Locus 4785

Sequence ID X_DroMel_CAF1
Location 12,432,504 – 12,432,637
Length 133
Max. P 0.912951
window7831 window7832 window7833

overview

Window 1

Location 12,432,504 – 12,432,610
Length 106
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 72.53
Mean single sequence MFE -35.85
Consensus MFE -15.88
Energy contribution -17.29
Covariance contribution 1.41
Combinations/Pair 1.17
Mean z-score -1.85
Structure conservation index 0.44
SVM decision value 0.56
SVM RNA-class probability 0.783556
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12432504 106 + 22224390
AUAAUGGCAGAUCCUGCAGCAGGAGCUCCAUCG---CCUCCAGCUCCUGCUGCUGCAAUUGCUCCUGUGGCACCAGUAGCACCAAUUCCGCCACCAGCAGAUCAGCUCU
.....(((.((((..((((((((((((......---.....))))))))))))......((((...(((((..................))))).)))))))).))).. ( -39.77)
>DroSec_CAF1 5889 106 + 1
AUAAUGACAGACCCUGCGGCAGGGGCUCCAUCG---CCUCCAGCUCCUGUUGCUGCAAUUGCUCCUGUGGCACCAGUCGCAGCAAUUCCGCCACCAGCAGAACAGCUCU
.............((((((((((((((......---.....))))))))))((.(.(((((((...(((((....))))))))))))).)).....))))......... ( -32.90)
>DroEre_CAF1 5939 103 + 1
AUAAUGGCUGAUCCUGCGGCAGGAGCUCCAUCG---CCUCCAGCAGC---UGCUGCAAUGGCUCCUGUGGCAGCAAUAGCAGCAAUUCCGCCACCAGCUGAGCAGCUCU
....((((.((..((((.((.(((((......)---.)))).)).((---(((..((........))..)))))....))))....)).))))..((((....)))).. ( -37.80)
>DroYak_CAF1 11639 103 + 1
AUUAUGGCCGAUCCUGCGGCAGGCGCUCCAUCG---CCCCAGGCACC---UGCUGCAAUGGCUCCAGUGGCACCAAUAGCAGCAAUUCCGCCACCAGCUGAGCAGCUCU
.....(((((....(((((((((.(((......---.....))).))---))))))).)))))...(((((..................))))).((((....)))).. ( -34.17)
>DroAna_CAF1 5677 86 + 1
AUUCUGGCCAGUCCGGCAGGAGGAGCACCAGGAGGAGCACCAGC------------AGUAGCACCAGUAGCUCCAGUAGCAUC------GCCCCUGGU-----GGCUCC
..(((.(((.....))).)))(((((((((((.(((((((..((------------....))....)).)))))....((...------)).))))))-----.))))) ( -34.60)
>consensus
AUAAUGGCAGAUCCUGCGGCAGGAGCUCCAUCG___CCUCCAGCACC___UGCUGCAAUGGCUCCUGUGGCACCAGUAGCAGCAAUUCCGCCACCAGCAGAGCAGCUCU
...((((....(((((...)))))...))))....................((((...(((((...(((((..................))))).)))))..))))... (-15.88 = -17.29 +   1.41)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,432,504 – 12,432,610
Length 106
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 72.53
Mean single sequence MFE -43.16
Consensus MFE -20.66
Energy contribution -22.60
Covariance contribution 1.94
Combinations/Pair 1.25
Mean z-score -1.98
Structure conservation index 0.48
SVM decision value 1.09
SVM RNA-class probability 0.912951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12432504 106 - 22224390
AGAGCUGAUCUGCUGGUGGCGGAAUUGGUGCUACUGGUGCCACAGGAGCAAUUGCAGCAGCAGGAGCUGGAGG---CGAUGGAGCUCCUGCUGCAGGAUCUGCCAUUAU
..(((......)))(((((((((.....((((.(((......))).))))......((((((((((((.....---......))))))))))))....))))))))).. ( -48.40)
>DroSec_CAF1 5889 106 - 1
AGAGCUGUUCUGCUGGUGGCGGAAUUGCUGCGACUGGUGCCACAGGAGCAAUUGCAGCAACAGGAGCUGGAGG---CGAUGGAGCCCCUGCCGCAGGGUCUGUCAUUAU
..(((......)))(((((((((....(((((.(((.(((..(((......)))..))).)))..((.((.((---(......))))).)))))))..))))))))).. ( -39.10)
>DroEre_CAF1 5939 103 - 1
AGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUAUUGCUGCCACAGGAGCCAUUGCAGCA---GCUGCUGGAGG---CGAUGGAGCUCCUGCCGCAGGAUCAGCCAUUAU
.(.((((.((....((((((((.....)))))))).((((..((((((((((((((((.---...)))....)---)))))..)))))))..)))))).)))))..... ( -42.70)
>DroYak_CAF1 11639 103 - 1
AGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUAUUGGUGCCACUGGAGCCAUUGCAGCA---GGUGCCUGGGG---CGAUGGAGCGCCUGCCGCAGGAUCGGCCAUAAU
..((((....)))).(((((.((.(((((((...((((.((...)).))))..))))))---)...((((.((---((..((....)))))).)))).)).)))))... ( -45.80)
>DroAna_CAF1 5677 86 - 1
GGAGCC-----ACCAGGGGC------GAUGCUACUGGAGCUACUGGUGCUACU------------GCUGGUGCUCCUCCUGGUGCUCCUCCUGCCGGACUGGCCAGAAU
(((((.-----(((((((((------...)))...(((((.((..((......------------))..))))))).)))))))))))..(((((.....)).)))... ( -39.80)
>consensus
AGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUACUGGUGCCACAGGAGCAAUUGCAGCA___GGAGCUGGAGG___CGAUGGAGCUCCUGCCGCAGGAUCGGCCAUUAU
...(((((...(((((((((((.....)))))))))))((.......))....)))))...................(((((...(((((...)))))....))))).. (-20.66 = -22.60 +   1.94)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,432,541 – 12,432,637
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 86.74
Mean single sequence MFE -36.98
Consensus MFE -25.19
Energy contribution -27.38
Covariance contribution 2.19
Combinations/Pair 1.07
Mean z-score -1.85
Structure conservation index 0.68
SVM decision value 0.31
SVM RNA-class probability 0.681968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12432541 96 - 22224390
CUCCAUGAGCUUCUGCUGGCAUACCAAAGAGCUGAUCUGCUGGUGGCGGAAUUGGUGCUACUGGUGCCACAGGAGCAAUUGCAGCAGCAGGAGCUG
((((....(((((((.((((..((((.((.((..((((((.....)))).))..)).))..)))))))))))))))...(((....)))))))... ( -39.40)
>DroSec_CAF1 5926 96 - 1
CUCCAUGAGCUUCUGGUGACACACCAAAGAGCUGUUCUGCUGGUGGCGGAAUUGCUGCGACUGGUGCCACAGGAGCAAUUGCAGCAACAGGAGCUG
((((.(((((((.(((((...)))))..)))))(((((((.....)))))))((((((((.((.(.(....).).)).)))))))).))))))... ( -36.60)
>DroEre_CAF1 5976 93 - 1
CUCCUUGAGGUUCUGCUGGCAAACCAAAGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUAUUGCUGCCACAGGAGCCAUUGCAGCA---GCUGCUG
........((((((..(((((........((((....))))((((((((.....))))))))..)))))..))))))....((((.---...)))) ( -32.90)
>DroYak_CAF1 11676 93 - 1
CUCCAUGAGCCUCUGCUGGCAGACCAAAGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUAUUGGUGCCACUGGAGCCAUUGCAGCA---GGUGCCU
........(((.((((((((((.(......))))).)))).)).)))((..(((((((...((((.((...)).))))..))))))---)...)). ( -39.00)
>consensus
CUCCAUGAGCUUCUGCUGGCAAACCAAAGAGCUGCUCAGCUGGUGGCGGAAUUGCUGCUACUGGUGCCACAGGAGCAAUUGCAGCA___GGAGCUG
........(((((((.((((((.......(((......)))((((((((.....)))))))).))))))))))))).....((((.......)))) (-25.19 = -27.38 +   2.19)

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 11:33:06 2006