Locus 7465

Sequence ID 3L_DroMel_CAF1
Location 20,025,192 – 20,025,325
Length 133
Max. P 0.979548
window12134 window12135 window12136 window12137

overview

Window 4

Location 20,025,192 – 20,025,298
Length 106
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 88.42
Mean single sequence MFE -22.98
Consensus MFE -16.58
Energy contribution -17.18
Covariance contribution 0.60
Combinations/Pair 1.08
Mean z-score -2.91
Structure conservation index 0.72
SVM decision value 1.47
SVM RNA-class probability 0.956525
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20025192 106 + 23771897
UUUCCCUCUCAGCUGCUCAGUUGACGGUGAACUUCGCUGUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUGUGUGUACAUAUAUAUGUAUA
.........(((((....)))))((((((.....)))))).....(((((.((((.(((((((((..(((.((....)).))).))))))))).)))).))))).. ( -26.70)
>DroSec_CAF1 16903 102 + 1
UUUCCCUCUCAGCUGCUCAGUUGACGCUGAACUUCGCUGUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACAUACU----UAUA
......((.((((.(.(((((....))))).)...)))).))..((((....))))((((((((((.(((......))).))))...)))))).....----.... ( -21.40)
>DroSim_CAF1 11547 102 + 1
UUUCCCUCUCAGCUGCUCAGUUGACGCUGAACUUCGCUGUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACCUACA----UAUA
......((.((((.(.(((((....))))).)...)))).))...........(((((((((((((.(((......))).))))...)))))))))..----.... ( -25.90)
>DroEre_CAF1 16280 94 + 1
UUUCCCUCUCAGCUGCUCAGUUGACGCUGAACUUUGCUGUGUUUCUAUAUUUAUAGGUACAUACAUAUGUUUGCCUACAUAUGUUUUAUGUAC------------A
.......(.((((.(.(((((....))))).)...)))).)...((((....))))((((((((((((((......))))))))...))))))------------. ( -24.50)
>DroYak_CAF1 18582 102 + 1
UUUCCCUCUCAGUUGCUCAGUUGACGCUGAACUUUGCUGUGAUUCUAUAUUUAUAAGUUCAUACAUAUGUUUGUCUACAUUUGUUUUAUUUACUUACU----UAUA
......((.((((.(.(((((....))))).)...)))).))...........(((((....(((.((((......)))).))).......)))))..----.... ( -16.40)
>consensus
UUUCCCUCUCAGCUGCUCAGUUGACGCUGAACUUCGCUGUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACAUACA____UAUA
......((.((((.(.(((((....))))).)...)))).))..............((((((((((.(((......))).))))...))))))............. (-16.58 = -17.18 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,025,192 – 20,025,298
Length 106
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 88.42
Mean single sequence MFE -23.94
Consensus MFE -16.94
Energy contribution -17.98
Covariance contribution 1.04
Combinations/Pair 1.04
Mean z-score -3.34
Structure conservation index 0.71
SVM decision value 1.65
SVM RNA-class probability 0.969844
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20025192 106 - 23771897
UAUACAUAUAUAUGUACACACAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCACAGCGAAGUUCACCGUCAACUGAGCAGCUGAGAGGGAAA
..(((((((((.(((...((((.....)))).....))).))))))))).((((....))))..((.((((...(((((........))))).)))).))...... ( -24.20)
>DroSec_CAF1 16903 102 - 1
UAUA----AGUAUGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCACAGCGAAGUUCAGCGUCAACUGAGCAGCUGAGAGGGAAA
....----.(((.(((((....((((.(((......))).)))).))))).)))..........((.((((...((((((......)))))).)))).))...... ( -23.20)
>DroSim_CAF1 11547 102 - 1
UAUA----UGUAGGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCACAGCGAAGUUCAGCGUCAACUGAGCAGCUGAGAGGGAAA
(((.----((((((((((....((((.(((......))).)))).)))))))))).))).....((.((((...((((((......)))))).)))).))...... ( -31.00)
>DroEre_CAF1 16280 94 - 1
U------------GUACAUAAAACAUAUGUAGGCAAACAUAUGUAUGUACCUAUAAAUAUAGAAACACAGCAAAGUUCAGCGUCAACUGAGCAGCUGAGAGGGAAA
.------------((((((...((((((((......))))))))))))))((((....)))).....((((...((((((......)))))).))))......... ( -25.40)
>DroYak_CAF1 18582 102 - 1
UAUA----AGUAAGUAAAUAAAACAAAUGUAGACAAACAUAUGUAUGAACUUAUAAAUAUAGAAUCACAGCAAAGUUCAGCGUCAACUGAGCAACUGAGAGGGAAA
....----.((((((..((...(((.((((......)))).)))))..))))))..........((.(((....((((((......))))))..))).))...... ( -15.90)
>consensus
UAUA____AGUAUGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCACAGCGAAGUUCAGCGUCAACUGAGCAGCUGAGAGGGAAA
.............(((((....((((.(((......))).)))).)))))((((....))))..((.((((...((((((......)))))).)))).))...... (-16.94 = -17.98 +   1.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,025,230 – 20,025,325
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 87.10
Mean single sequence MFE -16.40
Consensus MFE -10.71
Energy contribution -10.53
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.65
SVM decision value 0.43
SVM RNA-class probability 0.731760
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20025230 95 + 23771897
GUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUGUGUGUACAUAUAUAUGUAUAUACUCGUAUUUUUCCUCAUAUAUUGAU
((((.........((..((((.((((((.(((.(((.(((((.....))))).))).))).)))))).))))..)).......))))........ ( -19.79)
>DroSec_CAF1 16941 91 + 1
GUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACAUACU----UAUAUACUCGUGUUUUUCCUCAUAUAUUGAU
((((..((((....))))((((((((((.(((......))).))))...)))))).....----...................))))........ ( -12.10)
>DroSim_CAF1 11585 91 + 1
GUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACCUACA----UAUAUACUCGUAUUUUUCCUCAUAUAUUGAU
.......(((((...(((((((((((((.(((......))).))))...)))))))))..----.))))).............(((.....))). ( -17.00)
>DroEre_CAF1 16318 83 + 1
GUGUUUCUAUAUUUAUAGGUACAUACAUAUGUUUGCCUACAUAUGUUUUAUGUAC------------AUACAAGUAUUUUUCCUCAUAUAUUGAA
(((.....((((((.((.((((((((((((((......))))))))...))))))------------.)).)))))).......)))........ ( -16.70)
>consensus
GUGAUUCUAUAUUUAUAGGUACAUACAUUUGUUUGUCCACAUAUGUUUUGUGUACAUACA____UAUAUACUCGUAUUUUUCCUCAUAUAUUGAU
(((...((((....))))((((((((((.(((......))).))))...)))))).............)))............(((.....))). (-10.71 = -10.53 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,025,230 – 20,025,325
Length 95
Sequences 4
Columns 95
Reading direction reverse
Mean pairwise identity 87.10
Mean single sequence MFE -17.30
Consensus MFE -12.73
Energy contribution -12.97
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -3.37
Structure conservation index 0.74
SVM decision value 1.84
SVM RNA-class probability 0.979548
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20025230 95 - 23771897
AUCAAUAUAUGAGGAAAAAUACGAGUAUAUACAUAUAUAUGUACACACAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCAC
.....(((((.(((....(((....))).(((((((((.(((...((((.....)))).....))).))))))))))))....)))))....... ( -16.70)
>DroSec_CAF1 16941 91 - 1
AUCAAUAUAUGAGGAAAAACACGAGUAUAUA----AGUAUGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCAC
.....(((((.(((..........((((((.----...))))))(((..((((.(((......))).)))).))).)))....)))))....... ( -14.00)
>DroSim_CAF1 11585 91 - 1
AUCAAUAUAUGAGGAAAAAUACGAGUAUAUA----UGUAGGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCAC
......................((.(((((.----((((((((((....((((.(((......))).)))).)))))))))).)))))...)).. ( -20.70)
>DroEre_CAF1 16318 83 - 1
UUCAAUAUAUGAGGAAAAAUACUUGUAU------------GUACAUAAAACAUAUGUAGGCAAACAUAUGUAUGUACCUAUAAAUAUAGAAACAC
(((...(((..((........))..)))------------((((((...((((((((......))))))))))))))...........))).... ( -17.80)
>consensus
AUCAAUAUAUGAGGAAAAAUACGAGUAUAUA____UGUAUGUACACAAAACAUAUGUGGACAAACAAAUGUAUGUACCUAUAAAUAUAGAAUCAC
.....(((((.(((..........(((((((......)))))))(((..((((.(((......))).)))).))).)))....)))))....... (-12.73 = -12.97 +   0.25)

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 12:47:52 2006