Locus 2335

Sequence ID 2L_DroMel_CAF1
Location 6,332,926 – 6,333,067
Length 141
Max. P 0.997987
window3763 window3764 window3765

overview

Window 3

Location 6,332,926 – 6,333,041
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 96.61
Mean single sequence MFE -27.24
Consensus MFE -24.38
Energy contribution -25.14
Covariance contribution 0.76
Combinations/Pair 1.03
Mean z-score -2.31
Structure conservation index 0.90
SVM decision value 2.98
SVM RNA-class probability 0.997987
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6332926 115 + 22407834
UACACAUGUAUAAAUAGUUCGGCUUUAAACCUAAGCCCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAU
.......((((((((((((.(((((.......))))).)))))))(((((.((((.(((((...(((((............)))))....))))).))))..)))))...))))) ( -28.90)
>DroSec_CAF1 24047 115 + 1
UACACAUGUAUAAAUAGUUCGGCUUUAAACCUAAGCCCAAUUGUUGGGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAU
.......(((((((.(((.(((...........(((((........)))))((((((.(((...(((((............))))).)))))))))....)))..)))))))))) ( -27.70)
>DroSim_CAF1 25983 115 + 1
UACACAUGUAUAAAUAGUUCGGCUUUAAACCUAAGCCCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAU
.......((((((((((((.(((((.......))))).)))))))(((((.((((.(((((...(((((............)))))....))))).))))..)))))...))))) ( -28.90)
>DroEre_CAF1 24503 115 + 1
UACACAUGUAUAAAUACAUCGGCUUUAAACCUAAGCCCAAUUUUGGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUGCGCUAUUUUUAUAU
.......(((((((......(((((.......))))).......(((((((((((.(((((...(((((............)))))....))))).))))).))))))))))))) ( -25.30)
>DroYak_CAF1 24001 115 + 1
UACACAUGUAUAAAUAGUUCGGCUUUAUACCUAAGCCCAAUUUUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUUCGCUAUUUUUAUAU
.....(((((.(((((((..(((((.......)))))........((((..((((((.(((...(((((............))))).)))))))))))))..))))))).))))) ( -25.40)
>consensus
UACACAUGUAUAAAUAGUUCGGCUUUAAACCUAAGCCCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAU
.......((((((((((((.(((((.......))))).)))))).(((((.((((.(((((...(((((............)))))....))))).))))..)))))..)))))) (-24.38 = -25.14 +   0.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,332,926 – 6,333,041
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 96.61
Mean single sequence MFE -25.82
Consensus MFE -22.54
Energy contribution -22.70
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.45
Structure conservation index 0.87
SVM decision value 0.53
SVM RNA-class probability 0.770878
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6332926 115 - 22407834
AUAUAAAAGUAGCGGAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCACAACAAUUGGGCUUAGGUUUAAAGCCGAACUAUUUAUACAUGUGUA
.(((((((((..(((...((((((((..((((((............)))))).))))).)))..((((.((.....))))))...........))).))).))))))........ ( -25.70)
>DroSec_CAF1 24047 115 - 1
AUAUAAAAGUAGCGGAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCCCAACAAUUGGGCUUAGGUUUAAAGCCGAACUAUUUAUACAUGUGUA
.(((((((((..(((...((((((((..((((((............)))))).))))).)))..(((((........)))))...........))).))).))))))........ ( -27.90)
>DroSim_CAF1 25983 115 - 1
AUAUAAAAGUAGCGGAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCACAACAAUUGGGCUUAGGUUUAAAGCCGAACUAUUUAUACAUGUGUA
.(((((((((..(((...((((((((..((((((............)))))).))))).)))..((((.((.....))))))...........))).))).))))))........ ( -25.70)
>DroEre_CAF1 24503 115 - 1
AUAUAAAAAUAGCGCAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCACCAAAAUUGGGCUUAGGUUUAAAGCCGAUGUAUUUAUACAUGUGUA
...........((((((.((((((((..((((((............)))))).))))).)))((((((..........)))...(((.....)))..)))........)))))). ( -26.00)
>DroYak_CAF1 24001 115 - 1
AUAUAAAAAUAGCGAAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCACAAAAAUUGGGCUUAGGUAUAAAGCCGAACUAUUUAUACAUGUGUA
......((((((......((((((((..((((((............)))))).))))).)))..((((.((.....))))))..(((.....)))...))))))........... ( -23.80)
>consensus
AUAUAAAAGUAGCGGAUAGGUAGUUGUUUUGGCAAGCCAGUAAAAAUGCCAGUUAACUAACCACAGCCACAACAAUUGGGCUUAGGUUUAAAGCCGAACUAUUUAUACAUGUGUA
......((((((......((((((((..((((((............)))))).))))).)))..((((.((.....))))))..(((.....)))...))))))........... (-22.54 = -22.70 +   0.16)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,332,962 – 6,333,067
Length 105
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 90.76
Mean single sequence MFE -25.16
Consensus MFE -19.13
Energy contribution -19.69
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.08
Structure conservation index 0.76
SVM decision value 0.85
SVM RNA-class probability 0.865732
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6332962 105 + 22407834
CCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAUU------UAUGUAUGUAUCUAUAAAGUGGCCA
....(((((.((((...(((((((..............))))))).)))).)))))..........((((((((.(((..------(((....)))..))))))))))).. ( -25.84)
>DroSec_CAF1 24083 101 + 1
CCAAUUGUUGGGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAUU------UAUGU----AUUUAUAAAGUGGCCA
.........(((...((((((.(((...(((((............))))).)))))))))...)))((((((((.((((.------...))----))....)))))))).. ( -25.30)
>DroSim_CAF1 26019 101 + 1
CCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAUU------UAUGU----AUUUAUAAAGUGGCCA
....(((((.((((...(((((((..............))))))).)))).)))))..........((((((((.((((.------...))----))....)))))))).. ( -25.24)
>DroEre_CAF1 24539 107 + 1
CCAAUUUUGGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUGCGCUAUUUUUAUAUACGAGUAUAUGU----AUGUAUAAAGUGGCCA
........(((((.(((.(((((....)))))........(((....)))..))).)))))..((.((((((((((((((((......)))----))))).)))))))))) ( -28.50)
>DroYak_CAF1 24037 97 + 1
CCAAUUUUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUUCGCUAUUUUUAUAUA----------U----AUGUAUAAAGUGGCCA
..........(((((((((((.(((...(((((............))))).)))))))))...........((((((((.----------.----..)))))))).))))) ( -20.90)
>consensus
CCAAUUGUUGUGGCUGUGGUUAGUUAACUGGCAUUUUUACUGGCUUGCCAAAACAACUACCUAUCCGCUACUUUUAUAUU______UAUGU____AUGUAUAAAGUGGCCA
....(((((.((((...(((((((..............))))))).)))).)))))..........((((((((.(((....................))))))))))).. (-19.13 = -19.69 +   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 10:25:34 2006