Locus 1927

Sequence ID 3R_DroMel_CAF1
Location 5,446,679 – 5,446,846
Length 167
Max. P 0.814279
window3169 window3170 window3171

overview

Window 9

Location 5,446,679 – 5,446,796
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.37
Mean single sequence MFE -31.47
Consensus MFE -20.83
Energy contribution -20.62
Covariance contribution -0.21
Combinations/Pair 1.16
Mean z-score -2.22
Structure conservation index 0.66
SVM decision value 0.66
SVM RNA-class probability 0.814279
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5446679 117 + 27905053
CACAACACAACACGAGACGAGACGAGACCGAAAGGGAAAAAAACACUUUAAAGCUGC---UGUCGAGUGUUAAUCAUGGUGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGC
.......((((................((....)).................((.((---((..((((((((((..((((...........))))))))))))))..)))).)).)))). ( -29.30)
>DroEre_CAF1 33840 99 + 1
CACAACA-----CGAG----------ACCAAGAGG--AA-AAACACUUUACAGCUGC---UGCCGAGUGUUAAUCAUGGGGUAAUUUAUUAGUCAGUUGACACUUUUUGGUCUCAGUUGC
..((((.-----.(((----------(((((((((--..-.(((((((..(((...)---))..)))))))....................(((....))).)))))))))))).)))). ( -31.50)
>DroYak_CAF1 34539 109 + 1
CACAACA-----CGAGAC----UGAGACCAAGAGG--AAAAAACACUUUACAGCUGCUGCUGCCAAGUGUUAAUCAUGGGGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGC
.......-----...(((----((.(.((((((((--....(((((((..((((....))))..)))))))..(((..((.(((....))).))...)))..)))))))).).))))).. ( -33.60)
>consensus
CACAACA_____CGAGAC_____GAGACCAAGAGG__AAAAAACACUUUACAGCUGC___UGCCGAGUGUUAAUCAUGGGGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGC
...........................((....))...............(((((((....(((((((((((((..(((.............)))))))))))))...))).))))))). (-20.83 = -20.62 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,446,719 – 5,446,836
Length 117
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.40
Mean single sequence MFE -36.30
Consensus MFE -30.40
Energy contribution -30.19
Covariance contribution -0.21
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.84
SVM decision value 0.57
SVM RNA-class probability 0.784297
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5446719 117 + 27905053
AAACACUUUAAAGCUGC---UGUCGAGUGUUAAUCAUGGUGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAU
...((((....((((((---.(((((((((((((..((((...........))))))))))))))...))).))))))...........((((((....))))))......))))..... ( -34.80)
>DroEre_CAF1 33862 117 + 1
AAACACUUUACAGCUGC---UGCCGAGUGUUAAUCAUGGGGUAAUUUAUUAGUCAGUUGACACUUUUUGGUCUCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAU
...(((((..((((((.---.(((((((((((((....((.(((....))).)).))))))))))...)))..))))))..))......((((((....)))))).......)))..... ( -33.10)
>DroYak_CAF1 34568 120 + 1
AAACACUUUACAGCUGCUGCUGCCAAGUGUUAAUCAUGGGGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAU
...((((...((((.(((((.(((((((((((((....((.(((....))).)).)))))))))...)))).))))).)).........((((((....))))))))....))))..... ( -41.00)
>consensus
AAACACUUUACAGCUGC___UGCCGAGUGUUAAUCAUGGGGUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAU
...(((((..(((((((....(((((((((((((..(((.............)))))))))))))...))).)))))))..))......((((((....)))))).......)))..... (-30.40 = -30.19 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,446,756 – 5,446,846
Length 90
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -30.80
Consensus MFE -22.10
Energy contribution -22.80
Covariance contribution 0.70
Combinations/Pair 1.09
Mean z-score -1.50
Structure conservation index 0.72
SVM decision value 0.20
SVM RNA-class probability 0.631236
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5446756 90 + 27905053
GUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAUGUUGGGA------------------------------GUG
.((((((((((.((((((.((....(((..((((....))))..)))...(((((....))))))).)))))))))))).))))...------------------------------... ( -25.00)
>DroEre_CAF1 33899 120 + 1
GUAAUUUAUUAGUCAGUUGACACUUUUUGGUCUCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAUGUUGGCAGUUGAGUGUGCGAAUUAUACCCAAUGAUGGGUG
................(((((((((....(((...(((((.(...((((((((((....)))..)))))))..).)))))...)))....)))))).)))....((((((....)))))) ( -32.00)
>DroYak_CAF1 34608 120 + 1
GUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAUGUUGCGAGCUGGAAGUGCGAAUUAUACCCGAUGAUGGGUG
(((((((((((.((((((.((....(((..((((....))))..)))...(((((....))))))).)))))))))))).)))))..((.......))......(((((......))))) ( -35.40)
>consensus
GUAAUUUAUUAGCCAGUUGACACUUUUUGGCCGCAGUUGCGGAAAAAUUCACUCGAAAUCGGGUGUGAAUUGGUGGUAAUGUUGGGAG_UG___GUGCGAAUUAUACCC_AUGAUGGGUG
.((((((((((.((((((.((....(((..((((....))))..)))...(((((....))))))).)))))))))))).)))).....................(((((....))))). (-22.10 = -22.80 +   0.70)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:05 2006