Locus 6076

Sequence ID 3L_DroMel_CAF1
Location 16,156,422 – 16,156,580
Length 158
Max. P 0.975752
window9753 window9754 window9755 window9756

overview

Window 3

Location 16,156,422 – 16,156,540
Length 118
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 98.06
Mean single sequence MFE -33.94
Consensus MFE -34.05
Energy contribution -33.86
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.02
Structure conservation index 1.00
SVM decision value 0.91
SVM RNA-class probability 0.880586
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156422 118 + 23771897
--UAUUUGCCCUGGUCCGUUGUCUCGCUUAACUUUUUUAUUGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAU
--........((((.(.((.((((.((..............)).))))(((((((((((.((.(((((..((....))..).)))).)).)))))))))))......)).).)))).... ( -33.54)
>DroSec_CAF1 13808 120 + 1
UCUAUUUGCCCUGGUCCGUUGUCUCGCUUAACUUUUUUAUUGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAU
..........((((.(.((.((((.((..............)).))))(((((((((((.((.(((((..((....))..).)))).)).)))))))))))......)).).)))).... ( -33.54)
>DroSim_CAF1 15130 120 + 1
UCUAUUUGCCCUGGUCCGUUGUCUCGCUUAACUUUUUUAUUGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAU
..........((((.(.((.((((.((..............)).))))(((((((((((.((.(((((..((....))..).)))).)).)))))))))))......)).).)))).... ( -33.54)
>DroEre_CAF1 13384 120 + 1
UGUAUUUGCUCCGGUCCGUUGUCUCGCUUAACUUUUUUAUUGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAU
....((((...((((.((((((((.((..............)).))))(((((((((((.((.(((((..((....))..).)))).)).)))))))))))))))..))))..))))... ( -35.14)
>consensus
UCUAUUUGCCCUGGUCCGUUGUCUCGCUUAACUUUUUUAUUGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAU
....((((...((((.((((((((.((..............)).))))(((((((((((.((.(((((..((....))..).)))).)).)))))))))))))))..))))..))))... (-34.05 = -33.86 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,156,422 – 16,156,540
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.06
Mean single sequence MFE -35.63
Consensus MFE -36.01
Energy contribution -35.63
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -2.74
Structure conservation index 1.01
SVM decision value 1.76
SVM RNA-class probability 0.975752
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156422 118 - 23771897
AUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCAAUAAAAAAGUUAAGCGAGACAACGGACCAGGGCAAAUA--
.(((((((.((........(((((((((((.........(((............)))....)))))))))))((((.((..............)).))))..))..))).))))....-- ( -35.66)
>DroSec_CAF1 13808 120 - 1
AUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCAAUAAAAAAGUUAAGCGAGACAACGGACCAGGGCAAAUAGA
.(((((((.((........(((((((((((.........(((............)))....)))))))))))((((.((..............)).))))..))..))).))))...... ( -35.66)
>DroSim_CAF1 15130 120 - 1
AUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCAAUAAAAAAGUUAAGCGAGACAACGGACCAGGGCAAAUAGA
.(((((((.((........(((((((((((.........(((............)))....)))))))))))((((.((..............)).))))..))..))).))))...... ( -35.66)
>DroEre_CAF1 13384 120 - 1
AUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCAAUAAAAAAGUUAAGCGAGACAACGGACCGGAGCAAAUACA
.(((((((.((........(((((((((((.........(((............)))....)))))))))))((((.((..............)).))))..))..))))).))...... ( -35.56)
>consensus
AUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCAAUAAAAAAGUUAAGCGAGACAACGGACCAGGGCAAAUAGA
.(((((((.((........(((((((((((.........(((............)))....)))))))))))((((.((..............)).))))..))..))))).))...... (-36.01 = -35.63 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 16,156,460 – 16,156,580
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.58
Mean single sequence MFE -38.33
Consensus MFE -38.17
Energy contribution -38.42
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 1.00
SVM decision value 0.62
SVM RNA-class probability 0.800941
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156460 120 + 23771897
UGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAUCGAUGUAGACCUAGACGUUUGACGUAGACUUUGUCAAAUG
........(((((((((((.((.(((((..((....))..).)))).)).)))))))))))((((((........))))))..............(((((((((.......))))))))) ( -39.00)
>DroSec_CAF1 13848 120 + 1
UGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAUCGAUGUAGACCUAGACGUUUGACGUAGACUUUGUCAAAUG
........(((((((((((.((.(((((..((....))..).)))).)).)))))))))))((((((........))))))..............(((((((((.......))))))))) ( -39.00)
>DroSim_CAF1 15170 120 + 1
UGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAUCGAUGUAGACCUAGACGUUUGACGUAGACUUUGUCAAAUG
........(((((((((((.((.(((((..((....))..).)))).)).)))))))))))((((((........))))))..............(((((((((.......))))))))) ( -39.00)
>DroEre_CAF1 13424 120 + 1
UGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAUCGAUGUAGACCUAGACGCUUGACGUAGACUUUGUCAAAUG
.((.....(((((((((((.((.(((((..((....))..).)))).)).)))))))))))((((((........))))))...............))((((((.......))))))... ( -36.30)
>consensus
UGCCAGACGAAGCGCAAACAUUUGCGAGUAUUAAUUAACGCUUUGUUGAAGUUUGCGCUUCGAUGUCGCCGCCCAGACAUCGAUGUAGACCUAGACGUUUGACGUAGACUUUGUCAAAUG
........(((((((((((.((.(((((..((....))..).)))).)).)))))))))))((((((........))))))..............(((((((((.......))))))))) (-38.17 = -38.42 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 16,156,460 – 16,156,580
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 99.58
Mean single sequence MFE -36.57
Consensus MFE -36.76
Energy contribution -36.57
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -2.33
Structure conservation index 1.01
SVM decision value 0.84
SVM RNA-class probability 0.863696
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16156460 120 - 23771897
CAUUUGACAAAGUCUACGUCAAACGUCUAGGUCUACAUCGAUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCA
..((((((.........))))))((((((((((......)))..)))))))((.(...((((((((((((.........(((............)))....))))))))))))..).)). ( -36.72)
>DroSec_CAF1 13848 120 - 1
CAUUUGACAAAGUCUACGUCAAACGUCUAGGUCUACAUCGAUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCA
..((((((.........))))))((((((((((......)))..)))))))((.(...((((((((((((.........(((............)))....))))))))))))..).)). ( -36.72)
>DroSim_CAF1 15170 120 - 1
CAUUUGACAAAGUCUACGUCAAACGUCUAGGUCUACAUCGAUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCA
..((((((.........))))))((((((((((......)))..)))))))((.(...((((((((((((.........(((............)))....))))))))))))..).)). ( -36.72)
>DroEre_CAF1 13424 120 - 1
CAUUUGACAAAGUCUACGUCAAGCGUCUAGGUCUACAUCGAUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCA
..((((((.........))))))((((((((((......)))..)))))))((.(...((((((((((((.........(((............)))....))))))))))))..).)). ( -36.12)
>consensus
CAUUUGACAAAGUCUACGUCAAACGUCUAGGUCUACAUCGAUGUCUGGGCGGCGACAUCGAAGCGCAAACUUCAACAAAGCGUUAAUUAAUACUCGCAAAUGUUUGCGCUUCGUCUGGCA
..((((((.........))))))((((((((((......)))..)))))))((.(...((((((((((((.........(((............)))....))))))))))))..).)). (-36.76 = -36.57 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:20 2006