Locus 7860

Sequence ID 3R_DroMel_CAF1
Location 21,034,641 – 21,034,731
Length 90
Max. P 0.848042
window12661 window12662

overview

Window 1

Location 21,034,641 – 21,034,731
Length 90
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -24.22
Consensus MFE -16.22
Energy contribution -16.78
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.67
SVM decision value 0.65
SVM RNA-class probability 0.812818
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21034641 90 + 27905053
AUUUGCUUGCCCAAAU--GCAUUGUAAACUCGAAUGCGUCACGCGGAUUUUUCCCGCG--------------A-AAAAAGGUCAAAACCUCUCUUAAGACACAUUCA
.(((((.(((......--)))..)))))...(((((.(((.(((((.......)))))--------------.-....((((....)))).......))).))))). ( -26.10)
>DroSec_CAF1 39309 92 + 1
AUUUGCUUGCCCAAAUGUGCAUUGUAAACUCGUAUGCGUCACGCGGAGUUUCCCCGCG--------------A-AAAAAGGGCAAAACCUCUUUUAAGACACAUUCA
.(((((.(((.(....).)))..)))))...(.(((.(((.(((((.......)))))--------------.-.(((((((......)))))))..))).))).). ( -24.10)
>DroSim_CAF1 39505 90 + 1
AUUUGCUUGCCCAAAU--GCAUUGUAAACUCGAAUGCGUCACGCGGAUUUUCCCCGCG--------------A-AAAAAGGGCAAAACCUCUCUUAAGACACAUUCA
.(((((.(((......--)))..)))))...(((((.(((.(((((.......)))))--------------.-....(((......))).......))).))))). ( -26.30)
>DroEre_CAF1 42957 104 + 1
ACCUGUUUGGCCAACU--GCAUUGUAAACUCGAAUGCGUCACCCGGAUUUUCCCCGCGGGUCAGUGCUAGCGA-AAAAAGUUCAAAACGUCUCUUAAGACACAUUCA
....((((((...((.--((((((......).)))))))...))(((((((...(((.(((....))).))).-..))))))).))))((((....))))....... ( -19.50)
>DroYak_CAF1 43334 105 + 1
ACUUGUUUGCCCAAAU--GCAUUGUAAACGCGAAUGCGUCACGCGGAUUUUCCCCGCGGACCAGUGCUAGCCAAAAAAAGUGCAAAACAUCUCUUAAGACACAUUCC
....((((((......--.....))))))..(((((.(((.(((((.......))))).....(..((..........))..)..............))).))))). ( -25.10)
>consensus
AUUUGCUUGCCCAAAU__GCAUUGUAAACUCGAAUGCGUCACGCGGAUUUUCCCCGCG______________A_AAAAAGGGCAAAACCUCUCUUAAGACACAUUCA
......((((((......((((((......)).))))....(((((.......))))).....................))))))...................... (-16.22 = -16.78 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,034,641 – 21,034,731
Length 90
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -29.66
Consensus MFE -23.46
Energy contribution -24.26
Covariance contribution 0.80
Combinations/Pair 1.07
Mean z-score -1.90
Structure conservation index 0.79
SVM decision value 0.78
SVM RNA-class probability 0.848042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21034641 90 - 27905053
UGAAUGUGUCUUAAGAGAGGUUUUGACCUUUUU-U--------------CGCGGGAAAAAUCCGCGUGACGCAUUCGAGUUUACAAUGC--AUUUGGGCAAGCAAAU
.(((((((((..(((((((((....))))))))-)--------------((((((.....)))))).)))))))))..........(((--......)))....... ( -30.30)
>DroSec_CAF1 39309 92 - 1
UGAAUGUGUCUUAAAAGAGGUUUUGCCCUUUUU-U--------------CGCGGGGAAACUCCGCGUGACGCAUACGAGUUUACAAUGCACAUUUGGGCAAGCAAAU
.(.(((((((..((((((((......)))))))-)--------------((((((....).))))).))))))).)..........(((........)))....... ( -27.70)
>DroSim_CAF1 39505 90 - 1
UGAAUGUGUCUUAAGAGAGGUUUUGCCCUUUUU-U--------------CGCGGGGAAAAUCCGCGUGACGCAUUCGAGUUUACAAUGC--AUUUGGGCAAGCAAAU
.(((((((((..((((((((......)))))))-)--------------((((((.....)))))).)))))))))..........(((--......)))....... ( -29.90)
>DroEre_CAF1 42957 104 - 1
UGAAUGUGUCUUAAGAGACGUUUUGAACUUUUU-UCGCUAGCACUGACCCGCGGGGAAAAUCCGGGUGACGCAUUCGAGUUUACAAUGC--AGUUGGCCAAACAGGU
.((((((.((....)).))))))...((((.((-(.((((((....(((((.((......)))))))...(((((.(......))))))--.)))))).))).)))) ( -28.30)
>DroYak_CAF1 43334 105 - 1
GGAAUGUGUCUUAAGAGAUGUUUUGCACUUUUUUUGGCUAGCACUGGUCCGCGGGGAAAAUCCGCGUGACGCAUUCGCGUUUACAAUGC--AUUUGGGCAAACAAGU
.(((((((((..(((((.((.....)))))))...(((((....)))))((((((.....)))))).)))))))))((((.....))))--(((((......))))) ( -32.10)
>consensus
UGAAUGUGUCUUAAGAGAGGUUUUGCCCUUUUU_U______________CGCGGGGAAAAUCCGCGUGACGCAUUCGAGUUUACAAUGC__AUUUGGGCAAGCAAAU
.(((((((((...(((((((......)))))))................((((((.....)))))).)))))))))..((((.(((.......)))...)))).... (-23.46 = -24.26 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:31 2006