Locus 3336

Sequence ID 2L_DroMel_CAF1
Location 9,664,783 – 9,664,916
Length 133
Max. P 0.563474
window5289 window5290 window5291

overview

Window 9

Location 9,664,783 – 9,664,893
Length 110
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.27
Mean single sequence MFE -30.23
Consensus MFE -12.49
Energy contribution -15.97
Covariance contribution 3.47
Combinations/Pair 1.08
Mean z-score -2.60
Structure conservation index 0.41
SVM decision value 0.01
SVM RNA-class probability 0.536889
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9664783 110 + 22407834
GCUUGCCAAAAGGAAAAUGGAGGCAGC--AU-AAAAGGAAACGGAAAAAGUUGCGAAUAAAUGGAAUUAUAUC-------CUUGGCAAUGGCUGCAGUCGAGCAGAAAUGAUCAACUGCU
((((((((..((((........(((((--..-....(....).......)))))..((((......)))).))-------)))))))..))).(((((.((.((....)).)).))))). ( -31.22)
>DroPse_CAF1 44464 117 + 1
GCUUGCCAAAACUGAGAUAAAAAUCAC--GA-GAAAAGAGUGGGAAAACUUUGCAAAUAAAUGGAAUUAUUUCCAGGGGCCUUGACAGUGGCUGCACUCGAGCAGAAAUGAUCAACUGCA
((..(((...((((.(((....))).(--((-(...(((((......)))))((.......(((((....)))))...)))))).))))))).))......((((..........)))). ( -26.00)
>DroSec_CAF1 23010 112 + 1
GCUUGCCAAAAGGAAAGUGGAGGCAGCGCCU-AAAAGGAAACGGAAAAAGUUGCGAAUAAAUGGAAUUAUAUC-------CUUGGCAAUGGCUGCAGUCGAGCAGAAAUGAUCAACUGCU
((((((((..((((........(((((....-....(....).......)))))..((((......)))).))-------)))))))..))).(((((.((.((....)).)).))))). ( -32.16)
>DroYak_CAF1 23131 110 + 1
GCUUGCCAAAAGGAAAGUGGAGGCAGC--AU-GAAAGGAAACGGAAUAAGUUGCGAAUAAAUGGAAUUAUAUC-------CUUGGCAAUGGCUGCAGUCGAGCAGAAAUGAUCAACUGCU
((((((((..((((........(((((--..-....(....).......)))))..((((......)))).))-------)))))))..))).(((((.((.((....)).)).))))). ( -31.22)
>DroAna_CAF1 25999 111 + 1
GCUUGCCAAACGGAAAGUGGAGGCCAA--ACAGAAAGGAAACGGAAAAAGUUGCGAAUAAAUGCAAUUAUAUC-------CUUGGCAAUGGCAGCAGUCGAGCAGAAAUGAUCAACUGUA
...(((((.((.....))....(((((--.......(....)(((.(.(((((((......))))))).).))-------))))))..)))))(((((.((.((....)).)).))))). ( -32.80)
>DroPer_CAF1 44646 117 + 1
GCUUGCCAAAACUGAGAGAAAAAUCAA--GG-GAAAAGAGUGGGAAAACUUUGCAAAUAAAUGGAAUUAUUUCCAGGGGCCUUGACAGUGGCUGCACGCGAGCAGAAAUGAUCAACUGCA
((.(((....((((.........((((--((-....(((((......))))).........(((((....)))))....))))))))))....))).))..((((..........)))). ( -28.00)
>consensus
GCUUGCCAAAAGGAAAAUGGAGGCAAC__AU_GAAAGGAAACGGAAAAAGUUGCGAAUAAAUGGAAUUAUAUC_______CUUGGCAAUGGCUGCAGUCGAGCAGAAAUGAUCAACUGCA
(((((((((...........................(....)......((((.((......)).)))).............))))))..))).(((((.((.((....)).)).))))). (-12.49 = -15.97 +   3.47)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,664,783 – 9,664,893
Length 110
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.27
Mean single sequence MFE -24.59
Consensus MFE -13.52
Energy contribution -13.80
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -1.92
Structure conservation index 0.55
SVM decision value 0.06
SVM RNA-class probability 0.563474
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9664783 110 - 22407834
AGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGUUUCCUUUU-AU--GCUGCCUCCAUUUUCCUUUUGGCAAGC
.((((((((.((....)).)))))))).....((((((((-------((......)))........(((.(.................-..--).))).............))))))).. ( -25.31)
>DroPse_CAF1 44464 117 - 1
UGCAGUUGAUCAUUUCUGCUCGAGUGCAGCCACUGUCAAGGCCCCUGGAAAUAAUUCCAUUUAUUUGCAAAGUUUUCCCACUCUUUUC-UC--GUGAUUUUUAUCUCAGUUUUGGCAAGC
((((.((((.((....)).)))).)))).....(((((((((...((.((((((......)))))).))...................-..--(.(((....))).).)))))))))... ( -23.90)
>DroSec_CAF1 23010 112 - 1
AGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGUUUCCUUUU-AGGCGCUGCCUCCACUUUCCUUUUGGCAAGC
.((((((((.((....)).)))))))).....((((((((-------((......)))..............................-((((...))))...........))))))).. ( -27.90)
>DroYak_CAF1 23131 110 - 1
AGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUAUUCCGUUUCCUUUC-AU--GCUGCCUCCACUUUCCUUUUGGCAAGC
.((((((((.((....)).)))))))).....((((((((-------((......)))........(((.(.................-..--).))).............))))))).. ( -25.31)
>DroAna_CAF1 25999 111 - 1
UACAGUUGAUCAUUUCUGCUCGACUGCUGCCAUUGCCAAG-------GAUAUAAUUGCAUUUAUUCGCAACUUUUUCCGUUUCCUUUCUGU--UUGGCCUCCACUUUCCGUUUGGCAAGC
..(((((((.((....)).)))))))......((((((((-------((.....((((........)))).....))).............--.(((...)))........))))))).. ( -23.90)
>DroPer_CAF1 44646 117 - 1
UGCAGUUGAUCAUUUCUGCUCGCGUGCAGCCACUGUCAAGGCCCCUGGAAAUAAUUCCAUUUAUUUGCAAAGUUUUCCCACUCUUUUC-CC--UUGAUUUUUCUCUCAGUUUUGGCAAGC
.((((..........))))..((.(((....((((((((((....((.((((((......)))))).)).(((......)))......-))--)))).........))))....))).)) ( -21.20)
>consensus
AGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG_______GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGUUUCCUUUC_AU__GCGGCCUCCACUUUCCUUUUGGCAAGC
.((((((((.((....)).)))))))).((..((((((((.......((.((((......)))))).............................((....)).......)))))))))) (-13.52 = -13.80 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,664,820 – 9,664,916
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.10
Mean single sequence MFE -23.60
Consensus MFE -14.52
Energy contribution -14.72
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -1.74
Structure conservation index 0.62
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9664820 96 - 22407834
CCUUCGUCGGU-----------------CGUCCUGCCUGCAGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGU
.......(((.-----------------.....(((..((.((((((((.((....)).)))))))).)).........(-------((......)))........))).......))). ( -22.12)
>DroPse_CAF1 44501 120 - 1
CCAUCAUCCGGCUGCUGGCUGCUGGCUGCCGCCUGCCGGCUGCAGUUGAUCAUUUCUGCUCGAGUGCAGCCACUGUCAAGGCCCCUGGAAAUAAUUCCAUUUAUUUGCAAAGUUUUCCCA
.........((((..((((.((.(((....))).)).(((((((.((((.((....)).)))).)))))))...)))).))))..((.((((((......)))))).))........... ( -40.70)
>DroSec_CAF1 23049 92 - 1
CCCUCGU---------------------CGUCCUGCCUGCAGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGU
.......---------------------.(((((((..((.((((((((.((....)).)))))))).))....))..))-------))).............................. ( -19.70)
>DroEre_CAF1 22843 92 - 1
CCCUCGU---------------------CGUCCUGCCUGCAGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUAUUCCGU
.......---------------------.(((((((..((.((((((((.((....)).)))))))).))....))..))-------))).............................. ( -19.70)
>DroYak_CAF1 23168 92 - 1
CCUUCGU---------------------CGUCCUGCCUGCAGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG-------GAUAUAAUUCCAUUUAUUCGCAACUUAUUCCGU
.......---------------------.(((((((..((.((((((((.((....)).)))))))).))....))..))-------))).............................. ( -19.70)
>DroAna_CAF1 26037 92 - 1
CCUUCCC---------------------AGUCCUGCCUGCUACAGUUGAUCAUUUCUGCUCGACUGCUGCCAUUGCCAAG-------GAUAUAAUUGCAUUUAUUCGCAACUUUUUCCGU
.......---------------------.(((((((..((..(((((((.((....)).)))))))..))....))..))-------)))....((((........)))).......... ( -19.70)
>consensus
CCUUCGU_____________________CGUCCUGCCUGCAGCAGUUGAUCAUUUCUGCUCGACUGCAGCCAUUGCCAAG_______GAUAUAAUUCCAUUUAUUCGCAACUUUUUCCGU
.................................(((..((.((((((((.((....)).)))))))).)).................((.((((......)))))))))........... (-14.52 = -14.72 +   0.20)

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 10:50:03 2006