Locus 9308

Sequence ID 3R_DroMel_CAF1
Location 24,777,805 – 24,777,979
Length 174
Max. P 0.682405
window14880 window14881

overview

Window 0

Location 24,777,805 – 24,777,912
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.57
Mean single sequence MFE -26.10
Consensus MFE -17.80
Energy contribution -18.10
Covariance contribution 0.30
Combinations/Pair 1.13
Mean z-score -1.45
Structure conservation index 0.68
SVM decision value 0.09
SVM RNA-class probability 0.577336
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24777805 107 + 27905053
AGCGAAAGCA--------GGGAAA---CAAAAAAAAAAAAACAACGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGCCAAGGUGUGCAUGGGCGGG--GGCGUGGAUU
.((....)).--------.(....---)...............((((.......(((((......)))))...((((((...(((.(((....))))))...))))))--.))))..... ( -29.50)
>DroSec_CAF1 8930 95 + 1
AGCGCAAGCU--------GGGAAA----AA-------------AAGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGCCAAGGUGUGCAUGGGGGGGAGGGCGUUUCUU
(((....)))--------((((((----..-------------..((.......(((((......))))).(.(((.(((((.((.(((....)))))))))).))).)..)).)))))) ( -26.00)
>DroSim_CAF1 4310 96 + 1
AGCGAAAGCA--------GGGAAA---AAA-------------AAGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGCCAAGGUGUGCAUGGGGGGAGGGGUGUUUCUU
.((....)).--------((((((---...-------------....((((..(....)..))))..((..(.(((.((...(((.(((....))))))...)).))).)..)))))))) ( -23.30)
>DroEre_CAF1 17898 87 + 1
------------------GGGAAACAAAAA-------------ACGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGGUGAGGUGUGCAUGGGCGGG--GGCCUGGCGC
------------------.(....).....-------------...........(((((......)))))((.((.(((((....))))))).))((((.(((((...--.))))))))) ( -21.20)
>DroYak_CAF1 9483 106 + 1
AGCGAAAGCAGAAAGGCAGGCAAGCAAAAA-------------ACGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGGCAAGGUGUGCAUGGGCGGG-GGGCGUGGCUU
.((....))...(((.((.((..((.....-------------((((.......(((((......))))).....((((((....))))))..))))......))...-..)).)).))) ( -30.50)
>consensus
AGCGAAAGCA________GGGAAA___AAA_____________ACGCGAAUUGAUUGAUUGAUUUAUCAAAUGUCUGCCAUGGCAAUGCCAAGGUGUGCAUGGGCGGG_GGGCGUGGCUU
.((....))...................................((((......(((((......)))))...((((((...(((.(((....))))))...))))))....)))).... (-17.80 = -18.10 +   0.30)

alignment

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secondary structure

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dotplot

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Window 1

Location 24,777,874 – 24,777,979
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 83.21
Mean single sequence MFE -46.90
Consensus MFE -27.94
Energy contribution -28.82
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.60
SVM decision value 0.31
SVM RNA-class probability 0.682405
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24777874 105 + 27905053
UGGCAAUGCCAAGGUGUGCAUGGGCGGG--GGCGUGGAUUUCUCCAAAGCGAAAAGGGGGU----------GUGGCU---GGCUGGUGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUUUG
..(((.(((....))))))(((((((((--(.((((....(((((..........)))))(----------(..(((---(.(....).))))..)).)))).))))))))))....... ( -45.40)
>DroSec_CAF1 8985 107 + 1
UGGCAAUGCCAAGGUGUGCAUGGGGGGGAGGGCGUUUCUUCCUCCAAAGGGGAAAGGGGGU----------GUGGCU---GGCUGGUGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUUUG
.(((...)))(((((((......(((((((((....))))))))).....(((.((((.((----------((.((.---(((((....))))))).))))..)))).)))))))))).. ( -44.80)
>DroSim_CAF1 4366 107 + 1
UGGCAAUGCCAAGGUGUGCAUGGGGGGAGGGGUGUUUCUUCCUCCAAAGGGGAAAGGGGGU----------GUGGCU---GGCUGGUGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUUUG
.(((...)))(((((((...(((((((((((....)))))))))))....(((.((((.((----------((.((.---(((((....))))))).))))..)))).)))))))))).. ( -45.90)
>DroEre_CAF1 17947 114 + 1
UGGCAAUGGUGAGGUGUGCAUGGGCGGG--GGCCUGGCGCUCUCCAAA----AAGGGGGGUGUGGCAGUGGGUGGCUGGUGGCUGGCGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUCUG
..........(((((....(((((((((--(.(((((((((((((...----..))))))))).(((((..((.((..(...)..)).)).)))))..)).))))))))))))))))).. ( -54.20)
>DroYak_CAF1 9550 102 + 1
UGGCAAUGGCAAGGUGUGCAUGGGCGGG-GGGCGUGGCUUCCUCCAAA----AGAGGGA------------GUGGCUG-AGGCUGGUGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUUUG
........(((.....)))(((((((((-.(.(((.((((((((....----.))))))------------)).((((-.(((((....))))).))))))).))))))))))....... ( -44.20)
>consensus
UGGCAAUGCCAAGGUGUGCAUGGGCGGG_GGGCGUGGCUUCCUCCAAAG_G_AAAGGGGGU__________GUGGCU___GGCUGGUGGCAGCUGCGGCAUGGCCCUGUCCAUAUCUUUG
..(((.(((....))))))((((((((...(((.......(((((..........)))))..............(((...(((((....)))))..)))...)))))))))))....... (-27.94 = -28.82 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:14 2006