Locus 1626

Sequence ID 2R_DroMel_CAF1
Location 6,094,385 – 6,094,484
Length 99
Max. P 0.858985
window2721 window2722

overview

Window 1

Location 6,094,385 – 6,094,484
Length 99
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 88.82
Mean single sequence MFE -24.30
Consensus MFE -18.85
Energy contribution -19.05
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.78
SVM decision value 0.82
SVM RNA-class probability 0.858985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6094385 99 + 20766785
CGCCGUCGCUUCUGCCGCCGGCAAAAUUAGCAGAGGCGUCAGCAACAAC------AACUAAAUGGGAAAAUUGUAGCGACUACUUACUAUGGAAAAGUGGAAACA
(((.(.(((((((((..............))))))))).).((((....------..((....)).....)))).))).((((((.........))))))..... ( -22.94)
>DroSec_CAF1 112109 97 + 1
CGCCGUCGCUUCUGCCGCCGGCGAAAUUAGCAGAGGCGACAGCAACAAC------AACUAAAUGUGAAAAUUGAAGCAACUACUUACUAAGGAAAAGUC--AACA
..(((((((((((((((....))......))))))))))).((..(((.------.((.....)).....)))..)).............)).......--.... ( -24.20)
>DroSim_CAF1 116776 97 + 1
CGCCGUCGCUUCUGCCGCCGGCGAAAUUAGCAGAGGCGACAGCAACAAC------AACUAAAUGGGAAAAUUGAAGCAACUACUUACUAUGGAAAAGUC--AACA
.((.(((((((((((((....))......))))))))))).))......------...............((((.....(((.......))).....))--)).. ( -23.80)
>DroEre_CAF1 115810 103 + 1
UUCCGUCGCUUCUGCCGCCGGCAAAAUCAGCAGAGGCGACAGCAACAACAACAACAGCUAAAUGGGAAAAUAAAGGCAACUACUUACCAUGGAAAAGUC--AACA
(((((((((((((((..............)))))))))))(((.............)))..((((........((....)).....)))))))).....--.... ( -28.08)
>DroYak_CAF1 114005 103 + 1
CUCCGUCGCUUCUGCCGCCGGCAAAAUCAGCAGAGGCGACAGCAACAACAACAACAACUAAAUGGGAAAAUAAAAGCAACUACUUACUAUGGAAAAGUC--AACA
.((((((((((((((..............))))))))))).((...........((......))...........)).............)))......--.... ( -22.49)
>consensus
CGCCGUCGCUUCUGCCGCCGGCAAAAUUAGCAGAGGCGACAGCAACAAC______AACUAAAUGGGAAAAUUGAAGCAACUACUUACUAUGGAAAAGUC__AACA
..(((((((((((((..............))))))))))).((................................)).............))............. (-18.85 = -19.05 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,094,385 – 6,094,484
Length 99
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 88.82
Mean single sequence MFE -27.98
Consensus MFE -24.12
Energy contribution -24.20
Covariance contribution 0.08
Combinations/Pair 1.04
Mean z-score -1.29
Structure conservation index 0.86
SVM decision value -0.05
SVM RNA-class probability 0.506427
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6094385 99 - 20766785
UGUUUCCACUUUUCCAUAGUAAGUAGUCGCUACAAUUUUCCCAUUUAGUU------GUUGUUGCUGACGCCUCUGCUAAUUUUGCCGGCGGCAGAAGCGACGGCG
......................((((...))))..............(((------((((((.(((.((((...((.......)).)))).))).))))))))). ( -24.70)
>DroSec_CAF1 112109 97 - 1
UGUU--GACUUUUCCUUAGUAAGUAGUUGCUUCAAUUUUCACAUUUAGUU------GUUGUUGCUGUCGCCUCUGCUAAUUUCGCCGGCGGCAGAAGCGACGGCG
.(((--((.........(((((....))))))))))...........(((------((((((.((((((((...((.......)).)))))))).))))))))). ( -28.60)
>DroSim_CAF1 116776 97 - 1
UGUU--GACUUUUCCAUAGUAAGUAGUUGCUUCAAUUUUCCCAUUUAGUU------GUUGUUGCUGUCGCCUCUGCUAAUUUCGCCGGCGGCAGAAGCGACGGCG
.(((--((.........(((((....))))))))))...........(((------((((((.((((((((...((.......)).)))))))).))))))))). ( -28.60)
>DroEre_CAF1 115810 103 - 1
UGUU--GACUUUUCCAUGGUAAGUAGUUGCCUUUAUUUUCCCAUUUAGCUGUUGUUGUUGUUGCUGUCGCCUCUGCUGAUUUUGCCGGCGGCAGAAGCGACGGAA
....--.....((((((((.((((((......))))))..))))............((((((.((((((((...((.......)).)))))))).)))))))))) ( -30.80)
>DroYak_CAF1 114005 103 - 1
UGUU--GACUUUUCCAUAGUAAGUAGUUGCUUUUAUUUUCCCAUUUAGUUGUUGUUGUUGUUGCUGUCGCCUCUGCUGAUUUUGCCGGCGGCAGAAGCGACGGAG
....--......(((..(((((....))))).........................((((((.((((((((...((.......)).)))))))).))))))))). ( -27.20)
>consensus
UGUU__GACUUUUCCAUAGUAAGUAGUUGCUUCAAUUUUCCCAUUUAGUU______GUUGUUGCUGUCGCCUCUGCUAAUUUUGCCGGCGGCAGAAGCGACGGCG
.............((..(((((....))))).........................((((((.((((((((...((.......)).)))))))).)))))))).. (-24.12 = -24.20 +   0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:10 2006