Locus 7345

Sequence ID X_DroMel_CAF1
Location 18,334,497 – 18,334,697
Length 200
Max. P 0.959729
window12032 window12033 window12034 window12035

overview

Window 2

Location 18,334,497 – 18,334,617
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.75
Mean single sequence MFE -33.80
Consensus MFE -29.42
Energy contribution -29.82
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.69
Structure conservation index 0.87
SVM decision value 1.51
SVM RNA-class probability 0.959729
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18334497 120 + 22224390
GCUACGCGAUCAUCAAUGAUCCUGGCAUACAAUUGGUUGCCAUGGACACACUCAGCGAAUUCUACUGGCUAGAUGAGCCUAAGAUUGCCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAU
((((.(.(((((....)))))))))).......((((...((((((((..(((.((((..(((...((((.....))))..)))))))...)))..))))))))....))))........ ( -36.90)
>DroSec_CAF1 12496 120 + 1
GCUACGCGAUCAUCAAUGAUCCUGGCAUACAACUGGUUGCCAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGAUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAU
((((.(.(((((....)))))))))).......((((...((((((((..(((.......(((...((((.....))))..))).......)))..))))))))....))))........ ( -34.34)
>DroSim_CAF1 12331 120 + 1
GCUACGCGAUCAUCAAUGAUCCUGGCAUACAACUGGUUGCCAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGCUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAU
((((.(.(((((....)))))))))).......((((...((((((((..((((((.(.......).)))....((((....)))).....)))..))))))))....))))........ ( -32.80)
>DroEre_CAF1 12178 120 + 1
GCUAUGCGAUCAUCAAUGAUCCUGCCAUACAACUGGUUGCCAUGGACACACUCAGCGAAUUCUACUGGCUGGACGAGCUUAAGAUAACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAC
((...(((((((....)))))..((((......)))).))((((((((..(((.......(((...((((.....))))..))).......)))..))))))))....)).......... ( -28.94)
>DroYak_CAF1 12455 120 + 1
GCUAUGCGAUUAUCAAUGAUCCUGGCAUACAACUGGUGGCCAUGGACACACUCAGCGAAUUCUACUGGCUGGACGACCUAAAGUUAAGCAAGAGAAUGUCCAUGUACCGCCACUAUCGAU
((((.(.(((((....)))))))))).......(((((((((((((((..(((...(....).....(((.(((........))).)))..)))..))))))))....)))))))..... ( -36.00)
>consensus
GCUACGCGAUCAUCAAUGAUCCUGGCAUACAACUGGUUGCCAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGAUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAU
((((.(.(((((....)))))))))).......((((...((((((((..(((.......(((...((((.....))))..))).......)))..))))))))....))))........ (-29.42 = -29.82 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 18,334,537 – 18,334,657
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.25
Mean single sequence MFE -37.00
Consensus MFE -33.00
Energy contribution -33.24
Covariance contribution 0.24
Combinations/Pair 1.10
Mean z-score -1.21
Structure conservation index 0.89
SVM decision value 0.22
SVM RNA-class probability 0.640895
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18334537 120 + 22224390
CAUGGACACACUCAGCGAAUUCUACUGGCUAGAUGAGCCUAAGAUUGCCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAUUGCUCCAGGCGCGCCUGGAGAAGCUCUGCAAGGAUGCCAU
((((((((..(((.((((..(((...((((.....))))..)))))))...)))..)))))))).((((.......))))..(((((((....)))))))..(((((....))).))... ( -40.20)
>DroSec_CAF1 12536 120 + 1
CAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGAUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAUUGCUCCAGGCGCGCCUGGAGAAGUUCUGCAAGGACGCCAU
((((((((..(((.......(((...((((.....))))..))).......)))..))))))))....((............(((((((....)))))))..((((.....))))))... ( -39.04)
>DroSim_CAF1 12371 120 + 1
CAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGCUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAUUGCUCCAGGCGCGCCUGGAGAAGCUCUGCAAGGACGCCAU
((((((((..((((((.(.......).)))....((((....)))).....)))..))))))))...((((...........(((((((....)))))))..((...))..)).)).... ( -36.20)
>DroEre_CAF1 12218 120 + 1
CAUGGACACACUCAGCGAAUUCUACUGGCUGGACGAGCUUAAGAUAACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGACUGCUCCAGGCGCGCCUGGAGAAGCUCUGCAAAGACGCCAU
((((((((..(((.......(((...((((.....))))..))).......)))..))))))))..................(((((((....)))))))..(((((....))).))... ( -36.24)
>DroYak_CAF1 12495 120 + 1
CAUGGACACACUCAGCGAAUUCUACUGGCUGGACGACCUAAAGUUAAGCAAGAGAAUGUCCAUGUACCGCCACUAUCGAUUGCUCCUGGCGCGCCUGGAGAAGCUCUGCAAGGACGCCAU
((((((((..(((...(....).....(((.(((........))).)))..)))..))))))))....((((..............))))(((((((.((.....)).).))).)))... ( -33.34)
>consensus
CAUGGACACACUCAGCGAAUUCUACUGGCUAGACGAGCCUAAGAUUACCAAGAGAAUGUCCAUGUAUCGCCACUAUCGAUUGCUCCAGGCGCGCCUGGAGAAGCUCUGCAAGGACGCCAU
((((((((..(((.......(((...((((.....))))..))).......)))..))))))))..................(((((((....)))))))..(((((....))).))... (-33.00 = -33.24 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 18,334,537 – 18,334,657
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -41.84
Consensus MFE -35.68
Energy contribution -37.12
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -1.31
Structure conservation index 0.85
SVM decision value 0.19
SVM RNA-class probability 0.628111
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18334537 120 - 22224390
AUGGCAUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGCAAUCUUAGGCUCAUCUAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
((.((...((....((....(((((((....)))))))...))...))..)).)).(((((((((...((..(((((((..((((.....))))...)).))).))..)).))))))))) ( -43.30)
>DroSec_CAF1 12536 120 - 1
AUGGCGUCCUUGCAGAACUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAUCUUAGGCUCGUCUAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
....((((((....((....(((((((....)))))))...))...)).))))...(((((((((...((..((..(((..((((.....))))...)))....))..)).))))))))) ( -43.10)
>DroSim_CAF1 12371 120 - 1
AUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAGCUUAGGCUCGUCUAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
....((((((....((....(((((((....)))))))...))...)).))))...(((((((((...((..((...((..((((.....))))...)).....))..)).))))))))) ( -43.30)
>DroEre_CAF1 12218 120 - 1
AUGGCGUCUUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAGUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUUAUCUUAAGCUCGUCCAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
....((((.(((..((.((.(((((((....))))))).))))..))).))))...(((((((((...((..((..(((...(((.....)))....)))....))..)).))))))))) ( -42.00)
>DroYak_CAF1 12495 120 - 1
AUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCAGGAGCAAUCGAUAGUGGCGGUACAUGGACAUUCUCUUGCUUAACUUUAGGUCGUCCAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
.((((((.((((.((.....)).)))).))))))...((...(....)..))....(((((((((.(((..((....((...(((......)))...)).....)).))).))))))))) ( -37.50)
>consensus
AUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAUCUUAGGCUCGUCUAGCCAGUAGAAUUCGCUGAGUGUGUCCAUG
....((((.(((..((....(((((((....)))))))...))..))).))))...(((((((((...((((((..(((..((((.....))))...)))....)))))).))))))))) (-35.68 = -37.12 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 18,334,577 – 18,334,697
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.25
Mean single sequence MFE -42.00
Consensus MFE -36.96
Energy contribution -38.04
Covariance contribution 1.08
Combinations/Pair 1.06
Mean z-score -1.30
Structure conservation index 0.88
SVM decision value 0.45
SVM RNA-class probability 0.740052
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18334577 120 - 22224390
CUCCAGAAAGGCAGACUCCACCGUGUACAUGCCGCAGACGAUGGCAUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGCAAUCUU
.....(..(((.(((.....(((((((..((((((...((((.(((....))).......(((((((....)))))))..))))...)))))).)))))))....))))))..)...... ( -39.60)
>DroSec_CAF1 12576 120 - 1
CUCCAGGAAGGCAGACUCCACCGUGUAGAUGCCGCACACGAUGGCGUCCUUGCAGAACUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAUCUU
..((((((.((......)).(((((((..((((((...((((.(((....))).......(((((((....)))))))..))))...)))))).)))))))......))))))....... ( -44.50)
>DroSim_CAF1 12411 120 - 1
CUCCAGGAAGGCAGACUCCACCGUGUAGAUGCCGCACACGAUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAGCUU
..((((((.((......)).(((((((..((((((...((((.(((....))).......(((((((....)))))))..))))...)))))).)))))))......))))))....... ( -44.50)
>DroEre_CAF1 12258 120 - 1
CUCCAGGAAGGCGGACUCCACCGUGUAGAUUCCGCAGACGAUGGCGUCUUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAGUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUUAUCUU
..((((((.((......)).(((((((....(((((((((....))))).....((.((.(((((((....))))))).))))....))))...)))))))......))))))....... ( -43.30)
>DroYak_CAF1 12535 120 - 1
CUCCAGGAACACAGACUCCACCGUGUACAUUCCGCAAACGAUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCAGGAGCAAUCGAUAGUGGCGGUACAUGGACAUUCUCUUGCUUAACUU
.....(((........))).((((((((...((((...((((.((.((((.((...(((......)))..)).)))))).))))...))))..))))))))................... ( -38.10)
>consensus
CUCCAGGAAGGCAGACUCCACCGUGUAGAUGCCGCACACGAUGGCGUCCUUGCAGAGCUUCUCCAGGCGCGCCUGGAGCAAUCGAUAGUGGCGAUACAUGGACAUUCUCUUGGUAAUCUU
..((((((.((......)).(((((((..((((((...((((.(((....))).......(((((((....)))))))..))))...)))))).)))))))......))))))....... (-36.96 = -38.04 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:35 2006