Locus 1540

Sequence ID 2L_DroMel_CAF1
Location 4,159,508 – 4,159,603
Length 95
Max. P 0.940470
window2490 window2491

overview

Window 0

Location 4,159,508 – 4,159,603
Length 95
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 89.83
Mean single sequence MFE -17.34
Consensus MFE -14.32
Energy contribution -14.76
Covariance contribution 0.44
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.83
SVM decision value 0.87
SVM RNA-class probability 0.871077
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4159508 95 + 22407834
UUCCAUUUAAUCAAGUUCAACUUA-GGUAUUGAAAUAUUGCCUUCGACUUAACCCCCUUCAAUCAGCGACUAAAUCGGCGCUCCAUCCGAAAAUUU
..........(((((((......(-((((.........)))))..)))))..............((((.((.....))))))......))...... ( -10.20)
>DroSec_CAF1 289769 95 + 1
UUCUCUUUAAUCAAGUUCUACUUA-GGUGUCGAAGUAUUGCCUUCGACUUACGCCUCUUCAAUCAGCGCCUCAAUCGGCGCUCCAUCCGCAAAUUU
.......................(-((((((((((......)))))))....))))........((((((......)))))).............. ( -22.10)
>DroSim_CAF1 292346 95 + 1
UUCCAUUUAAUCAAGUUCUACUUA-GGUGUCGAAAUAUUGCCUUCGACUUACGCCUCUUCAAUCAGCGCCUCAAUCGGCGCUCCAUCCGCAAAUUU
.......................(-(((((((((........))))))....))))........((((((......)))))).............. ( -19.30)
>DroEre_CAF1 304243 96 + 1
UUCCAUUUUAUCUAGUUCUACUUAAGGAGUCGAAAUAUUUCCUUCGACUUACGCCUCCUCAAUCAGCGCCUCAACCGGCGCUUCAUCCGCAAAUUU
.........................(((((((((........))))))................((((((......))))))...)))........ ( -20.70)
>DroYak_CAF1 311231 95 + 1
UUCCAUUUAAUCAAGUUCUACUUA-GGGGUCGAAAUAUUUGCUUCGACUUACGCCUCCUCAAUCAGCACCUCAACCGGCGCUCCAUCCGCAAAUUU
........................-(((((((((........)))))))...............(((.((......)).)))))............ ( -14.40)
>consensus
UUCCAUUUAAUCAAGUUCUACUUA_GGUGUCGAAAUAUUGCCUUCGACUUACGCCUCUUCAAUCAGCGCCUCAAUCGGCGCUCCAUCCGCAAAUUU
.........................((.((((((........))))))................((((((......))))))....))........ (-14.32 = -14.76 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,159,508 – 4,159,603
Length 95
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -25.28
Consensus MFE -20.36
Energy contribution -20.48
Covariance contribution 0.12
Combinations/Pair 1.15
Mean z-score -2.00
Structure conservation index 0.81
SVM decision value 1.29
SVM RNA-class probability 0.940470
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4159508 95 - 22407834
AAAUUUUCGGAUGGAGCGCCGAUUUAGUCGCUGAUUGAAGGGGGUUAAGUCGAAGGCAAUAUUUCAAUACC-UAAGUUGAACUUGAUUAAAUGGAA
.........(((.(((.(((((((((..(.((.......)).)..))))))...))).....((((((...-...))))))))).)))........ ( -19.00)
>DroSec_CAF1 289769 95 - 1
AAAUUUGCGGAUGGAGCGCCGAUUGAGGCGCUGAUUGAAGAGGCGUAAGUCGAAGGCAAUACUUCGACACC-UAAGUAGAACUUGAUUAAAGAGAA
...(((((....((((((((......))))))................(((((((......))))))).))-...))))).(((.....))).... ( -29.10)
>DroSim_CAF1 292346 95 - 1
AAAUUUGCGGAUGGAGCGCCGAUUGAGGCGCUGAUUGAAGAGGCGUAAGUCGAAGGCAAUAUUUCGACACC-UAAGUAGAACUUGAUUAAAUGGAA
...(((((....((((((((......))))))................(((((((......))))))).))-...)))))................ ( -25.70)
>DroEre_CAF1 304243 96 - 1
AAAUUUGCGGAUGAAGCGCCGGUUGAGGCGCUGAUUGAGGAGGCGUAAGUCGAAGGAAAUAUUUCGACUCCUUAAGUAGAACUAGAUAAAAUGGAA
...(((((......((((((......))))))..((((((((((....))(((((......))))).)))))))))))))................ ( -30.20)
>DroYak_CAF1 311231 95 - 1
AAAUUUGCGGAUGGAGCGCCGGUUGAGGUGCUGAUUGAGGAGGCGUAAGUCGAAGCAAAUAUUUCGACCCC-UAAGUAGAACUUGAUUAAAUGGAA
..............((((((......))))))(((..((...((....(((((((......)))))))...-...))....))..)))........ ( -22.40)
>consensus
AAAUUUGCGGAUGGAGCGCCGAUUGAGGCGCUGAUUGAAGAGGCGUAAGUCGAAGGCAAUAUUUCGACACC_UAAGUAGAACUUGAUUAAAUGGAA
..(((((.((....((((((......))))))................(((((((......))))))).)).)))))................... (-20.36 = -20.48 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:04 2006