Locus 1237

Sequence ID 2R_DroMel_CAF1
Location 4,852,374 – 4,852,510
Length 136
Max. P 0.969443
window2149 window2150 window2151

overview

Window 9

Location 4,852,374 – 4,852,478
Length 104
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 96.15
Mean single sequence MFE -33.75
Consensus MFE -29.67
Energy contribution -30.01
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.88
SVM decision value 0.13
SVM RNA-class probability 0.597531
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4852374 104 + 20766785
GCAGAUGAGUGGCCAUAUGAAUGUGGGCGUAAGAGUGUGCACCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCAAAAGUCAGAGACAUCUGACACUUCACA
((...(((.(((((((((.....((((((.............))))))........))).))))))..)))...))....((((((....))))))........ ( -31.94)
>DroEre_CAF1 8761 104 + 1
GCAGAUGAGUGGCCAUAUGAAUGUGGGCGUAAGAGUGUUUGCCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACA
((...(((.(((((((((.....((((((((((....)))).))))))........))).))))))..)))...))(((.((((((....))))))..)))... ( -34.02)
>DroYak_CAF1 13207 104 + 1
GCAGAUGAGUGGCCAUAUGAAUGUGGGCGUAAGAGUGUGUGCCACCCGUUGCAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACA
(((.(((.((((((((((..(((....)))....))))).))))).))))))....(((..((((........)))....((((((....)))))).)..))). ( -35.30)
>consensus
GCAGAUGAGUGGCCAUAUGAAUGUGGGCGUAAGAGUGUGUGCCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACA
((...(((.(((((((((.....((((((.............))))))........))).))))))..)))...))....((((((....))))))........ (-29.67 = -30.01 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,852,374 – 4,852,478
Length 104
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 96.15
Mean single sequence MFE -31.39
Consensus MFE -30.56
Energy contribution -30.12
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.45
Structure conservation index 0.97
SVM decision value 1.64
SVM RNA-class probability 0.969443
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4852374 104 - 20766785
UGUGAAGUGUCAGAUGUCUCUGACUUUUGCCUUUGACUUGGCCAGCACUUUUCCAACGGGCGGUGCACACUCUUACGCCCACAUUCAUAUGGCCACUCAUCUGC
.(..(((.((((((....)))))))))..)...(((..((((((.............(((((.............))))).........)))))).)))..... ( -28.77)
>DroEre_CAF1 8761 104 - 1
UGUGAAGUGUCAGAUGUCUCUGACUUUCGCCUUUGACUUGGCCAGCACUUUUCCAACGGGCGGCAAACACUCUUACGCCCACAUUCAUAUGGCCACUCAUCUGC
.((((((.((((((....))))))))))))...(((..((((((.............(((((.............))))).........)))))).)))..... ( -31.17)
>DroYak_CAF1 13207 104 - 1
UGUGAAGUGUCAGAUGUCUCUGACUUUCGCCUUUGACUUGGCCAGCACUUUUGCAACGGGUGGCACACACUCUUACGCCCACAUUCAUAUGGCCACUCAUCUGC
.((((((.((((((....))))))))))))...(((..(((((((((....)))...(((((.............))))).........)))))).)))..... ( -34.22)
>consensus
UGUGAAGUGUCAGAUGUCUCUGACUUUCGCCUUUGACUUGGCCAGCACUUUUCCAACGGGCGGCACACACUCUUACGCCCACAUUCAUAUGGCCACUCAUCUGC
.((((((.((((((....))))))))))))...(((..(((((((........)...(((((.............))))).........)))))).)))..... (-30.56 = -30.12 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,852,407 – 4,852,510
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 95.47
Mean single sequence MFE -36.03
Consensus MFE -32.71
Energy contribution -32.60
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.83
Structure conservation index 0.91
SVM decision value 0.22
SVM RNA-class probability 0.639525
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4852407 103 + 20766785
AGUGUGCACCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCAAAAGUCAGAGACAUCUGACACUUCACAUGCUCGGAUGAGGGCGCCUUAUUGGCCUCAAG
.....((((..((....))....)))).((((((....(((((....((((((....)))))).........((((......))))))))).))))))..... ( -37.30)
>DroEre_CAF1 8794 103 + 1
AGUGUUUGCCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACAUGCUCGGAUGAGGGCGCCUUAUUGGCCUCAAG
((..(((....((....))..)))..))((((((....((((((((.((((((....))))))..)))....((((......))))))))).))))))..... ( -36.50)
>DroYak_CAF1 13240 103 + 1
AGUGUGUGCCACCCGUUGCAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACAUGCUCGGAUGAGGGUGCCUUAUUGGCCUCAAG
((..(.(((........)))...)..))((((((....((((((((.((((((....))))))..)))....((((......))))))))).))))))..... ( -34.30)
>consensus
AGUGUGUGCCGCCCGUUGGAAAAGUGCUGGCCAAGUCAAAGGCGAAAGUCAGAGACAUCUGACACUUCACAUGCUCGGAUGAGGGCGCCUUAUUGGCCUCAAG
((..(...(((.....)))....)..))((((((....(((((....((((((....)))))).........((((......))))))))).))))))..... (-32.71 = -32.60 +  -0.11)

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 09:59:47 2006