Locus 7471

Sequence ID 3L_DroMel_CAF1
Location 20,033,945 – 20,034,094
Length 149
Max. P 0.927640
window12146 window12147 window12148

overview

Window 6

Location 20,033,945 – 20,034,055
Length 110
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 92.31
Mean single sequence MFE -23.00
Consensus MFE -22.48
Energy contribution -22.59
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.98
SVM decision value 1.18
SVM RNA-class probability 0.927640
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20033945 110 + 23771897
CAAAUUGAGGUCACACCAUCGCCACCACCACACCAUCAGUUCCACGCACACUAUUAUCUAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGU
......((((.....)).))..............(((.(((((((((................)))))))))))).(((((((.(((......)))...))).))))... ( -23.59)
>DroSec_CAF1 1086 102 + 1
CAAAUUGAGGUCACACCAUCGCCAUCA-----CCAUCAGUUCCACACACACUA---UCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUAAAGGAAGU
.....((((((.........))).)))-----((....(((((((((......---.......)))))))))(((((....)))))..................)).... ( -20.92)
>DroSim_CAF1 1082 105 + 1
CAAAUUGAGGUCACACCAUCGCCAUCA-----CCAUCAGUUCCACACACACUAUCAUCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGU
.....((((((.........))).)))-----..(((.(((((((((................)))))))))))).(((((((.(((......)))...))).))))... ( -24.49)
>consensus
CAAAUUGAGGUCACACCAUCGCCAUCA_____CCAUCAGUUCCACACACACUAU_AUCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGU
......((((.....)).))..............(((.(((((((((................)))))))))))).(((((((.(((......)))...))).))))... (-22.48 = -22.59 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,033,975 – 20,034,094
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.72
Mean single sequence MFE -30.75
Consensus MFE -26.88
Energy contribution -27.69
Covariance contribution 0.81
Combinations/Pair 1.03
Mean z-score -1.80
Structure conservation index 0.87
SVM decision value 0.86
SVM RNA-class probability 0.867527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20033975 119 + 23771897
CACCAUCAGUUCCACGCACACUAUUAUCUAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGUAUGUAGAACCGGAGGUGCGAGGGCUAACUACCCACUUCC-
....(((.(((((((((................)))))))))))).(((((((.(((......)))...))).)))).............(((((((.(.((.....)).).)))))))- ( -31.89)
>DroSec_CAF1 1113 114 + 1
--CCAUCAGUUCCACACACACUA---UCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUAAAGGAAGUAUGCAGAACCGGAGGUGCGAGGGCUAACUACCCACUUCC-
--..(((.(((((((((......---.......)))))))))))).((((.((.(((......)))...))..)))).............(((((((.(.((.....)).).)))))))- ( -28.72)
>DroSim_CAF1 1109 117 + 1
--CCAUCAGUUCCACACACACUAUCAUCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGUAUGUAGAGCCGGAGGUGCGAGGGCUAACUACCCACUUCC-
--..(((.(((((((((................))))))))))))....((((.(((......)))...)))).((((((..((((((((...........))))..))))..))))))- ( -32.89)
>DroYak_CAF1 1004 103 + 1
--CCAUCAGUUCCACACACU-------------UUGUGGAACCAUAUCCUCG--UCUAGACAAAGACAAGUGAACGAAGUAUGCAAAACCGGAGGUGCGAGGGCUAACUACCCACUUCCA
--......((((((((....-------------.))))))))(((((..(((--(((......))))..(....))).))))).......(((((((.(.((.....)).).))))))). ( -29.50)
>consensus
__CCAUCAGUUCCACACACACUA___UCCAUCAGUGUGGAACGAUAUCCUCGUGUCUAGACAAAGAAAAAUGAAGGAAGUAUGCAGAACCGGAGGUGCGAGGGCUAACUACCCACUUCC_
........(((((((((................)))))))))....(((((((.(((......)))...))).)))).............(((((((.(.((.....)).).))))))). (-26.88 = -27.69 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,033,975 – 20,034,094
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 86.72
Mean single sequence MFE -37.41
Consensus MFE -30.42
Energy contribution -31.04
Covariance contribution 0.62
Combinations/Pair 1.09
Mean z-score -2.01
Structure conservation index 0.81
SVM decision value 0.99
SVM RNA-class probability 0.896822
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20033975 119 - 23771897
-GGAAGUGGGUAGUUAGCCCUCGCACCUCCGGUUCUACAUACUUCCUUCAUUUUUCUUUGUCUAGACACGAGGAUAUCGUUCCACACUGAUAGAUAAUAGUGUGCGUGGAACUGAUGGUG
-....(.((((.....)))).).((((..(((((((((................(((((((......)))))))........(((((((........))))))).)))))))))..)))) ( -37.00)
>DroSec_CAF1 1113 114 - 1
-GGAAGUGGGUAGUUAGCCCUCGCACCUCCGGUUCUGCAUACUUCCUUUAUUUUUCUUUGUCUAGACACGAGGAUAUCGUUCCACACUGAUGGA---UAGUGUGUGUGGAACUGAUGG--
-(((((((.((((..((((...........)))))))).)))))))........(((((((......)))))))(((((((((((((.......---......))))))))).)))).-- ( -36.32)
>DroSim_CAF1 1109 117 - 1
-GGAAGUGGGUAGUUAGCCCUCGCACCUCCGGCUCUACAUACUUCCUUCAUUUUUCUUUGUCUAGACACGAGGAUAUCGUUCCACACUGAUGGAUGAUAGUGUGUGUGGAACUGAUGG--
-(((((((.((((..((((...........)))))))).)))))))........(((((((......)))))))(((((((((((((..((........))..))))))))).)))).-- ( -38.60)
>DroYak_CAF1 1004 103 - 1
UGGAAGUGGGUAGUUAGCCCUCGCACCUCCGGUUUUGCAUACUUCGUUCACUUGUCUUUGUCUAGA--CGAGGAUAUGGUUCCACAA-------------AGUGUGUGGAACUGAUGG--
.....(.((((.....)))).)...((..((((((..(((((((.((..((((((((((((....)--)))))))).)))...)).)-------------))))))..))))))..))-- ( -37.70)
>consensus
_GGAAGUGGGUAGUUAGCCCUCGCACCUCCGGUUCUACAUACUUCCUUCAUUUUUCUUUGUCUAGACACGAGGAUAUCGUUCCACACUGAUGGA___UAGUGUGUGUGGAACUGAUGG__
.(((((((.((((..((((...........)))))))).)))))))........(((((((......)))))))(((((((((((((................))))))))).))))... (-30.42 = -31.04 +   0.62)

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 12:48:02 2006