Locus 4877

Sequence ID 2L_DroMel_CAF1
Location 13,894,955 – 13,895,085
Length 130
Max. P 0.687264
window7734 window7735

overview

Window 4

Location 13,894,955 – 13,895,045
Length 90
Sequences 6
Columns 90
Reading direction forward
Mean pairwise identity 77.22
Mean single sequence MFE -13.78
Consensus MFE -10.37
Energy contribution -10.65
Covariance contribution 0.28
Combinations/Pair 1.20
Mean z-score -1.01
Structure conservation index 0.75
SVM decision value 0.32
SVM RNA-class probability 0.687264
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13894955 90 + 22407834
CUUUCCCUUGCCAAUUGCCAACCCUUUGCCAUUUUAAAUUCAUUCUAUGAUUUUUCGUCUUUUUCCCUUACAGUUCGCUGGCUGGGUGGA
.................(((.(((...(((................((((....)))).............((....))))).)))))). ( -13.90)
>DroSec_CAF1 38686 90 + 1
CUUUCCCUUGCCAAUUGCCAACCCUUUGCCAUUUUAUACUCAUUAUAUGAUUUUUCGUCUUUUUCCCUUACAGUUCGCUGGCUGGGUGGA
.................(((.(((...(((................((((....)))).............((....))))).)))))). ( -13.90)
>DroSim_CAF1 40939 90 + 1
CUUUCCCUUGCCAAUUGCCAACCCUUUGCCAUUUUAUACUCAUUAUAUGAUUUUUCGUCUUUUUCCCUUGCAGUUCGCUGGCUGGGUGGA
.................(((.(((...((((...............((((....))))...........((.....)))))).)))))). ( -15.80)
>DroEre_CAF1 38803 90 + 1
CUUUCCCUUCCCAACUGCCAACCCUUUGCCAUUCCUAACUCAUUAUAUGAUUUUUCGUCCUUUUUCCUUACAGUUCGCUGGCUGGGUGGA
.................(((.(((...(((................((((....)))).............((....))))).)))))). ( -13.90)
>DroYak_CAF1 40872 73 + 1
----------------GCCAACCCUUUGCCGUUCUUAACUCAUUAUAUGAUUUUUCGUC-UUUUUCCUUACAGUUCGCUGGCUGGGUGGA
----------------.(((.(((...(((................((((....)))).-...........((....))))).)))))). ( -13.90)
>DroPer_CAF1 49792 73 + 1
A--UCCCUUG-----UGC---CCCUUUCUCAUGCAUACCU-------UUCCCUUGCACACAUUCUCCUUACAGUUCGCUGGCUGGGUGGA
.--(((....-----.((---((........((((.....-------......)))).............(((....)))...))))))) ( -11.30)
>consensus
CUUUCCCUUGCCAAUUGCCAACCCUUUGCCAUUCUAAACUCAUUAUAUGAUUUUUCGUCUUUUUCCCUUACAGUUCGCUGGCUGGGUGGA
.................(((.(((...(((................((((....)))).............((....))))).)))))). (-10.37 = -10.65 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,894,988 – 13,895,085
Length 97
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 76.64
Mean single sequence MFE -26.30
Consensus MFE -19.76
Energy contribution -18.85
Covariance contribution -0.91
Combinations/Pair 1.35
Mean z-score -0.83
Structure conservation index 0.75
SVM decision value 0.06
SVM RNA-class probability 0.566142
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13894988 97 + 22407834
UUAAAUUCAUUCUA-------UGAUUUUUCGUC----UUUUUCCCUUACAGUUCGCUGGCUGGGUGGAUGCGGUAAUCUUUGUGUUCAGCCUGGAGAACGAGGGCAGC
..............-------.........(((----((((((((...(((....)))...((.(((((((((......))))))))).)).)).))).))))))... ( -23.70)
>DroGri_CAF1 46607 100 + 1
UUUAACUAAUUCUCUUUCGCUCUCGUUGCGCUCU--------UUCUUUCAGUUCGCUGGCUGGGUGGAUGCGGUAAUCUUUGUGUUUAGCCUGGAGAACGAGGGCAGC
..................((((((((((((..((--------.......))..)))...(..(((((((((((......))))))))).))..)..)))))))))... ( -29.20)
>DroEre_CAF1 38836 97 + 1
CCUAACUCAUUAUA-------UGAUUUUUCGUC----CUUUUUCCUUACAGUUCGCUGGCUGGGUGGAUGCGGUAAUCUUCGUGUUCAGUCUGGAGAACGAGGGCAGC
..............-------.........(((----((((((((...(((....)))...((.(((((((((......))))))))).)).)))))..))))))... ( -26.90)
>DroWil_CAF1 54722 100 + 1
U--CACUCAUUUCGUUUUU--CUCUCUUUCUCA----CUUUAUCUUUACAGUUCGCUGGCUGGGUGGAUGCGGUAAUAUUUGUAUUUAGCCUGGAAAACGAGGGCAGU
.--.(((..((((((((((--(...........----...........(((....)))...((.(((((((((......))))))))).)).)))))))))))..))) ( -24.90)
>DroYak_CAF1 40889 96 + 1
CUUAACUCAUUAUA-------UGAUUUUUCGUC-----UUUUUCCUUACAGUUCGCUGGCUGGGUGGAUGCGGUAAUCUUCGUGUUCAGCCUGGAAAACGAGGGCAGC
.....(((.....(-------(((....)))).-----.((((((...(((....)))...((.(((((((((......))))))))).)).)))))).)))...... ( -25.60)
>DroAna_CAF1 36081 94 + 1
UU---CUCA---UA-------CUAUUUUGCAUC-CUCUCGUAUCCUUACAGUUCGCUGGCUGGGUGGAUGCCGUAAUCUUCGUGUUCAGCCUGGAGAACGAGGGCAGU
..---....---..-------.....((((..(-(((..(((....))).((((.(((((((..(((((......))))....)..))))).)).)))))))))))). ( -27.50)
>consensus
UUUAACUCAUUAUA_______CGAUUUUUCGUC_____UUUUUCCUUACAGUUCGCUGGCUGGGUGGAUGCGGUAAUCUUCGUGUUCAGCCUGGAGAACGAGGGCAGC
..........................................(((((.(((....))).(..(((((((((((......))))))))).))..).....))))).... (-19.76 = -18.85 +  -0.91)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:56 2006