUUACUCGUUUUGUGUGUCAAAUGGCACACAAUGGCUUACUCACAUGUGAGUCCGUUUUUACUGU
------(((((.......)))))......((((....((...............(((((((((....))))))))).(((((((......))))))).))....)))). ( -26.40)
>DroEre_CAF1 30997 109 + 1
UUCUGCGGUAGGUUAUAUCCAAUGAUUCCUAGUUUUUGCCCCUCUUUAUUCGUUUUGUGUGUCAAAUGGCACACAAUGGCUUACUCACAUGUGAGUCCAUUUUUACUGU
....((((((((......))((((..............................(((((((((....))))))))).(((((((......)))))))))))..)))))) ( -27.30)
>DroYak_CAF1 27909 109 + 1
UUCUCCGGUAGGAUUUAGCCAUGAGUUCCUAGUUUUUGCCCCUCUUUAUUCGUUUUGUGUGUCAAAUGGCACACAAUGGCUUACUCACAUGUGAGUCUGCUUUUACUGU
.....((((((((...(((((((((...(........)...)))...........((((((((....)))))))))))))).(((((....)))))....)))))))). ( -29.60)
>consensus
UUCU_CGUUGGGUAUCAACCAAUAGUCCCUAGUUUUUACCCCUCUUUAUUCGUUUUGUGUGUCAAAUGGCACACAAUGGCUUACUCACAUGUGAGUCCGUUUUUACUGU
..........((......)).........((((....((...............(((((((((....))))))))).(((((((......))))))).))....)))). (-22.54 = -22.06 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 24,203,738 – 24,203,852
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.85
Mean single sequence MFE -30.03
Consensus MFE -19.86
Energy contribution -20.76
Covariance contribution 0.90
Combinations/Pair 1.38
Mean z-score -1.57
Structure conservation index 0.66
SVM decision value 0.55
SVM RNA-class probability 0.778563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24203738 114 + 27905053
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC-UGUGCAAUCUAUGACACAAGCGGUCCUUCGAUCUUU-GAAGCCUUC----GGCUCUUUGGUCACUUUGGCGCAUUUAAAACGCCACGG
............((((((((((.((......-((((((.....)).))))..(((..((((((...))-))))...))----)))))))))).)))..(((((.........)))))... ( -29.90)
>DroPse_CAF1 27822 104 + 1
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC-UGUGCAAUCUAUGACACAGACGGCCCUGC-----------GCCUUC----GGCUCUUUGGUCACUUUGGCACAUUUAAAACGCCACGA
............(((((((((........((-((((((.....)).)))))).((((..(.-----------(((...----))).)...)))).)))))))))................ ( -31.90)
>DroGri_CAF1 429 106 + 1
UAAAUGAAACACGUUGGACGGAAGCAAUUUCGUGUGCAAUCUAUGGCGCAAACUGUGCC--------U-GAGGCCCUCUUGGCGCUCCUUGGUCGCUUUUACACAUUUUAAACGG-----
...........(((((.((((((....)))))).)((.(((...(((((.....)))))--------.-((((((.....))).)))...))).))..............)))).----- ( -27.00)
>DroEre_CAF1 31106 114 + 1
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC-UGUGCAAUCUAUGACACAAGCGGUCCUUCGAUCCUU-CAGGCCUCC----GGCUCCUUGGUCACUUUGGCGCAUUUAAAACGCCACGA
............((((((((((.((......-((((((.....)).))))..(((.(((..((....)-))))...))----)))))))))).)))..(((((.........)))))... ( -32.80)
>DroAna_CAF1 24654 103 + 1
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC-UGUGCAAUCUAUGACACAAGCGGUCC---GGUCCUUCGAAUCCUCC----GCCUCU---------UUGGCACAUUUAAAACGCCACGA
............((((((((((.((......-((((((.....)).))))((.(((.(---((....))).)))))..----)).)))---------)))))))................ ( -26.70)
>DroPer_CAF1 27815 104 + 1
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC-UGUGCAAUCUAUGACACAGACGGCCCUGC-----------GCCUUC----GGCUCUUUGGUCACUUUGGCACAUUUAAAACGCCACGA
............(((((((((........((-((((((.....)).)))))).((((..(.-----------(((...----))).)...)))).)))))))))................ ( -31.90)
>consensus
UAAAUGAAACACGUGCCAAGGAAGCAAUUUC_UGUGCAAUCUAUGACACAAACGGUCCU_C______U_GA_GCCUUC____GGCUCUUUGGUCACUUUGGCACAUUUAAAACGCCACGA
............(((((((((..(((........)))......((((.((((.((((.........................)))).)))))))))))))))))................ (-19.86 = -20.76 +   0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:25:34 2006