Locus 3788

Sequence ID 2L_DroMel_CAF1
Location 11,061,929 – 11,062,059
Length 130
Max. P 0.955624
window5969 window5970 window5971

overview

Window 9

Location 11,061,929 – 11,062,029
Length 100
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 88.45
Mean single sequence MFE -35.44
Consensus MFE -25.62
Energy contribution -26.02
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.20
Structure conservation index 0.72
SVM decision value 0.69
SVM RNA-class probability 0.822646
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11061929 100 + 22407834
UCAGACGACAGACUGACUGCAGAGUCGUUGGCUUUGGGUUUGGGCUUGGUCUUUGGGCUUUGGGCCUUGGGUAGAGGGACCUGAGACUGAGACCUGGG-------AU
...((((((...(((....))).))))))...((..(((((.((((((((((((((((.....)))).......))))))).))).)).)))))..))-------.. ( -33.61)
>DroSec_CAF1 50621 94 + 1
UCAGACGACAGACUGACUGCAGAGUCGUUGGCUUUGGGUUU------GGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGG-------AU
.........((((..(.(.((((((.....)))))).).).------.))))(..((.(((.(((((..(((......)))..))))).)))))..).-------.. ( -35.10)
>DroSim_CAF1 50838 94 + 1
UCAGACGACAGACUGACUGCAGAGUCGUUGGCUUUGGGUUU------GGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGG-------AU
.........((((..(.(.((((((.....)))))).).).------.))))(..((.(((.(((((..(((......)))..))))).)))))..).-------.. ( -35.10)
>DroEre_CAF1 53367 107 + 1
UCAGACGACAGACUGACUGCAGAGUCGUUGGGUUUGGGUUUGGGUUUGGUCUUUGGGCUUUGGGCCUUGGGUAGAGGGACCUGAGACUGAGACCUGGGAUCUGGGAU
(((((((((.((((........))))))))..((..(((((.((((((((((((((((.....)))).......)))))))..))))).)))))..)).)))))... ( -36.91)
>DroYak_CAF1 53067 93 + 1
UCAGACGACAGACUGACAACAGAGUCGUUGGGUUUGUGUUUGGGUUUGGUCUUU-------GGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGG-------AU
((((((.(((((((..((((......)))))))))))))))))....((((((.-------.(((((..(((......)))..)))))))))))....-------.. ( -36.50)
>consensus
UCAGACGACAGACUGACUGCAGAGUCGUUGGCUUUGGGUUUGGG_UUGGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGG_______AU
...((((((...(((....))).))))))..................((((((.........(((((..(((......)))..)))))))))))............. (-25.62 = -26.02 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,061,929 – 11,062,029
Length 100
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 88.45
Mean single sequence MFE -19.79
Consensus MFE -17.84
Energy contribution -17.60
Covariance contribution -0.24
Combinations/Pair 1.05
Mean z-score -1.75
Structure conservation index 0.90
SVM decision value 1.46
SVM RNA-class probability 0.955624
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11061929 100 - 22407834
AU-------CCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGGCCCAAAGCCCAAAGACCAAGCCCAAACCCAAAGCCAACGACUCUGCAGUCAGUCUGUCGUCUGA
..-------....((.((..((((..(((......)))...(((.....)))...))))..)).))...........(((((((.(((....)))...))))).)). ( -19.20)
>DroSec_CAF1 50621 94 - 1
AU-------CCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGACCCAAAGCCCAAAGACC------AAACCCAAAGCCAACGACUCUGCAGUCAGUCUGUCGUCUGA
..-------....(((((..((((..(((......)))..))))...........)))))------...........(((((((.(((....)))...))))).)). ( -18.32)
>DroSim_CAF1 50838 94 - 1
AU-------CCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGACCCAAAGCCCAAAGACC------AAACCCAAAGCCAACGACUCUGCAGUCAGUCUGUCGUCUGA
..-------....(((((..((((..(((......)))..))))...........)))))------...........(((((((.(((....)))...))))).)). ( -18.32)
>DroEre_CAF1 53367 107 - 1
AUCCCAGAUCCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGGCCCAAAGCCCAAAGACCAAACCCAAACCCAAACCCAACGACUCUGCAGUCAGUCUGUCGUCUGA
....(((((..(((((((........(((......)))...(((.....)))...))))).....................((((....))))....))..))))). ( -21.00)
>DroYak_CAF1 53067 93 - 1
AU-------CCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGACCC-------AAAGACCAAACCCAAACACAAACCCAACGACUCUGUUGUCAGUCUGUCGUCUGA
..-------....(((((..((((..(((......)))..))))..-------..))))).................(((((((.(((....)))...))))).)). ( -22.10)
>consensus
AU_______CCCAGGUCUCAGUCUCAGGUCCCUCUACCCAAGACCCAAAGCCCAAAGACCAA_CCCAAACCCAAAGCCAACGACUCUGCAGUCAGUCUGUCGUCUGA
.............(((((..((((..(((......)))..))))...........))))).................(((((((.(((....)))...))))).)). (-17.84 = -17.60 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,061,969 – 11,062,059
Length 90
Sequences 3
Columns 90
Reading direction forward
Mean pairwise identity 93.94
Mean single sequence MFE -31.53
Consensus MFE -27.60
Energy contribution -27.93
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.88
SVM decision value 0.07
SVM RNA-class probability 0.567129
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11061969 90 + 22407834
UGGGCUUGGUCUUUGGGCUUUGGGCCUUGGGUAGAGGGACCUGAGACUGAGACCUGGGAUCUGAGACCAAGUCAGGCCAAGUCAAGUCGA
..((((((((((((((..((..(..((..(((...((.........))...)))..))..)..)).))))...))))))))))....... ( -34.60)
>DroSec_CAF1 50661 84 + 1
U------GGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGGAUCUGAGACCAAGUCAGGCCAAGUCAAGUCGA
(------((((((..((.(((.(((((..(((......)))..))))).)))))..)((..((....))..))))))))........... ( -30.00)
>DroSim_CAF1 50878 84 + 1
U------GGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGGAUCUGAGACCAAGUCAGGCCAAGUCAACUCGA
(------((((((..((.(((.(((((..(((......)))..))))).)))))..)((..((....))..))))))))........... ( -30.00)
>consensus
U______GGUCUUUGGGCUUUGGGUCUUGGGUAGAGGGACCUGAGACUGAGACCUGGGAUCUGAGACCAAGUCAGGCCAAGUCAAGUCGA
.......(((((((((..((..(((((..(((...((.........))...)))..)))))..)).))))...)))))............ (-27.60 = -27.93 +   0.33)

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 11:01:17 2006