Locus 4342

Sequence ID 3R_DroMel_CAF1
Location 11,460,478 – 11,460,626
Length 148
Max. P 0.997401
window7099 window7100 window7101

overview

Window 9

Location 11,460,478 – 11,460,586
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.71
Mean single sequence MFE -33.68
Consensus MFE -29.10
Energy contribution -29.42
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -1.37
Structure conservation index 0.86
SVM decision value 0.49
SVM RNA-class probability 0.755123
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460478 108 + 27905053
UGGCCAGGGGAGAGCUCCUUUGGCCUGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAGCCACCUUCGUCCUUUCCCAACAG------------UUUCUGCUGAUGUCGCCCGCCA
.((((((((((....)))))))))).((((((...((((((.....((((.(((.....))))))).....(........))))))------------)...)))....)))........ ( -31.20)
>DroSec_CAF1 193005 108 + 1
UGGCCAGGGGAGAGCUCCUUUGGCCUGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAGCCGCCUUCGUCCUUUCCCAGCAG------------UUUCUGCUGAUGUCGCCUGCCA
.((((((((((....)))))))))).....................(((((.((..........((....))........((((((------------...)))))).....)).))))) ( -33.80)
>DroSim_CAF1 188122 108 + 1
UGGCCAGGGGAGAGCUCCUUUGGCCCGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAGCCGCCUUCGUCCUUUCCCAGCAG------------UUUCUGCUGAUGUCGCCUGCCA
.((((((((((....))))))))))((((..................(((.(((.....))))))...............((((((------------...))))))..))))....... ( -34.00)
>DroEre_CAF1 182133 110 + 1
UGGCCGGAGGAGGGCUCCUUUGGCCUGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAGCCGCCUUCGUCCUUUCCCAGCAGC----------AUUUCCGCCGAUGUCGCCUGCCA
.(((.(((.((((((......(((..((((((.....((((......)))))))))).....))))))))).))).......((.((----------(((......))))).))..))). ( -33.70)
>DroYak_CAF1 186224 120 + 1
UGGCCAGGGGAGAGCUCCUUUGGCCUGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAUCCGCCUUCGUCCUUUCCCAGCAGUUUCUGUUCCUGUUUCUGCUGAUGUCGCCUGCCA
.(((.(((((((((..(....(((..((((((.....((((......)))).......)))))).)))...)..))))))((((((...(.......)...))))))......)))))). ( -35.70)
>consensus
UGGCCAGGGGAGAGCUCCUUUGGCCUGAUGCAUUUACUGUUUAAUUUGGCAUGCAUUUUGUAGCCGCCUUCGUCCUUUCCCAGCAG____________UUUCUGCUGAUGUCGCCUGCCA
.((((((((((....)))))))))).....................(((((.((.....((....)).............((((((...............)))))).....)).))))) (-29.10 = -29.42 +   0.32)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,460,478 – 11,460,586
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.71
Mean single sequence MFE -33.51
Consensus MFE -31.68
Energy contribution -31.28
Covariance contribution -0.40
Combinations/Pair 1.19
Mean z-score -1.88
Structure conservation index 0.95
SVM decision value 2.85
SVM RNA-class probability 0.997401
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460478 108 - 27905053
UGGCGGGCGACAUCAGCAGAAA------------CUGUUGGGAAAGGACGAAGGUGGCUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCAGGCCAAAGGAGCUCUCCCCUGGCCA
(((((.(((...(((((((...------------)))))))......((....))..........))).))))).....................(((((..(((....)))..))))). ( -30.80)
>DroSec_CAF1 193005 108 - 1
UGGCAGGCGACAUCAGCAGAAA------------CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCAGGCCAAAGGAGCUCUCCCCUGGCCA
..(((.((....(((((((...------------)))))))...........((((((........)).))))..........))...)))....(((((..(((....)))..))))). ( -34.90)
>DroSim_CAF1 188122 108 - 1
UGGCAGGCGACAUCAGCAGAAA------------CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCGGGCCAAAGGAGCUCUCCCCUGGCCA
..(((.((....(((((((...------------)))))))...........((((((........)).))))..........))...)))....(((((..(((....)))..))))). ( -34.70)
>DroEre_CAF1 182133 110 - 1
UGGCAGGCGACAUCGGCGGAAAU----------GCUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCAGGCCAAAGGAGCCCUCCUCCGGCCA
..(((.((....(((((((....----------.)))))))...........((((((........)).))))..........))...)))....((((..((((....))))..)))). ( -34.80)
>DroYak_CAF1 186224 120 - 1
UGGCAGGCGACAUCAGCAGAAACAGGAACAGAAACUGCUGGGAAAGGACGAAGGCGGAUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCAGGCCAAAGGAGCUCUCCCCUGGCCA
(((((.(((...(((((((...............))))))).......((....)).........))).))))).....................(((((..(((....)))..))))). ( -32.36)
>consensus
UGGCAGGCGACAUCAGCAGAAA____________CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAAACAGUAAAUGCAUCAGGCCAAAGGAGCUCUCCCCUGGCCA
..(((.((....(((((((...............)))))))...........((((((........)).))))..........))...)))....(((((..(((....)))..))))). (-31.68 = -31.28 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,460,518 – 11,460,626
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.48
Mean single sequence MFE -35.04
Consensus MFE -30.22
Energy contribution -29.66
Covariance contribution -0.56
Combinations/Pair 1.21
Mean z-score -1.73
Structure conservation index 0.86
SVM decision value 1.37
SVM RNA-class probability 0.946762
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11460518 108 - 27905053
GGUUGGAUGACACUAUCGCCAUUUUGUUGUCAGCUGCUUCUGGCGGGCGACAUCAGCAGAAA------------CUGUUGGGAAAGGACGAAGGUGGCUACAAAAUGCAUGCCAAAUUAA
..((((....((((.(((((....(((((((.(((......))).)))))))(((((((...------------)))))))....)).))).))))((........))...))))..... ( -34.00)
>DroSec_CAF1 193045 108 - 1
GGCAGGAUGACACUAUCGCCAUUUUGUUGUCAUCUGCUUCUGGCAGGCGACAUCAGCAGAAA------------CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAA
((((............((((..(((((((((..((((.....))))..))).(((((((...------------))))))).....))))))))))((........)).))))....... ( -37.20)
>DroSim_CAF1 188162 108 - 1
GGCAGGAUGACACUAUCGCCAUUUUGUUGUCAGCUGCUUCUGGCAGGCGACAUCAGCAGAAA------------CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAA
((((.((((....))))((.(((((((....((((((((.((...(....).(((((((...------------))))))).......)).))))))))))))))))).))))....... ( -35.20)
>DroEre_CAF1 182173 109 - 1
GG-UGGACGACACUAUCGCCAUUUUGUUGUCAGCUGCUUUUGGCAGGCGACAUCGGCGGAAAU----------GCUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAA
((-((.....)))).(((((....(((((((.(((......))).)))))))(((((((....----------.)))))))....)).))).((((((........)).))))....... ( -36.30)
>DroYak_CAF1 186264 120 - 1
GGUUGGAUGACACUAUCGCCAUUUUGUUGUCAGCUGCUCCUGGCAGGCGACAUCAGCAGAAACAGGAACAGAAACUGCUGGGAAAGGACGAAGGCGGAUACAAAAUGCAUGCCAAAUUAA
(((((.((.......(((((..(((((((((..((((.....))))..))).(((((((...............))))))).....))))))))))).......)).)).)))....... ( -32.50)
>consensus
GGCUGGAUGACACUAUCGCCAUUUUGUUGUCAGCUGCUUCUGGCAGGCGACAUCAGCAGAAA____________CUGCUGGGAAAGGACGAAGGCGGCUACAAAAUGCAUGCCAAAUUAA
(((.............((((..(((((((((..((((.....))))..))).(((((((...............))))))).....))))))))))((........))..)))....... (-30.22 = -29.66 +  -0.56)

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 11:26:48 2006