Locus 4476

Sequence ID 3L_DroMel_CAF1
Location 12,967,412 – 12,967,527
Length 115
Max. P 0.846583
window6979 window6980

overview

Window 9

Location 12,967,412 – 12,967,527
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 89.13
Mean single sequence MFE -25.88
Consensus MFE -17.34
Energy contribution -17.27
Covariance contribution -0.06
Combinations/Pair 1.12
Mean z-score -1.89
Structure conservation index 0.67
SVM decision value 0.02
SVM RNA-class probability 0.541696
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12967412 115 + 23771897
UACUGCACUUCUUAGUUGACAACAUAUGGAGCUGAAUGCUACAGUAAAAUUUUAAUAAAGUCCACCAUCGACUUGGUGACCCUUGCAAUUCAUUUCAUUUCCAUAUGCUGACUCU
...................((.(((((((((.(((((((....))).............(((.((((......))))))).............)))).))))))))).))..... ( -23.40)
>DroSec_CAF1 84684 115 + 1
GACUCAAAUUCUUAGUUGACAACAUAUGGAGCUGAGUGCUAGAGUAAAAUUUUAAUAAAAUCCACCAUCGACUUGGUGACCCUUGCUUUUCAUUUCAUUUCCAUAUGCUGACUCU
...((((........))))((.(((((((((.((((....(((((((..(((....)))...(((((......)))))....)))))))....)))).))))))))).))..... ( -26.50)
>DroSim_CAF1 89592 115 + 1
GACUCAAAUUCUUAGUUGACAACAUAUGGAGCUGAGUGCUAGAGUAAGAUUUUAAUAAAGUCCACCAUCGACUUGGUGACCCUUGCAUUUCAUUUCAUUUCCAUAUGCUGACUCU
...((((........))))((.(((((((((.(((((((.((.((..(((((.....)))))(((((......))))))).)).))))......))).))))))))).))..... ( -27.80)
>DroEre_CAF1 90548 110 + 1
GUCUCGAAUUCUUAAUUGAGAACAUAUGUGCCUGAGUGGUACAGUAAAAUUUUAAUAAAGUCCACCAUCGACUUGGUGGCCCGUGCAUUU-----CAUUUCCAUAUGCUGACUCU
(((.((....(((.(((((((.....((((((.....))))))......))))))).))).((((((......))))))..)).((((..-----.........)))).)))... ( -25.80)
>consensus
GACUCAAAUUCUUAGUUGACAACAUAUGGAGCUGAGUGCUACAGUAAAAUUUUAAUAAAGUCCACCAUCGACUUGGUGACCCUUGCAUUUCAUUUCAUUUCCAUAUGCUGACUCU
...................((.((((((((((.....)))......................(((((......)))))......................))))))).))..... (-17.34 = -17.27 +  -0.06)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 0

Location 12,967,412 – 12,967,527
Length 115
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 89.13
Mean single sequence MFE -28.31
Consensus MFE -23.48
Energy contribution -23.73
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.83
SVM decision value 0.77
SVM RNA-class probability 0.846583
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12967412 115 - 23771897
AGAGUCAGCAUAUGGAAAUGAAAUGAAUUGCAAGGGUCACCAAGUCGAUGGUGGACUUUAUUAAAAUUUUACUGUAGCAUUCAGCUCCAUAUGUUGUCAACUAAGAAGUGCAGUA
...(.(((((((((((..((((.((...(((((((..(((((......)))))..)))..............)))).))))))..))))))))))).)................. ( -30.43)
>DroSec_CAF1 84684 115 - 1
AGAGUCAGCAUAUGGAAAUGAAAUGAAAAGCAAGGGUCACCAAGUCGAUGGUGGAUUUUAUUAAAAUUUUACUCUAGCACUCAGCUCCAUAUGUUGUCAACUAAGAAUUUGAGUC
...(.(((((((((((..(((..(....)((.((((((((((......)))))(((((.....)))))..))))).))..)))..))))))))))).)................. ( -30.20)
>DroSim_CAF1 89592 115 - 1
AGAGUCAGCAUAUGGAAAUGAAAUGAAAUGCAAGGGUCACCAAGUCGAUGGUGGACUUUAUUAAAAUCUUACUCUAGCACUCAGCUCCAUAUGUUGUCAACUAAGAAUUUGAGUC
...(.(((((((((((..(((.......(((.((((((((((......)))))((.(((....)))))..))))).))).)))..))))))))))).)................. ( -28.70)
>DroEre_CAF1 90548 110 - 1
AGAGUCAGCAUAUGGAAAUG-----AAAUGCACGGGCCACCAAGUCGAUGGUGGACUUUAUUAAAAUUUUACUGUACCACUCAGGCACAUAUGUUCUCAAUUAAGAAUUCGAGAC
.(((..((((((((....((-----((((....(((((((((......)))))).))).......))))))(((.......)))...)))))))))))................. ( -23.90)
>consensus
AGAGUCAGCAUAUGGAAAUGAAAUGAAAUGCAAGGGUCACCAAGUCGAUGGUGGACUUUAUUAAAAUUUUACUCUAGCACUCAGCUCCAUAUGUUGUCAACUAAGAAUUUGAGUC
...(.(((((((((((...............((((.((((((......)))))).)))).................((.....))))))))))))).)................. (-23.48 = -23.73 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:15 2006