Locus 4384

Sequence ID 3R_DroMel_CAF1
Location 11,593,341 – 11,593,450
Length 109
Max. P 0.990644
window7163 window7164

overview

Window 3

Location 11,593,341 – 11,593,450
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 93.85
Mean single sequence MFE -34.42
Consensus MFE -27.94
Energy contribution -31.00
Covariance contribution 3.06
Combinations/Pair 1.03
Mean z-score -2.58
Structure conservation index 0.81
SVM decision value 2.22
SVM RNA-class probability 0.990644
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11593341 109 + 27905053
UUUAAUAUGCAAAAUUGUGGAAGCCGUCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUUAACUCCCAAAGCUGGGAGCUUCCACACUUUGGAACGCCUGCUUUUGGGCG
.......(.((((..(((((((((..(((...((((....)))).((((.(((((.......))))).)))).)))))))))))).)))).).(((((......))))) ( -39.50)
>DroSec_CAF1 123192 109 + 1
UUUAAUAUGCAAAAUCGUGGAAGCCGUCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUUAACUCCCAAAGCUGGGCGCUUGCACACUUUGGAGCGCCUGCUUUUGGGCG
.......(.((((...(((.((((.((((...((((....)))).((((.(((((.......))))).)))))))))))).)))..)))).).(((((......))))) ( -36.60)
>DroSim_CAF1 126623 109 + 1
UUUAAUAUGCAAAAUCGUGGAAGCCGUCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUUAACUCCCAAAGCUGGGAGCUUGCACACUUUGGACCGCCUGCUUUUGGGCG
........((..((..(..(..((.(((((((.((.((((((...((((.(((((.......))))).))))..))..)))).)).))))))).)))..)..))..)). ( -34.80)
>DroEre_CAF1 125457 109 + 1
UUUAAUAUGCAAAAUCUACGAAGCCGCCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUGAACUCCCAAAGCUGGGAGCUACCACACUUUGGACCGCCUGCUUUUGGGCC
.........................((((((...(((((......(((((........))))).((((((.(((......)))..))))))......))))))))))). ( -28.60)
>DroYak_CAF1 124558 109 + 1
UUUAAUAUGCAAAAUCUCUGAAGCCGCCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUUAACUCCCAAAGCUGGGAGCUUCCACACUUUGGACUGCCUGCUUUGGGGCG
...............(((..((((..(((...((((....)))).((((.(((((.......))))).))))))).((.((((.....))))..))..))))..))).. ( -32.60)
>consensus
UUUAAUAUGCAAAAUCGUGGAAGCCGUCCAAAUUGAGCAAUCAAAAGUUCUGGGAAAUUAACUCCCAAAGCUGGGAGCUUCCACACUUUGGACCGCCUGCUUUUGGGCG
.........((((...((((((((..(((...((((....)))).((((.(((((.......))))).))))))).))))))))..))))....((((......)))). (-27.94 = -31.00 +   3.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,593,341 – 11,593,450
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 93.85
Mean single sequence MFE -35.26
Consensus MFE -26.72
Energy contribution -27.36
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.66
Structure conservation index 0.76
SVM decision value 1.13
SVM RNA-class probability 0.919294
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11593341 109 - 27905053
CGCCCAAAAGCAGGCGUUCCAAAGUGUGGAAGCUCCCAGCUUUGGGAGUUAAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGACGGCUUCCACAAUUUUGCAUAUUAAA
((((........))))...(((((((((((((((.((((.((((((((.....))))))))....((((....)))).))))..))))))))).))))))......... ( -37.00)
>DroSec_CAF1 123192 109 - 1
CGCCCAAAAGCAGGCGCUCCAAAGUGUGCAAGCGCCCAGCUUUGGGAGUUAAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGACGGCUUCCACGAUUUUGCAUAUUAAA
....((((((..((((((.((.....))..))))))....((((((((.....)))))))).))))))..(((..((((((((.....)))).))))..)))....... ( -30.60)
>DroSim_CAF1 126623 109 - 1
CGCCCAAAAGCAGGCGGUCCAAAGUGUGCAAGCUCCCAGCUUUGGGAGUUAAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGACGGCUUCCACGAUUUUGCAUAUUAAA
.((......))((((.(((((((.((.((((......((.((((((((.....)))))))).)).....)))).)).))))))).)))).................... ( -34.00)
>DroEre_CAF1 125457 109 - 1
GGCCCAAAAGCAGGCGGUCCAAAGUGUGGUAGCUCCCAGCUUUGGGAGUUCAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGGCGGCUUCGUAGAUUUUGCAUAUUAAA
.(((((((....(((((((.(((((.(((.(((((((......)))))))......)))..))))).)))))))...))))))).((............))........ ( -36.40)
>DroYak_CAF1 124558 109 - 1
CGCCCCAAAGCAGGCAGUCCAAAGUGUGGAAGCUCCCAGCUUUGGGAGUUAAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGGCGGCUUCAGAGAUUUUGCAUAUUAAA
(((((.(((...(((((((.(((((..((((((((((......))))))....))))....))))).)))))))...))))))))((............))........ ( -38.30)
>consensus
CGCCCAAAAGCAGGCGGUCCAAAGUGUGGAAGCUCCCAGCUUUGGGAGUUAAUUUCCCAGAACUUUUGAUUGCUCAAUUUGGACGGCUUCCACGAUUUUGCAUAUUAAA
((.(((((....(((((((.(((((......((.....))((((((((.....))))))))))))).)))))))...))))).))((............))........ (-26.72 = -27.36 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:48 2006