Locus 7720

Sequence ID 3L_DroMel_CAF1
Location 20,616,019 – 20,616,139
Length 120
Max. P 0.958499
window12567 window12568

overview

Window 7

Location 20,616,019 – 20,616,139
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.81
Mean single sequence MFE -23.05
Consensus MFE -20.23
Energy contribution -20.73
Covariance contribution 0.50
Combinations/Pair 1.08
Mean z-score -1.75
Structure conservation index 0.88
SVM decision value 0.77
SVM RNA-class probability 0.845604
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20616019 120 + 23771897
UAUCACAAACUUCGUGGAAACCCAUAUCUUCUGAAAUAUUUCGGUUCCCAUACCCAAUAAUGGAUUUCCACAUCCCUGGCGCUAUUGUGCAUGUCACUUGCUUUCCUUUUGUUUGCUUCU
.....(((((...(((((((.((((.......(((....)))(((......))).....)))).))))))).......((((....))))....................)))))..... ( -25.80)
>DroSec_CAF1 60821 120 + 1
UAUCACAAACUUCGUGGAAGCCCAUAUCUUCUGAAAUAUUUCGGUUCCCAUAGCCAAUAAUGGAUUUCCACAUCCCUGGCGCUAUUGUGCAUGUCACUUGCUUUCCUUUUGUUUGCUUCU
.....(((((...((((((..((((.......(((....)))((((.....))))....))))..)))))).......((((....))))....................)))))..... ( -26.40)
>DroSim_CAF1 55702 120 + 1
UAUCACAAACUUCGUGGAAACCCAUAUCUUCUGAAGUAUUUCGGUUCCCAUAGCCAAUAAUGGAUUUCCACAUCCCUGGCGCUAUUGUGCAUGUCACUUGCUUUCCUUUUGUUUGCUUCU
.....(((((...(((((((.((((.((....))........((((.....))))....)))).))))))).......((((....))))....................)))))..... ( -26.30)
>DroEre_CAF1 53263 110 + 1
AACUAUAAACUUCGUAGAAACCCAUA----------UAUUUCGGUUCCCAUAGCCAAUAAUAGAUUUCCACCUCCCUGGCGCUAUUGUGCAUGUCACUUGCUUUCCUUUUGUUUGCUUCU
.............(((((........----------......((((.....)))).(((((((....(((......)))..)))))))(((.......)))..........))))).... ( -13.70)
>consensus
UAUCACAAACUUCGUGGAAACCCAUAUCUUCUGAAAUAUUUCGGUUCCCAUAGCCAAUAAUGGAUUUCCACAUCCCUGGCGCUAUUGUGCAUGUCACUUGCUUUCCUUUUGUUUGCUUCU
.....(((((...(((((((.((((.((....))........((((.....))))....)))).))))))).......((((....))))....................)))))..... (-20.23 = -20.73 +   0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,616,019 – 20,616,139
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.81
Mean single sequence MFE -29.57
Consensus MFE -25.80
Energy contribution -26.55
Covariance contribution 0.75
Combinations/Pair 1.06
Mean z-score -2.23
Structure conservation index 0.87
SVM decision value 1.49
SVM RNA-class probability 0.958499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20616019 120 - 23771897
AGAAGCAAACAAAAGGAAAGCAAGUGACAUGCACAAUAGCGCCAGGGAUGUGGAAAUCCAUUAUUGGGUAUGGGAACCGAAAUAUUUCAGAAGAUAUGGGUUUCCACGAAGUUUGUGAUA
....((((((....((...((..(((.....)))....)).)).....(((((((((((((.(((.(((......)))(((....)))....))))))))))))))))..)))))).... ( -32.80)
>DroSec_CAF1 60821 120 - 1
AGAAGCAAACAAAAGGAAAGCAAGUGACAUGCACAAUAGCGCCAGGGAUGUGGAAAUCCAUUAUUGGCUAUGGGAACCGAAAUAUUUCAGAAGAUAUGGGCUUCCACGAAGUUUGUGAUA
....((((((....((...((..(((.....)))....)).)).....(((((((..((((.(((..((..((...))(((....)))))..)))))))..)))))))..)))))).... ( -29.20)
>DroSim_CAF1 55702 120 - 1
AGAAGCAAACAAAAGGAAAGCAAGUGACAUGCACAAUAGCGCCAGGGAUGUGGAAAUCCAUUAUUGGCUAUGGGAACCGAAAUACUUCAGAAGAUAUGGGUUUCCACGAAGUUUGUGAUA
....((((((....((...((..(((.....)))....)).)).....(((((((((((((.(((..((..((...........))..))..))))))))))))))))..)))))).... ( -33.00)
>DroEre_CAF1 53263 110 - 1
AGAAGCAAACAAAAGGAAAGCAAGUGACAUGCACAAUAGCGCCAGGGAGGUGGAAAUCUAUUAUUGGCUAUGGGAACCGAAAUA----------UAUGGGUUUCUACGAAGUUUAUAGUU
..((((.............((..(((.....)))....))(((((..((((....))))....)))))..((((((((.(....----------..).))))))))....))))...... ( -23.30)
>consensus
AGAAGCAAACAAAAGGAAAGCAAGUGACAUGCACAAUAGCGCCAGGGAUGUGGAAAUCCAUUAUUGGCUAUGGGAACCGAAAUAUUUCAGAAGAUAUGGGUUUCCACGAAGUUUGUGAUA
....((((((.........((..(((.....)))....))(((((....((((....))))..)))))..((((((((...(((((......))))).))))))))....)))))).... (-25.80 = -26.55 +   0.75)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:03 2006