Locus 2006

Sequence ID 2L_DroMel_CAF1
Location 5,438,632 – 5,438,749
Length 117
Max. P 0.963961
window3229 window3230

overview

Window 9

Location 5,438,632 – 5,438,725
Length 93
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 78.63
Mean single sequence MFE -26.53
Consensus MFE -18.28
Energy contribution -18.62
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.37
Structure conservation index 0.69
SVM decision value 1.56
SVM RNA-class probability 0.963961
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5438632 93 - 22407834
UAAGGCAAAUCAACCUCUUGACUUCCAAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCUC---------UCUGUCUCCGAU
..(((((..........(((((..(((.((......))...))).)))))..(((((((((((....)))))))))))...---------..)))))..... ( -24.70)
>DroPse_CAF1 68188 96 - 1
UGGGGGGCUCUAAC----UGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCUCAUCAG--AAUCUGUCUCUGGA
....((((......----((((..(((((..........))))).))))....((((((((((....)))))))))))))).((((--(.......))))). ( -29.90)
>DroGri_CAF1 92130 102 - 1
AAACGUAAAUAAAAUUAUUGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAUGCUCAUCAGCUGAAGUGUCUCUGCU
....(((........(((((((..(((((..........))))).)))))))..(((((((((....)))))))))))).....(((.((......)).))) ( -26.60)
>DroMoj_CAF1 94729 102 - 1
AAAAACAAACAAAAUUAUUGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAUGCUCAUCAGCUGAAGUGUCUCUGCU
...............(((((((..(((((..........))))).)))))))..(((((((((....)))))))))........(((.((......)).))) ( -25.60)
>DroAna_CAF1 62957 92 - 1
UAA-GCCAACUGACCUCUCGACUUUCCUCCGAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCUC---------UCUGUCUCCGGU
...-(((....(((.....(((...((.(.(.......).).)).)))....(((((((((((....)))))))))))...---------...)))...))) ( -22.50)
>DroPer_CAF1 67851 96 - 1
UGGGGGGCUCUAAC----UGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCUCAUCAG--AAUCUGUCUCUGGA
....((((......----((((..(((((..........))))).))))....((((((((((....)))))))))))))).((((--(.......))))). ( -29.90)
>consensus
UAAGGCAAACUAAC_U_UUGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCUCAUCAG___AUCUGUCUCUGGU
...................(((.............((((...))))......(((((((((((....)))))))))))...............)))...... (-18.28 = -18.62 +   0.33)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,438,645 – 5,438,749
Length 104
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 81.19
Mean single sequence MFE -26.07
Consensus MFE -16.96
Energy contribution -17.99
Covariance contribution 1.03
Combinations/Pair 1.05
Mean z-score -3.02
Structure conservation index 0.65
SVM decision value 1.25
SVM RNA-class probability 0.936510
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5438645 104 - 22407834
AAAAAAAAAAAAGGUUCCUAAG-----UCUAAGGCAAAUCAACCUCUUGACUUCCAAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
............((.....(((-----((..(((........)))...)))))))........(((((...))))).....(((((((((((....))))))))))).. ( -24.90)
>DroPse_CAF1 68208 92 - 1
--------ACCCGUCUCCCAAG-----UCUGGGGGGCUCUAAC----UGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
--------....((((((((..-----..))))))))......----((((..(((((..........))))).))))...(((((((((((....))))))))))).. ( -34.20)
>DroSec_CAF1 58218 103 - 1
A-AAGAAAAAAAGGUUCCUAAG-----UCUAAGGCAAAUCAACCUCUUGACUUCCAAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
.-..........((.....(((-----((..(((........)))...)))))))........(((((...))))).....(((((((((((....))))))))))).. ( -24.90)
>DroEre_CAF1 58981 97 - 1
A-------AAAAGGUUCCUAAG-----UCUAAGGCAAAUCAACCUCUCGACUUCCCAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
.-------...(((((.....(-----(.....)).....)))))...(((..(((((.........))).)).)))....(((((((((((....))))))))))).. ( -24.80)
>DroYak_CAF1 65304 97 - 1
A-------AAAAUGUUCCUAAG-----UCUAAGGCAAAUCAACCUCUUGACUUCCCAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
.-------..............-----.....(((...........(((((..(((((.........))).)).)))))...((((((((((....))))))))))))) ( -24.40)
>DroMoj_CAF1 94751 104 - 1
-----AAAAGACGAAUCCGAAAACAAAACAAAAACAAACAAAAUUAUUGACUUCCAUAUAAAAUCACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAUGCU
-----.......................................(((((((..(((((..........))))).)))))))..(((((((((....))))))))).... ( -23.20)
>consensus
A_______AAAAGGUUCCUAAG_____UCUAAGGCAAAUCAACCUCUUGACUUCCAAGUAAAAACACCUGUGGUGUCAAUAUUUCAACACUGCCAGCGGUGUUGAAGCU
................................(((...........(((((..(((..............))).)))))...((((((((((....))))))))))))) (-16.96 = -17.99 +   1.03)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:57 2006