Locus 6904

Sequence ID 3R_DroMel_CAF1
Location 18,236,626 – 18,236,787
Length 161
Max. P 0.993739
window11207 window11208 window11209

overview

Window 7

Location 18,236,626 – 18,236,725
Length 99
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 87.75
Mean single sequence MFE -29.24
Consensus MFE -22.62
Energy contribution -22.58
Covariance contribution -0.04
Combinations/Pair 1.13
Mean z-score -2.02
Structure conservation index 0.77
SVM decision value 0.94
SVM RNA-class probability 0.885442
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18236626 99 - 27905053
UAAAAAACGCCAGAUCUAGCUAGAAAAUGCUGAGUUGGCAGCACAGCUCGC-----AGUGUUACAAAAGCUUUGCAUGGAGCCGACGGGUCUUACCCUACACUA
........(((((.((.(((........))))).)))))....(.((((((-----((.(((.....))).))))...)))).)..(((.....)))....... ( -25.60)
>DroSec_CAF1 4858 103 - 1
UAAAAAACGCCAAGUCUAGCUACAAAAGGCUGAGUUGGCAGCACAGUUCGCG-GCCAGUGUUACAAAAGCUUUGCAUGCAGCCGACGGGCUUUACCCUACACUA
........(((((.((.((((......)))))).))))).....((((((((-((..((((............))))...)))).))))))............. ( -31.30)
>DroSim_CAF1 4862 103 - 1
UAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCAGCACAGUUCGCG-ACCAGUGUUACAAAAGCUUUGCAUGCAGCCGACGGGCUUUACCCUACACUA
........(((((.((.(((........))))).))))).((.......)).-...(((((....(((((((.((.....))....))))))).....))))). ( -26.30)
>DroEre_CAF1 4869 104 - 1
AGAAAAACGCCAACUCUAGCUACAAAAUGCUGAGCUGGCAACACUGUUCGCGUACCAGUGUUAGAAAAGCUUUGCAUGUAGCAGACGGGCUUUAACCUACACUA
........(((...(((.((((((...(((.(((((..((((((((.........))))))).)...))))).))))))))))))..))).............. ( -33.00)
>DroYak_CAF1 4841 100 - 1
A-AUAAACGCCAGGUCUAGCUACAAAAUGCUGAGCUGGCAACACUGUUCGCGUACCAGUGUUACAAAAGCUUUGCAUGUA---GACGGGCUUUAGCCUACACUA
.-......((.((((((..(((((...(((.(((((.(.(((((((.........))))))).)...))))).)))))))---)..))))))..))........ ( -30.00)
>consensus
UAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCAGCACAGUUCGCG_ACCAGUGUUACAAAAGCUUUGCAUGCAGCCGACGGGCUUUACCCUACACUA
........(((((.((.(((........))))).))))).................(((((....(((((((..(........)..))))))).....))))). (-22.62 = -22.58 +  -0.04)

alignment

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secondary structure

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Window 8

Location 18,236,661 – 18,236,751
Length 90
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 75.56
Mean single sequence MFE -25.50
Consensus MFE -16.96
Energy contribution -16.64
Covariance contribution -0.32
Combinations/Pair 1.20
Mean z-score -2.21
Structure conservation index 0.67
SVM decision value 2.09
SVM RNA-class probability 0.987634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18236661 90 - 27905053
-------------CAUGC-AAUGACACCUAAGUUCCGGAAUAAAAAACGCCAGAUCUAGCUAGAAAAUGCUGAGUUGGCAGCACAGCUCGC-----AGUGUUACAAAAG
-------------.....-..((((((.....................(((((.((.(((........))))).))))).((.......))-----.))))))...... ( -18.70)
>DroSec_CAF1 4893 94 - 1
-------------CAUGC-AAUGAUCCGUAAAUAGCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAGGCUGAGUUGGCAGCACAGUUCGCG-GCCAGUGUUACAAAAG
-------------..(((-..((((((((.....))))))))......(((((.((.((((......)))))).))))).)))..((.(((.-....)))..))..... ( -30.70)
>DroSim_CAF1 4897 95 - 1
-------------CAUGAAAAUGAUCUCUAAGUUGCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCAGCACAGUUCGCG-ACCAGUGUUACAAAAG
-------------(((....)))........((((((((((.......(((((.((.(((........))))).))))).....))))))))-)).............. ( -26.40)
>DroEre_CAF1 4904 98 - 1
AAAU-----AGUAA------GUAAUCCCUAAUUUCCUGCUAGAAAAACGCCAACUCUAGCUACAAAAUGCUGAGCUGGCAACACUGUUCGCGUACCAGUGUUAGAAAAG
...(-----((((.------(.(((.....))).).))))).......((((.(((.(((........)))))).))))(((((((.........)))))))....... ( -23.00)
>DroYak_CAF1 4873 107 - 1
GAUGACGAAAGUACAUGC-UAUAAUCCCUAAGUUCCGGCUA-AUAAACGCCAGGUCUAGCUACAAAAUGCUGAGCUGGCAACACUGUUCGCGUACCAGUGUUACAAAAG
.(((((....)).)))((-(..(((......)))..)))..-......(((((.((.(((........))))).)))))(((((((.........)))))))....... ( -28.70)
>consensus
_____________CAUGC_AAUGAUCCCUAAGUUCCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCAGCACAGUUCGCG_ACCAGUGUUACAAAAG
................................................(((((.((.(((........))))).)))))(((((.............)))))....... (-16.96 = -16.64 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,236,685 – 18,236,787
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.67
Mean single sequence MFE -23.38
Consensus MFE -14.02
Energy contribution -13.94
Covariance contribution -0.08
Combinations/Pair 1.20
Mean z-score -2.33
Structure conservation index 0.60
SVM decision value 2.42
SVM RNA-class probability 0.993739
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18236685 102 - 27905053
AUAAAAUUGGAAGCAUUUACCAAAUAACCGAAAGCA-----------------CAUGC-AAUGACACCUAAGUUCCGGAAUAAAAAACGCCAGAUCUAGCUAGAAAAUGCUGAGUUGGCA
......((((.........))))....(((...((.-----------------...))-...(((......))).)))..........(((((.((.(((........))))).))))). ( -18.90)
>DroSec_CAF1 4921 102 - 1
AUAAAAUUGGAAGCAUUUACCAAAUAACCGAAAGCC-----------------CAUGC-AAUGAUCCGUAAAUAGCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAGGCUGAGUUGGCA
......((((.........))))..........((.-----------------...))-..((((((((.....))))))))......(((((.((.((((......)))))).))))). ( -27.10)
>DroSim_CAF1 4925 103 - 1
AUAAAAUUGGAAUCAUUUACCAAAUAUUCGAAAGCC-----------------CAUGAAAAUGAUCUCUAAGUUGCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCA
......((((((((((((..((......(....)..-----------------..)).))))))).))))).................(((((.((.(((........))))).))))). ( -21.80)
>DroEre_CAF1 4933 109 - 1
AUGAAAUUGUAAGCAUUUCAUAAAUAACUGAAAGUAAUUUAAAU-----AGUAA------GUAAUCCCUAAUUUCCUGCUAGAAAAACGCCAACUCUAGCUACAAAAUGCUGAGCUGGCA
.((((((.(....)))))))(((((.((.....)).)))))..(-----((((.------(.(((.....))).).))))).......((((.(((.(((........)))))).)))). ( -20.40)
>DroYak_CAF1 4902 118 - 1
UUGAAAUUUAAAGCAUUUUCCAAAUAACUGAAAGGAAUUUGAUGACGAAAGUACAUGC-UAUAAUCCCUAAGUUCCGGCUA-AUAAACGCCAGGUCUAGCUACAAAAUGCUGAGCUGGCA
...........(((..((((.........))))(((((((((((((....)).)))..-.........)))))))).))).-......(((((.((.(((........))))).))))). ( -28.70)
>consensus
AUAAAAUUGGAAGCAUUUACCAAAUAACCGAAAGCA_________________CAUGC_AAUGAUCCCUAAGUUCCGGAUUAAAAAACGCCAAGUCUAGCUACAAAAUGCUGAGUUGGCA
........................................................................................(((((.((.(((........))))).))))). (-14.02 = -13.94 +  -0.08)

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 12:32:58 2006