Locus 1123

Sequence ID 2L_DroMel_CAF1
Location 3,044,875 – 3,045,013
Length 138
Max. P 0.958404
window1828 window1829

overview

Window 8

Location 3,044,875 – 3,044,983
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.59
Mean single sequence MFE -49.38
Consensus MFE -38.00
Energy contribution -38.84
Covariance contribution 0.84
Combinations/Pair 1.27
Mean z-score -2.02
Structure conservation index 0.77
SVM decision value 1.19
SVM RNA-class probability 0.927974
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3044875 108 - 22407834
-----------CAGCAGGCAGGGAGCAGGGAGCUGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGCUCUCGAGAUAGUC-GUCCAGCUCUCGACUGCGUGCACUGC
-----------..(((.(((((((((((((((((.((((.....)))).))))))))))).))......(((((((.((....(((.....))-).)).))))))).)))).)))..... ( -53.60)
>DroSec_CAF1 4613 108 - 1
-----------CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGCUCUCGAGAUAGUC-GUCCAGCUCUCGACUGCGUGCACUGC
-----------..(((.(((((((((((((((((.((((.....)))).))))))))))).))......(((((((.((....(((.....))-).)).))))))).)))).)))..... ( -52.60)
>DroSim_CAF1 4741 108 - 1
-----------CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGCUCUCGAGAUAGUC-GUCCAGCUCUCGACUGCGUGCACUGC
-----------..(((.(((((((((((((((((.((((.....)))).))))))))))).))......(((((((.((....(((.....))-).)).))))))).)))).)))..... ( -52.60)
>DroYak_CAF1 4685 119 - 1
AAAGCAGGAAACAGGGAGCUGGGAGCAGGGAGCUGGGUGUGGGUCACUGGGUUCCCUGUUGCCAAGUCACGGGAGUCGGCUCUCGAGAUAGUC-GUCCAGCUCUCGACUGCGUGCACUGC
...(((.(.....(((((((((((((((((((((.((((.....)))).))))))))))).....(((.((((((....)))))).)))....-.)))))))))).....).)))..... ( -60.30)
>DroAna_CAF1 4574 99 - 1
-------------------AGGGAG--GGAGGCCCGAUACGGAUCUUUUGAUUUCUUGUUGCCAGGUUGUGGGAGAAGGCUAUCGAGAUAGCCCAGACACCUCGCAACUGCGUGAACUGC
-------------------.(((..--.....)))..((((((((....))))....(((((.((((.((..(....((((((....)))))))..)))))).)))))..))))...... ( -27.80)
>consensus
___________CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGCUCUCGAGAUAGUC_GUCCAGCUCUCGACUGCGUGCACUGC
.............(((.((.((.(((((((((((.((((.....)))).))))))))))).)).((((.((((((....)))))).((.(((.......))).)))))))).)))..... (-38.00 = -38.84 +   0.84)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,044,914 – 3,045,013
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.66
Mean single sequence MFE -38.48
Consensus MFE -28.75
Energy contribution -27.80
Covariance contribution -0.95
Combinations/Pair 1.35
Mean z-score -1.31
Structure conservation index 0.75
SVM decision value 1.49
SVM RNA-class probability 0.958404
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3044914 99 - 22407834
UUCCACCACUCAGCAGAAUCCAACCUGAAG---------------------CAGCAGGCAGGGAGCAGGGAGCUGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGC
............((.((.(((..((((...---------------------...))))..((.(((((((((((.((((.....)))).))))))))))).))........))).)).)) ( -40.40)
>DroSec_CAF1 4652 99 - 1
UUCCACCACUCAGUAGAAUCCAACCUGGAG---------------------CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGC
.....((((((.((((..(((.....)))(---------------------(.....)).((.(((((((((((.((((.....)))).))))))))))).))...))))..)))).)). ( -43.30)
>DroSim_CAF1 4780 100 - 1
UUCCAACACUCAGUAGAAUCCAACCUGGAGC--------------------CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGC
((((....(((.((.(..(((.....)))..--------------------).)))))..((.(((((((((((.((((.....)))).))))))))))).)).......))))...... ( -41.70)
>DroYak_CAF1 4724 120 - 1
UUCGGCCACUCAGCAGAAUCCAAAACGGAGCAGAAAACAGAAAGCAGGAAACAGGGAGCUGGGAGCAGGGAGCUGGGUGUGGGUCACUGGGUUCCCUGUUGCCAAGUCACGGGAGUCGGC
...(((..((((((....(((.....))).................(....).....))))))(((((((((((.((((.....)))).))))))))))))))..(((((....)).))) ( -46.50)
>DroAna_CAF1 4614 87 - 1
UUCGCCAAUUCGACAUUUUUCGAAUUAU-------------------------------AGGGAG--GGAGGCCCGAUACGGAUCUUUUGAUUUCUUGUUGCCAGGUUGUGGGAGAAGGC
...((((((((((......)))))))((-------------------------------((((((--.(((..(((...)))..)))....))))))))..(((.....))).....))) ( -20.50)
>consensus
UUCCACCACUCAGCAGAAUCCAACCUGGAG_____________________CAGCGAGCAGGGAGCAGGGAGCCGGGUGCGGGUCACUGGGUUCCCUGUUGCCAAGUUACGGGAGUCGGC
...............((.(((................................(....).((.(((((((((((.((((.....)))).))))))))))).))........))).))... (-28.75 = -27.80 +  -0.95)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:17 2006