Locus 3300

Sequence ID 2L_DroMel_CAF1
Location 9,549,614 – 9,549,710
Length 96
Max. P 0.985541
window5242 window5243

overview

Window 2

Location 9,549,614 – 9,549,710
Length 96
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 67.30
Mean single sequence MFE -22.04
Consensus MFE -14.28
Energy contribution -14.95
Covariance contribution 0.67
Combinations/Pair 1.13
Mean z-score -2.05
Structure conservation index 0.65
SVM decision value 2.01
SVM RNA-class probability 0.985541
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9549614 96 + 22407834
CACGUUGAAAAUCAGGACGAGCAGCAUCAGCUGCUGGCGCACAAACCAGUCCUGGAUGG--AUAAACAACAUUG----AAUUAUAUUCAAAAU-------AUGGUGUUA
(((((((...((((((((.((((((....))))))((........)).))))).)))..--.....)))).(((----(((...))))))...-------...)))... ( -26.10)
>DroVir_CAF1 2779 81 + 1
CAUAUUGACAAAAAGCACGAGCAGCAUCAGCUGUCGUCGCACCAGCCAAUCCUGUCCAGAAAUAAAUGAAGUAG----CAUU-----UA--G-----------------
......((((....(.((((.((((....)))))))))((....))......))))......((((((......----))))-----))--.----------------- ( -15.90)
>DroGri_CAF1 2899 83 + 1
CACAUUGACAAACAGCACGAGCAGCAUCAGCUGUUGGCGCACAAACCAAUCCUGUCAA---AGAAAUUA---------UAAU-----UA--GU-------UGGACGAUA
...((((.......((.(.((((((....)))))).).)).....(((((.......(---(....)).---------....-----..--))-------))).)))). ( -18.04)
>DroSec_CAF1 37 75 + 1
CACGUUGAAAAUCAGGACGAGCAGCAUCAGCUGCUGACGCACAAACCAGUCCUGGAUA---AUAAACAACAUUG----AAUU---------------------------
...((((....(((((((.((((((....))))))(.....)......)))))))...---.....))))....----....--------------------------- ( -19.50)
>DroSim_CAF1 37 95 + 1
CACGUUGAAAAUCAGGACGAGCAGCAUCAGCUGCUGGCGCACAAACCAGUCCUGGAUA---AUAAACAACAUUG----AAUUAUAUUAAAAAU-------AUGGUGUUA
...(((.....(((((((.((((((....))))))((........)).)))))))...---...)))(((((((----.(((........)))-------.))))))). ( -25.20)
>DroEre_CAF1 625 106 + 1
CACGUUGAAAAUCAGGACGAGCAGCAUCAGCUGCUGGCGCACAAACCAGUCCUGGGUG---AUAAACAGCAUUCGUUCGAUUAGAUUCAAAUUGCAUUCCAUUGAAGCA
....((((((((((((((.((((((....))))))((........)).)))))(..((---(..........)))..)))))...)))))..(((.(((....)))))) ( -27.50)
>consensus
CACGUUGAAAAUCAGGACGAGCAGCAUCAGCUGCUGGCGCACAAACCAGUCCUGGAUA___AUAAACAACAUUG____AAUU_____CA__AU_______AUGG_G_UA
...........(((((((.((((((....))))))((........)).)))))))...................................................... (-14.28 = -14.95 +   0.67)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,549,614 – 9,549,710
Length 96
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 67.30
Mean single sequence MFE -23.97
Consensus MFE -14.86
Energy contribution -15.25
Covariance contribution 0.39
Combinations/Pair 1.27
Mean z-score -1.71
Structure conservation index 0.62
SVM decision value 1.47
SVM RNA-class probability 0.956501
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9549614 96 - 22407834
UAACACCAU-------AUUUUGAAUAUAAUU----CAAUGUUGUUUAU--CCAUCCAGGACUGGUUUGUGCGCCAGCAGCUGAUGCUGCUCGUCCUGAUUUUCAACGUG
...(((...-------...((((((...)))----))).((((...((--(.....(((((((((......))))(((((....)))))..))))))))...))))))) ( -26.10)
>DroVir_CAF1 2779 81 - 1
-----------------C--UA-----AAUG----CUACUUCAUUUAUUUCUGGACAGGAUUGGCUGGUGCGACGACAGCUGAUGCUGCUCGUGCUUUUUGUCAAUAUG
-----------------.--((-----((((----......))))))........((..((((((.((..(((.(.((((....))))))))..))....)))))).)) ( -21.50)
>DroGri_CAF1 2899 83 - 1
UAUCGUCCA-------AC--UA-----AUUA---------UAAUUUCU---UUGACAGGAUUGGUUUGUGCGCCAACAGCUGAUGCUGCUCGUGCUGUUUGUCAAUGUG
.........-------..--..-----....---------........---((((((((.(((((......)))))(((((((......))).)))))))))))).... ( -16.50)
>DroSec_CAF1 37 75 - 1
---------------------------AAUU----CAAUGUUGUUUAU---UAUCCAGGACUGGUUUGUGCGUCAGCAGCUGAUGCUGCUCGUCCUGAUUUUCAACGUG
---------------------------....----..((((((.....---.(((.(((((.(((....(((((((...))))))).))).))))))))...)))))). ( -25.10)
>DroSim_CAF1 37 95 - 1
UAACACCAU-------AUUUUUAAUAUAAUU----CAAUGUUGUUUAU---UAUCCAGGACUGGUUUGUGCGCCAGCAGCUGAUGCUGCUCGUCCUGAUUUUCAACGUG
.........-------...............----..((((((.....---.(((.(((((((((......))))(((((....)))))..))))))))...)))))). ( -25.80)
>DroEre_CAF1 625 106 - 1
UGCUUCAAUGGAAUGCAAUUUGAAUCUAAUCGAACGAAUGCUGUUUAU---CACCCAGGACUGGUUUGUGCGCCAGCAGCUGAUGCUGCUCGUCCUGAUUUUCAACGUG
((((((....))).)))..(((((.......(((((.....)))))..---....((((((((((......))))(((((....)))))..))))))...))))).... ( -28.80)
>consensus
UA_C_CCAU_______AC__UA_____AAUU____CAAUGUUGUUUAU___UAUCCAGGACUGGUUUGUGCGCCAGCAGCUGAUGCUGCUCGUCCUGAUUUUCAACGUG
.......................................................((((((((((......))))(((((....)))))..))))))............ (-14.86 = -15.25 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:16 2006