Locus 8017

Sequence ID 3R_DroMel_CAF1
Location 21,508,439 – 21,508,564
Length 125
Max. P 0.999082
window12902 window12903 window12904 window12905

overview

Window 2

Location 21,508,439 – 21,508,547
Length 108
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 86.29
Mean single sequence MFE -27.54
Consensus MFE -21.66
Energy contribution -21.26
Covariance contribution -0.40
Combinations/Pair 1.14
Mean z-score -3.87
Structure conservation index 0.79
SVM decision value 3.30
SVM RNA-class probability 0.998948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21508439 108 + 27905053
CUUAAUCACUAACUUUUUGGUUGCCUUA----UA--UCUUUUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUAUAAGAGGCUACUUAAAAUUUGUUUA
.........(((((....))))).....----..--......(((((((((((((((((..(((((((((..........))))))))).)))))).)))))))))))...... ( -28.60)
>DroSec_CAF1 27996 108 + 1
CUUAAUCACUAACUUUUUGGUA----UAGUUUAA--UCUUUUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUACAAGAGGCCACUUAAAAUUUGUUUA
.......(((((((....))).----))))....--......((((((((((.((((((..(((((((((..........))))))))).))))))..))))))))))...... ( -26.10)
>DroSim_CAF1 29162 110 + 1
CUUAAUCACUAACUUUUUGGUUUCCUUAGUUU----CCUUUUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUACAAGAGGCCACUUAAAAUUUGUUUA
.......(((((....)))))...........----......((((((((((.((((((..(((((((((..........))))))))).))))))..))))))))))...... ( -24.70)
>DroEre_CAF1 28487 110 + 1
CUUAACCACUAACUAAUUGGUUUCCUUU----UAGUUGUUUUUGUUUUAAGUACUUCUUCAUGGGUGACACAUGCUCGUUAGUUACCUAUAAGAGGCCACUUAAAAUGUGUUUA
......((((((((((..((...))..)----)))))).....(((((((((.((((((.(((((((((((......))..)))))))))))))))..)))))))))))).... ( -31.20)
>DroYak_CAF1 28834 108 + 1
CUUAACCACUAACUUUUUAGUUUCCUUA----UA--UCUUUUAGUUUUAAGUACUUCAUUAUGGGUAACACAUGCUCGUUGGUUACCUAUAAGAGGCCACUUAAAAUGUGUUUA
......(((.((((....))))......----..--.......(((((((((.((((.(((((((((((.((.......)))))))))))))))))..)))))))))))).... ( -27.10)
>consensus
CUUAAUCACUAACUUUUUGGUUUCCUUA____UA__UCUUUUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUAUAAGAGGCCACUUAAAAUUUGUUUA
.......(((((....))))).....................((((((((((.((((((..((((((((............)))))))).))))))..))))))))))...... (-21.66 = -21.26 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,508,439 – 21,508,547
Length 108
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 86.29
Mean single sequence MFE -22.16
Consensus MFE -15.82
Energy contribution -16.02
Covariance contribution 0.20
Combinations/Pair 1.08
Mean z-score -2.25
Structure conservation index 0.71
SVM decision value 0.82
SVM RNA-class probability 0.859930
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21508439 108 - 27905053
UAAACAAAUUUUAAGUAGCCUCUUAUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAAAAGA--UA----UAAGGCAACCAAAAAGUUAGUGAUUAAG
.........((((((((.(.((((...(((((((..........)))))))....)))).)))))))))(((((....--..----...(....).......)))))....... ( -21.29)
>DroSec_CAF1 27996 108 - 1
UAAACAAAUUUUAAGUGGCCUCUUGUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAAAAGA--UUAAACUA----UACCAAAAAGUUAGUGAUUAAG
........(((((((((.(.(((((..(((((((..........)))))))))))).)...)))))))))........--....((((----.((......))))))....... ( -20.90)
>DroSim_CAF1 29162 110 - 1
UAAACAAAUUUUAAGUGGCCUCUUGUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAAAAGG----AAACUAAGGAAACCAAAAAGUUAGUGAUUAAG
.........((((((((.(.(((((..(((((((..........)))))))))))).)...))))))))(((((.((.----...))..(....).......)))))....... ( -25.30)
>DroEre_CAF1 28487 110 - 1
UAAACACAUUUUAAGUGGCCUCUUAUAGGUAACUAACGAGCAUGUGUCACCCAUGAAGAAGUACUUAAAACAAAAACAACUA----AAAGGAAACCAAUUAGUUAGUGGUUAAG
....(((.(((((((((.(.((((...(((.((............)).)))....)))).)))))))))).......(((((----(..(....)...)))))).)))...... ( -20.60)
>DroYak_CAF1 28834 108 - 1
UAAACACAUUUUAAGUGGCCUCUUAUAGGUAACCAACGAGCAUGUGUUACCCAUAAUGAAGUACUUAAAACUAAAAGA--UA----UAAGGAAACUAAAAAGUUAGUGGUUAAG
....(((.(((((((((.(.((((((.((((((((.......)).)))))).)))).)).))))))))))........--..----..((....)).........)))...... ( -22.70)
>consensus
UAAACAAAUUUUAAGUGGCCUCUUAUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAAAAGA__UA____UAAGGAAACCAAAAAGUUAGUGAUUAAG
..(((...(((((((((.(.((((...((((((............))))))....)))).))))))))))...................(....)......))).......... (-15.82 = -16.02 +   0.20)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,508,473 – 21,508,564
Length 91
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 90.20
Mean single sequence MFE -25.38
Consensus MFE -20.64
Energy contribution -20.40
Covariance contribution -0.24
Combinations/Pair 1.12
Mean z-score -3.47
Structure conservation index 0.81
SVM decision value 3.36
SVM RNA-class probability 0.999082
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21508473 91 + 27905053
UUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUAUAAGAGGCUACUUAAAAUUUGUUUAUAUAAA--UUGGACUUAUG
..(((((((((((((((((..(((((((((..........))))))))).)))))).))))))))))).(((((......--.)))))..... ( -28.50)
>DroSec_CAF1 28030 91 + 1
UUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUACAAGAGGCCACUUAAAAUUUGUUUAUAUAAA--UUGGACCACUG
..((((((((((.((((((..(((((((((..........))))))))).))))))..)))))))))).(((((......--.)))))..... ( -25.00)
>DroSim_CAF1 29198 91 + 1
UUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUACAAGAGGCCACUUAAAAUUUGUUUAUAUAAA--UUGGACCACUG
..((((((((((.((((((..(((((((((..........))))))))).))))))..)))))))))).(((((......--.)))))..... ( -25.00)
>DroEre_CAF1 28523 91 + 1
UUUGUUUUAAGUACUUCUUCAUGGGUGACACAUGCUCGUUAGUUACCUAUAAGAGGCCACUUAAAAUGUGUUUAUAUAAA--UUCGACCACUG
...(((((((((.((((((.(((((((((((......))..)))))))))))))))..))))))))).............--........... ( -23.30)
>DroYak_CAF1 28868 93 + 1
UUAGUUUUAAGUACUUCAUUAUGGGUAACACAUGCUCGUUGGUUACCUAUAAGAGGCCACUUAAAAUGUGUUUAUAUAAUUUUUCGACAACUG
...(((((((((.((((.(((((((((((.((.......)))))))))))))))))..))))))))).......................... ( -25.10)
>consensus
UUAGUUUUAAGUACUUCUUCUUGGGUGACACAUGCUCGAUUGUCACCUAUAAGAGGCCACUUAAAAUUUGUUUAUAUAAA__UUGGACCACUG
..((((((((((.((((((..((((((((............)))))))).))))))..))))))))))......................... (-20.64 = -20.40 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,508,473 – 21,508,564
Length 91
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 90.20
Mean single sequence MFE -18.02
Consensus MFE -15.72
Energy contribution -15.72
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -1.61
Structure conservation index 0.87
SVM decision value 1.08
SVM RNA-class probability 0.912204
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21508473 91 - 27905053
CAUAAGUCCAA--UUUAUAUAAACAAAUUUUAAGUAGCCUCUUAUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAA
...........--..............(((((((((.(.((((...(((((((..........)))))))....)))).)))))))))).... ( -19.30)
>DroSec_CAF1 28030 91 - 1
CAGUGGUCCAA--UUUAUAUAAACAAAUUUUAAGUGGCCUCUUGUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAA
...........--..............(((((((((.(.(((((..(((((((..........)))))))))))).)...))))))))).... ( -19.90)
>DroSim_CAF1 29198 91 - 1
CAGUGGUCCAA--UUUAUAUAAACAAAUUUUAAGUGGCCUCUUGUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAA
...........--..............(((((((((.(.(((((..(((((((..........)))))))))))).)...))))))))).... ( -19.90)
>DroEre_CAF1 28523 91 - 1
CAGUGGUCGAA--UUUAUAUAAACACAUUUUAAGUGGCCUCUUAUAGGUAACUAACGAGCAUGUGUCACCCAUGAAGAAGUACUUAAAACAAA
..(((......--..........))).(((((((((.(.((((...(((.((............)).)))....)))).)))))))))).... ( -14.09)
>DroYak_CAF1 28868 93 - 1
CAGUUGUCGAAAAAUUAUAUAAACACAUUUUAAGUGGCCUCUUAUAGGUAACCAACGAGCAUGUGUUACCCAUAAUGAAGUACUUAAAACUAA
...........................(((((((((.(.((((((.((((((((.......)).)))))).)))).)).)))))))))).... ( -16.90)
>consensus
CAGUGGUCCAA__UUUAUAUAAACAAAUUUUAAGUGGCCUCUUAUAGGUGACAAUCGAGCAUGUGUCACCCAAGAAGAAGUACUUAAAACUAA
...........................(((((((((.(.((((...((((((............))))))....)))).)))))))))).... (-15.72 = -15.72 +  -0.00)

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 13:00:28 2006