Locus 6123

Sequence ID 3L_DroMel_CAF1
Location 16,219,816 – 16,219,935
Length 119
Max. P 0.827347
window9836 window9837

overview

Window 6

Location 16,219,816 – 16,219,935
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.08
Mean single sequence MFE -26.62
Consensus MFE -25.22
Energy contribution -25.42
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.95
SVM decision value 0.70
SVM RNA-class probability 0.827347
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16219816 119 + 23771897
CAAUUUGUCUCC-CUUUGUUGGCAGAAAUUCGGGUUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUGCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAUCUAACCCUUU
............-..((.((((((((((.(((((((((((((.((((((((....))))))))....)).))))))))))).))))(((......))))))))).))............. ( -26.60)
>DroSec_CAF1 38714 120 + 1
CAAUUUGUCUCCGCUUUGUUGGCAGAAAUUCGGGUUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUGCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAUCUAACCCUUU
((.(((((((..(((.....)))(((((.(((((((((((((.((((((((....))))))))....)).))))))))))).))))).))))))).))....((((.........)))). ( -28.60)
>DroSim_CAF1 40348 120 + 1
CAAUUUGUCUCCCCUUUGUUGGCAGAAAUUCGGGUUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUGCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAUCUAACCCUUU
...............((.((((((((((.(((((((((((((.((((((((....))))))))....)).))))))))))).))))(((......))))))))).))............. ( -26.60)
>DroEre_CAF1 38576 119 + 1
CAAUUUGUCUCC-CUUUGUUGGCAGAAAUUCGGGUUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUGCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAGCUAACCCUUU
............-....(((((((((((.(((((((((((((.((((((((....))))))))....)).))))))))))).))))).((((.....)).)).......))))))..... ( -27.60)
>DroYak_CAF1 75764 119 + 1
CAAUUUGUCUCC-CUUUGUUGGCAGAAUUUCGGGCUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUUCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAUCUAACCCUUU
...((((((...-.......)))))).....(((.....(((....((((((((..(((.((((((............))))))))).))))))))...)))..((....))..)))... ( -23.70)
>consensus
CAAUUUGUCUCC_CUUUGUUGGCAGAAAUUCGGGUUAAAGGCUUUUGUUUGUUUGCAGAUAAAUCAUGCAUUUUAAUUUGAUUUUUUAGGACAAACUGUGCCAAGGAUAUCUAACCCUUU
...((((((...........)))))).....(((((...(((....((((((((..(((.((((((............))))))))).))))))))...)))..((....)))))))... (-25.22 = -25.42 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,219,816 – 16,219,935
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.08
Mean single sequence MFE -23.86
Consensus MFE -19.57
Energy contribution -19.61
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.04
Structure conservation index 0.82
SVM decision value 0.65
SVM RNA-class probability 0.811434
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16219816 119 - 23771897
AAAGGGUUAGAUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGCAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAACCCGAAUUUCUGCCAACAAAG-GGAGACAAAUUG
...((((((((.......(((..((((((...........))))))....((((.((....))))))...........))))))))))).....(((.((......)-).)))....... ( -23.71)
>DroSec_CAF1 38714 120 - 1
AAAGGGUUAGAUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGCAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAACCCGAAUUUCUGCCAACAAAGCGGAGACAAAUUG
...((((((((.......(((..((((((...........))))))....((((.((....))))))...........)))))))))))...(((((((.......)))))))....... ( -25.21)
>DroSim_CAF1 40348 120 - 1
AAAGGGUUAGAUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGCAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAACCCGAAUUUCUGCCAACAAAGGGGAGACAAAUUG
...((((((((.......(((..((((((...........))))))....((((.((....))))))...........))))))))))).....(((.((.......)).)))....... ( -23.11)
>DroEre_CAF1 38576 119 - 1
AAAGGGUUAGCUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGCAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAACCCGAAUUUCUGCCAACAAAG-GGAGACAAAUUG
...((((((((((....))))...((((((......((((((............))))))....)))))).............)))))).....(((.((......)-).)))....... ( -24.40)
>DroYak_CAF1 75764 119 - 1
AAAGGGUUAGAUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGAAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAGCCCGAAAUUCUGCCAACAAAG-GGAGACAAAUUG
...((((((((.......(((...((((((......((((((............))))))........))))))....))))))))))).....(((.((......)-).)))....... ( -22.85)
>consensus
AAAGGGUUAGAUAUCCUUGGCACAGUUUGUCCUAAAAAAUCAAAUUAAAAUGCAUGAUUUAUCUGCAAACAAACAAAAGCCUUUAACCCGAAUUUCUGCCAACAAAG_GGAGACAAAUUG
...((((((((.......(((...((((((......((((((............))))))........))))))....))))))))))).....(((.((........)))))....... (-19.57 = -19.61 +   0.04)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:40 2006