Locus 4415

Sequence ID 3R_DroMel_CAF1
Location 11,650,199 – 11,650,319
Length 120
Max. P 0.999939
window7213 window7214

overview

Window 3

Location 11,650,199 – 11,650,319
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -33.02
Consensus MFE -28.26
Energy contribution -28.86
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -1.94
Structure conservation index 0.86
SVM decision value 1.63
SVM RNA-class probability 0.968524
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11650199 120 + 27905053
UAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUAGCCACCCAGGUUAGCCAUUUCCACCAGCUGGCUAAAGCCAGUCAAAAUGCCAGCCCGGGUUCCAAUUUCCUUU
......((((((.....((...(((((((...........)))))))...)).(.((((.((.((((......((((((....))))))..)))))).)))).))))))).......... ( -32.40)
>DroSec_CAF1 30994 120 + 1
UAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUAGCCACCCAGGUUUGCCAUUUCCACCAGCUGACUAAAGCCGGUCAAAAUGCCAGCCCGGGUUCCGAUUUCCUUU
.....(((((((.....((...(((((((...........)))))))...))...((.(((.(((((..(((.(((......))).)))..))))).))).)).)))))))......... ( -35.00)
>DroSim_CAF1 33178 120 + 1
UAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUAGCCACCCAGAUUUGCCAUUUCCACCAGCUGGCUAAAGCCGGUCAAAAUGCCAGCCCGGGUUCCGAUUUCCUUU
.....(((((((.((..((...(((((((...........)))))))...))..))..(((.(((((..(((.(((......))).)))..))))).)))....)))))))......... ( -31.50)
>DroEre_CAF1 28998 120 + 1
UAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUAUCCACCCAGGUUUGCCAUUUCCACCAUCUGGCUUAAGCCAGUCAAAAUGCCAGCCCGGGUUCCGAUUUCCUUU
.....(((((((.....((..((((((((...........))))))))..))...((.(((.(((((.......(((((....)))))...))))).))).)).)))))))......... ( -33.80)
>DroYak_CAF1 31678 120 + 1
CAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUGGCCACCCAGGUUUGCCAUUUCCACCACCUGGCUUAAGCCGGUCAAAAUGCCAGCCCGGGUUCCGAUUUCCUUU
.....(((((((...........((((((...........))))))(((......(((((((((...........))))..)))))(((......))).)))..)))))))......... ( -32.40)
>consensus
UAGUCCGGAACCACUUCGUACAUGUUUGCGCCCUUCAUGAGCAAAUAGCCACCCAGGUUUGCCAUUUCCACCAGCUGGCUAAAGCCGGUCAAAAUGCCAGCCCGGGUUCCGAUUUCCUUU
.....(((((((.....((...(((((((...........)))))))...)).(.((((.((.((((......((((((....))))))..)))))).)))).))))))))......... (-28.26 = -28.86 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,650,199 – 11,650,319
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.08
Mean single sequence MFE -44.70
Consensus MFE -42.40
Energy contribution -42.48
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -2.77
Structure conservation index 0.95
SVM decision value 4.69
SVM RNA-class probability 0.999939
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11650199 120 - 27905053
AAAGGAAAUUGGAACCCGGGCUGGCAUUUUGACUGGCUUUAGCCAGCUGGUGGAAAUGGCUAACCUGGGUGGCUAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUA
........((((((((((((.(((((((((.((..(((......)))..)).))))).)))).))))))).(((((((((((.....))))(((....)))...)))))))))))).... ( -44.00)
>DroSec_CAF1 30994 120 - 1
AAAGGAAAUCGGAACCCGGGCUGGCAUUUUGACCGGCUUUAGUCAGCUGGUGGAAAUGGCAAACCUGGGUGGCUAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUA
........((((((((((((.((.((((((.(((((((......))))))).)))))).))..))))))).(((((((((((.....))))(((....)))...)))))))))))).... ( -48.10)
>DroSim_CAF1 33178 120 - 1
AAAGGAAAUCGGAACCCGGGCUGGCAUUUUGACCGGCUUUAGCCAGCUGGUGGAAAUGGCAAAUCUGGGUGGCUAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUA
........((((((((((((.((.((((((.(((((((......))))))).)))))).))..))))))).(((((((((((.....))))(((....)))...)))))))))))).... ( -45.60)
>DroEre_CAF1 28998 120 - 1
AAAGGAAAUCGGAACCCGGGCUGGCAUUUUGACUGGCUUAAGCCAGAUGGUGGAAAUGGCAAACCUGGGUGGAUAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUA
........(((((((((((..((.((((((.((((((....)))....))).)))))).))..))...(((.((.(((((((......)).))))).)).)))...).)))))))).... ( -39.90)
>DroYak_CAF1 31678 120 - 1
AAAGGAAAUCGGAACCCGGGCUGGCAUUUUGACCGGCUUAAGCCAGGUGGUGGAAAUGGCAAACCUGGGUGGCCAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUG
........((((((((((((.((.((((((.((((.((......)).)))).)))))).))..))))))).(((((((((((.....))))(((....)))...)))))))))))).... ( -45.90)
>consensus
AAAGGAAAUCGGAACCCGGGCUGGCAUUUUGACCGGCUUUAGCCAGCUGGUGGAAAUGGCAAACCUGGGUGGCUAUUUGCUCAUGAAGGGCGCAAACAUGUACGAAGUGGUUCCGGACUA
........((((((((((((.((.((((((.(((((((......))))))).)))))).))..))))))).(((((((((((.....))))(((....)))...)))))))))))).... (-42.40 = -42.48 +   0.08)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:37 2006