Locus 7085

Sequence ID X_DroMel_CAF1
Location 17,767,873 – 17,768,004
Length 131
Max. P 0.988421
window11568 window11569 window11570

overview

Window 8

Location 17,767,873 – 17,767,977
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 90.54
Mean single sequence MFE -24.37
Consensus MFE -22.50
Energy contribution -22.38
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -1.36
Structure conservation index 0.92
SVM decision value 0.19
SVM RNA-class probability 0.627878
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17767873 104 - 22224390
AGAUCUAAGUCCAGAUCCUUCCCUACGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCAGACAGACAACCCUACACACACACACCCGAGUCAU
.(((((......))))).........(((((((((((........))))))))))).((((.........))))(((......................))).. ( -24.85)
>DroSec_CAF1 26794 102 - 1
AGAUCUAAGUCCAGACCCUUCCCUCCGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUUUCGGACACACAGACAGACCACCCCAC--ACACACACUCGAGUCAU
........((((.((....)).....(((((((((((........))))))))))).....)))).....(((.((.........--........))..))).. ( -23.53)
>DroEre_CAF1 25193 101 - 1
AGAUCUAAGUCCAGACCCUUCGCUCUGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCAGACAGACAACCC---ACACACAUACCCGAGUCAU
.....................((((.(((((((((((........)))))))))))(((((.........))))).......---............))))... ( -24.30)
>DroYak_CAF1 25532 104 - 1
AGAUCUAAGUCCAGACCCUUCGUUUCGAAGAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCAGACAGACAACCCCAUACACACAUACCCGAGUCAU
.............(((...(((....(((((((((((........)))))))))))(((((.........))))).....................)))))).. ( -24.80)
>consensus
AGAUCUAAGUCCAGACCCUUCCCUCCGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCAGACAGACAACCCCACACACACACACCCGAGUCAU
.............(((.(........(((((((((((........)))))))))))(((((.........)))))......................).))).. (-22.50 = -22.38 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 17,767,907 – 17,768,004
Length 97
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 87.16
Mean single sequence MFE -32.85
Consensus MFE -28.84
Energy contribution -29.40
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.22
Structure conservation index 0.88
SVM decision value 1.63
SVM RNA-class probability 0.968773
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17767907 97 + 22224390
UGCGUGUUCGACAAGAAAAGGGGAGGUGCCAAGCCCCCCUUUUCGUAGGGAAGGAUCUGGACUUAGAUCUAGGUAACUAGAGCCAAGGCUUAUAAUU-----------
.((.(((((.....(((((((((.(((.....)))))))))))).(((..(.(((((((....)))))))...)..)))))))..).))........----------- ( -31.90)
>DroSec_CAF1 26826 97 + 1
UGUGUGUCCGAAAAGAAAAGGGGAGGUGCCAAGCCCCCCUUUUCGGAGGGAAGGGUCUGGACUUAGAUCUAGGUUACUAGAGACAAGGCUUAUAAUU-----------
..(((((((.....(((((((((.(((.....))))))))))))....(((....))))))).....(((((....))))).)))............----------- ( -31.60)
>DroEre_CAF1 25224 108 + 1
UGCGUGUUCGACAAGAAAAGGGGAGGUGCCAAGCCCCCCUUUUCAGAGCGAAGGGUCUGGACUUAGAUCUAGGUAACUAGAGCCAAGGCUUAUAAUUAUAAUAUAAGA
......((((....(((((((((.(((.....))))))))))))....))))((.((((((((((....)))))..))))).))....((((((.......)))))). ( -37.30)
>DroYak_CAF1 25566 101 + 1
UGCGUGUUCGACAAGAAAAGGGGAGGUGCCAAGCCCCCCUCUUCGAAACGAAGGGUCUGGACUUAGAUCUAGGUAACUAGCGCCAAGGCUUAUGAUUA-------CGA
..((((((((....(((.(((((.(((.....)))))))).)))....)))).((((((((((((....)))))..)))).)))............))-------)). ( -30.60)
>consensus
UGCGUGUUCGACAAGAAAAGGGGAGGUGCCAAGCCCCCCUUUUCGGAGCGAAGGGUCUGGACUUAGAUCUAGGUAACUAGAGCCAAGGCUUAUAAUU___________
.((...........(((((((((.(((.....))))))))))))........((.((((((((((....)))))..))))).))...))................... (-28.84 = -29.40 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,767,907 – 17,768,004
Length 97
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 87.16
Mean single sequence MFE -28.77
Consensus MFE -25.50
Energy contribution -26.38
Covariance contribution 0.88
Combinations/Pair 1.07
Mean z-score -2.51
Structure conservation index 0.89
SVM decision value 2.12
SVM RNA-class probability 0.988421
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17767907 97 - 22224390
-----------AAUUAUAAGCCUUGGCUCUAGUUACCUAGAUCUAAGUCCAGAUCCUUCCCUACGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCA
-----------........(((((((.(((((....))))).))))).................(((((((((((........)))))))))))...........)). ( -28.30)
>DroSec_CAF1 26826 97 - 1
-----------AAUUAUAAGCCUUGUCUCUAGUAACCUAGAUCUAAGUCCAGACCCUUCCCUCCGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUUUCGGACACACA
-----------................(((((....))))).....((((.((....)).....(((((((((((........))))))))))).....))))..... ( -26.00)
>DroEre_CAF1 25224 108 - 1
UCUUAUAUUAUAAUUAUAAGCCUUGGCUCUAGUUACCUAGAUCUAAGUCCAGACCCUUCGCUCUGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCA
.((((((.......)))))).(((((.(((((....))))).))))).........(((((...(((((((((((........)))))))))))..).))))...... ( -31.90)
>DroYak_CAF1 25566 101 - 1
UCG-------UAAUCAUAAGCCUUGGCGCUAGUUACCUAGAUCUAAGUCCAGACCCUUCGUUUCGAAGAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCA
...-------.........(((((((..((((....))))..))))).........((((....(((((((((((........)))))))))))....))))...)). ( -28.90)
>consensus
___________AAUUAUAAGCCUUGGCUCUAGUUACCUAGAUCUAAGUCCAGACCCUUCCCUCCGAAAAGGGGGGCUUGGCACCUCCCCUUUUCUUGUCGAACACGCA
...................(((((((.(((((....))))).))))).........((((....(((((((((((........)))))))))))....))))...)). (-25.50 = -26.38 +   0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:46 2006