Locus 7558

Sequence ID X_DroMel_CAF1
Location 18,830,765 – 18,830,918
Length 153
Max. P 0.751670
window12402 window12403 window12404

overview

Window 2

Location 18,830,765 – 18,830,878
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.62
Mean single sequence MFE -32.75
Consensus MFE -24.20
Energy contribution -24.12
Covariance contribution -0.08
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.74
SVM decision value 0.09
SVM RNA-class probability 0.577594
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18830765 113 + 22224390
UAUGAGCUAUUUUCC-CGAACGCCCCGCUCUGCGCUUCUCAUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUC
.(..(((........-.....(((.......(((((......)))))......)))(((---((((((.((.(---((.....))).)).((((....)))))))))))))..)))..). ( -33.62)
>DroSec_CAF1 67615 113 + 1
UAUGAGCUAAUUUCC-CGAGCGCCCCGUUCUGCGCUUCUCAUGGCGUUUACAUCGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUC
...............-((((((....((...(((((......)))))..)).....(((---((((((.((.(---((.....))).)).((((....))))))))))))).)))))).. ( -33.30)
>DroSim_CAF1 47843 113 + 1
UAUGAGCUAUUUUCC-CGAGCGCCCCGCUCUGCGCUUCUCAUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUC
.(..(((.......(-((((((...))))).(((((......)))))......)).(((---((((((.((.(---((.....))).)).((((....)))))))))))))..)))..). ( -35.70)
>DroEre_CAF1 65402 112 + 1
UAUGAGCUAUUUUC--CGAGUGCCCCUCUCCGCGCUUCUCAUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAAUGCGGCUUAGUUGCCAUUGCAUAAUCGCUUGUC
.(..(((.......--.....(((.......(((((......)))))......)))(((---(((((..((.(---((.....))).)).(((......))).))))))))..)))..). ( -28.02)
>DroYak_CAF1 64432 120 + 1
UAUGAGCUAUUUUCCCCAAGCGCCCCUCUCUGCGCUUCUCAUGGCAUUUACCUCGCUUAUGAUGCAACACACUUUGCAUCGUUUGAAUGCGGCUUAGUCGCCGUUGCAUAAUCGCUUGUC
.(..(((..........((((((........))))))...(((((..(((..((((..(((((((((......)))))))))......))))..)))..))))).........)))..). ( -33.10)
>consensus
UAUGAGCUAUUUUCC_CGAGCGCCCCGCUCUGCGCUUCUCAUGGCGUUUACCUGGCUUA___UGCAACACACU___CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUC
.(..(((..........((((((........))))))...(((((.........((.......)).....(((....(((((......)))))..))).))))).........)))..). (-24.20 = -24.12 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 18,830,804 – 18,830,918
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.73
Mean single sequence MFE -29.20
Consensus MFE -22.70
Energy contribution -23.10
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.78
SVM decision value 0.48
SVM RNA-class probability 0.751670
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18830804 114 + 22224390
AUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUCGCUUAAUCUAUUUAUUGAUUGACAAUAUUGAGACCCUUUA
..((.((((....((((((---((((((.((.(---((.....))).)).((((....)))))))))))))..)))(((((.(((((......))))).)))))......)))))).... ( -29.90)
>DroSec_CAF1 67654 114 + 1
AUGGCGUUUACAUCGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUCGCUUAAUUUAUUUAUUGAUUGACAAUAUUGAGACCCUUUA
..((.((((.((.((.(((---((((((.((.(---((.....))).)).((((....))))))))))))).)).((((((.(((((......))))).))))))...)))))))).... ( -31.50)
>DroSim_CAF1 47882 114 + 1
AUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUCGCUUAAUCUAUUUAUUGAUUGACAAUAUUGAGACCCUUUA
..((.((((....((((((---((((((.((.(---((.....))).)).((((....)))))))))))))..)))(((((.(((((......))))).)))))......)))))).... ( -29.90)
>DroEre_CAF1 65440 114 + 1
AUGGCGUUUACCUGGCUUA---UGCAACACACU---CGUCGUUUGAAUGCGGCUUAGUUGCCAUUGCAUAAUCGCUUGUCGCUUAAUCUACUUAUUGAUUGACAAUAUUGAGACCCUUUU
..((.((((....((((((---(((((..((.(---((.....))).)).(((......))).))))))))..)))(((((.(((((......))))).)))))......)))))).... ( -25.30)
>DroYak_CAF1 64472 120 + 1
AUGGCAUUUACCUCGCUUAUGAUGCAACACACUUUGCAUCGUUUGAAUGCGGCUUAGUCGCCGUUGCAUAAUCGCUUGUCGCUUAAUCUACUUAUUGAUUGACAAUAUUGAGACCCUUUA
...........(((((..(((((((((......))))))))).((...(((((......)))))..)).....))((((((.(((((......))))).))))))....)))........ ( -29.40)
>consensus
AUGGCGUUUACCUGGCUUA___UGCAACACACU___CGUCGUUUGAUUGCGGCUUAGUAGCCGUUGCAUAAUCGCUUGUCGCUUAAUCUAUUUAUUGAUUGACAAUAUUGAGACCCUUUA
..((.((((.....((......((((((............((......))(((......))))))))).....))((((((.(((((......))))).)))))).....)))))).... (-22.70 = -23.10 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,830,804 – 18,830,918
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.73
Mean single sequence MFE -29.04
Consensus MFE -21.30
Energy contribution -21.02
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -2.13
Structure conservation index 0.73
SVM decision value 0.10
SVM RNA-class probability 0.582961
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18830804 114 - 22224390
UAAAGGGUCUCAAUAUUGUCAAUCAAUAAAUAGAUUAAGCGACAAGCGAUUAUGCAACGGCUACUAAGCCGCAAUCAAACGACG---AGUGUGUUGCA---UAAGCCAGGUAAACGCCAU
....((((((...(((((.....)))))...))))...((.....))..(((((((((((((....))))(((.((.......)---).)))))))))---))).)).(((....))).. ( -28.60)
>DroSec_CAF1 67654 114 - 1
UAAAGGGUCUCAAUAUUGUCAAUCAAUAAAUAAAUUAAGCGACAAGCGAUUAUGCAACGGCUACUAAGCCGCAAUCAAACGACG---AGUGUGUUGCA---UAAGCGAUGUAAACGCCAU
.....(((....(((((((...................((.....))..(((((((((((((....))))(((.((.......)---).)))))))))---))))))))))....))).. ( -28.50)
>DroSim_CAF1 47882 114 - 1
UAAAGGGUCUCAAUAUUGUCAAUCAAUAAAUAGAUUAAGCGACAAGCGAUUAUGCAACGGCUACUAAGCCGCAAUCAAACGACG---AGUGUGUUGCA---UAAGCCAGGUAAACGCCAU
....((((((...(((((.....)))))...))))...((.....))..(((((((((((((....))))(((.((.......)---).)))))))))---))).)).(((....))).. ( -28.60)
>DroEre_CAF1 65440 114 - 1
AAAAGGGUCUCAAUAUUGUCAAUCAAUAAGUAGAUUAAGCGACAAGCGAUUAUGCAAUGGCAACUAAGCCGCAUUCAAACGACG---AGUGUGUUGCA---UAAGCCAGGUAAACGCCAU
....((((((...(((((.....)))))...))))...((.....))..((((((((((((......)))((((((.......)---)))))))))))---))).)).(((....))).. ( -29.00)
>DroYak_CAF1 64472 120 - 1
UAAAGGGUCUCAAUAUUGUCAAUCAAUAAGUAGAUUAAGCGACAAGCGAUUAUGCAACGGCGACUAAGCCGCAUUCAAACGAUGCAAAGUGUGUUGCAUCAUAAGCGAGGUAAAUGCCAU
.....((((((....(((((((((........))))....)))))((....((((((((((......)))(((((.....))))).......))))))).....)))))......))).. ( -30.50)
>consensus
UAAAGGGUCUCAAUAUUGUCAAUCAAUAAAUAGAUUAAGCGACAAGCGAUUAUGCAACGGCUACUAAGCCGCAAUCAAACGACG___AGUGUGUUGCA___UAAGCCAGGUAAACGCCAU
.....(((((...(((((.....)))))...)))))..(((((..((.....(((((((((......)))........((.((.....))))))))))......))...))...)))... (-21.30 = -21.02 +  -0.28)

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 12:41:58 2006