Locus 555

Sequence ID 3L_DroMel_CAF1
Location 1,586,717 – 1,586,815
Length 98
Max. P 0.908406
window850 window851

overview

Window 0

Location 1,586,717 – 1,586,815
Length 98
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 70.03
Mean single sequence MFE -30.78
Consensus MFE -14.65
Energy contribution -13.85
Covariance contribution -0.80
Combinations/Pair 1.52
Mean z-score -1.64
Structure conservation index 0.48
SVM decision value 0.33
SVM RNA-class probability 0.692512
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1586717 98 + 23771897
GAAUGCCAGGCACAUGGAGUGCCUGUUCGCCAAGUGGCUGGGGGACACUAGCUCGGUCAAUGGAGUGGG--UUAUAUGA---CCUGCGGUCAAAAUACCUA----------UU
(((...(((((((.....)))))))))).(((..((((((((.........)))))))).)))((((((--(....(((---((...)))))....)))))----------)) ( -36.00)
>DroSec_CAF1 5632 98 + 1
GAAUGCCAGGCACAUGGAGUGCCUGUUCGCCACGUGGCUGAGGGACAAUAACUCGGUCAAUGGAGUGGG--UUAUGUGA---CCUGCGGCCAAUAAACCUA----------UU
(((...(((((((.....))))))))))......(((((((((....((((((((.((....)).))))--))))....---))).)))))).........----------.. ( -37.50)
>DroSim_CAF1 5728 98 + 1
GAAUGCCAGGCACAUGGAGUGCCUGUUCGCCACGUGGCUGAGGGACAAUAACUCGGUCAAUGGAGUGGG--UUAUGUGA---CCUGCGGUCAAAAAACCUA----------UU
(((...(((((((.....)))))))))).(((..((((((((.........)))))))).)))((((((--((...(((---((...)))))...))))))----------)) ( -39.50)
>DroEre_CAF1 5574 103 + 1
GAAUGCCAGACACUUGGAGUGCCUGUUCACCAAGUGGAUGAGGGACAAUAACUCGAUCAAUGGAGUGGG--UGAUAUAUUUCCCUGUGGUCGAAAUACCUU--------AAAA
......((..(((((((.(........).)))))))..))(((((.(((((((((.((....)).))))--)....)))))))))..(((......)))..--------.... ( -25.30)
>DroWil_CAF1 10986 97 + 1
CAAUGCAAAAUAUAUGGAGUACUUAUUUUCAAAAUGGGUGAAAGAUGAAACUUCUGUUCAUGUGGUAUGAAUGAUA----------------AUGUACAAUUUUUUUUUGCUA
....((((((........(((((((((((((...((.((((((((.......))).))))).))...)))).))))----------------).)))).......)))))).. ( -18.16)
>DroYak_CAF1 5586 99 + 1
GAAUGCUAGGCACUUGGAGUGCCUGUUCGCCAAGUGGAUGAGGGACAAUAGCUCGGUCAAUGGAGUGGG--UGAUAUCAUUUCCUGUAGCUUAAAUACCUC------------
.......((((((.....))))))((((((...))))))((((......(((((((.....(((((((.--.....)))))))))).))))......))))------------ ( -28.20)
>consensus
GAAUGCCAGGCACAUGGAGUGCCUGUUCGCCAAGUGGCUGAGGGACAAUAACUCGGUCAAUGGAGUGGG__UGAUAUGA___CCUGCGGUCAAAAUACCUA__________UU
....(((((((((.....))))))..(((((...(((.((((.........)))).)))...).))))...................)))....................... (-14.65 = -13.85 +  -0.80) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,586,717 – 1,586,815
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 70.03
Mean single sequence MFE -25.48
Consensus MFE -12.29
Energy contribution -11.88
Covariance contribution -0.41
Combinations/Pair 1.53
Mean z-score -1.88
Structure conservation index 0.48
SVM decision value 1.06
SVM RNA-class probability 0.908406
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1586717 98 - 23771897
AA----------UAGGUAUUUUGACCGCAGG---UCAUAUAA--CCCACUCCAUUGACCGAGCUAGUGUCCCCCAGCCACUUGGCGAACAGGCACUCCAUGUGCCUGGCAUUC
..----------..(((......)))((.((---(((.....--..........)))))..)).(((((......(((....)))...(((((((.....)))))))))))). ( -30.66)
>DroSec_CAF1 5632 98 - 1
AA----------UAGGUUUAUUGGCCGCAGG---UCACAUAA--CCCACUCCAUUGACCGAGUUAUUGUCCCUCAGCCACGUGGCGAACAGGCACUCCAUGUGCCUGGCAUUC
..----------........((.(((((.((---(((.....--..........)))))(((.........)))......))))).))(((((((.....)))))))...... ( -29.86)
>DroSim_CAF1 5728 98 - 1
AA----------UAGGUUUUUUGACCGCAGG---UCACAUAA--CCCACUCCAUUGACCGAGUUAUUGUCCCUCAGCCACGUGGCGAACAGGCACUCCAUGUGCCUGGCAUUC
..----------..((((....))))((.((---(((.....--..........)))))(((.........))).(((....)))...(((((((.....))))))))).... ( -30.06)
>DroEre_CAF1 5574 103 - 1
UUUU--------AAGGUAUUUCGACCACAGGGAAAUAUAUCA--CCCACUCCAUUGAUCGAGUUAUUGUCCCUCAUCCACUUGGUGAACAGGCACUCCAAGUGUCUGGCAUUC
....--------..(((......)))...((((...(((...--...((((........)))))))..))))(((((.....))))).(((((((.....)))))))...... ( -23.50)
>DroWil_CAF1 10986 97 - 1
UAGCAAAAAAAAAUUGUACAU----------------UAUCAUUCAUACCACAUGAACAGAAGUUUCAUCUUUCACCCAUUUUGAAAAUAAGUACUCCAUAUAUUUUGCAUUG
..((((((.......((((.(----------------(((..((((.......((((.(((.......))))))).......)))).))))))))........)))))).... ( -13.60)
>DroYak_CAF1 5586 99 - 1
------------GAGGUAUUUAAGCUACAGGAAAUGAUAUCA--CCCACUCCAUUGACCGAGCUAUUGUCCCUCAUCCACUUGGCGAACAGGCACUCCAAGUGCCUAGCAUUC
------------((((.((...((((...((.((((......--.......))))..)).))))...)).)))).........((....((((((.....)))))).)).... ( -25.22)
>consensus
AA__________UAGGUAUUUUGACCGCAGG___UCAUAUAA__CCCACUCCAUUGACCGAGUUAUUGUCCCUCAGCCACUUGGCGAACAGGCACUCCAUGUGCCUGGCAUUC
..............(((......)))...............................(((((.................)))))....(((((((.....)))))))...... (-12.29 = -11.88 +  -0.41) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:15 2006