Locus 1664

Sequence ID 2R_DroMel_CAF1
Location 6,283,898 – 6,284,041
Length 143
Max. P 0.991396
window2781 window2782

overview

Window 1

Location 6,283,898 – 6,284,002
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.90
Mean single sequence MFE -24.46
Consensus MFE -7.30
Energy contribution -8.58
Covariance contribution 1.28
Combinations/Pair 1.08
Mean z-score -1.82
Structure conservation index 0.30
SVM decision value -0.03
SVM RNA-class probability 0.518446
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6283898 104 + 20766785
GCCGCCAACCAUUUUAGCUUUGACC--------AAGUUACGCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAAA-
(((((((....((((((.((((.((--------..(.....)..))))))))-------))))..........((...((((((....))))))..))......)))).))).......- ( -25.10)
>DroSec_CAF1 26512 101 + 1
GC---CAACCAUUUUAGCUUUGACC--------AAGUUACGCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAUA-
((---(.....((((((.((((.((--------..(.....)..))))))))-------))))..........((((((........))))))...(((......))).))).......- ( -22.50)
>DroEre_CAF1 27447 109 + 1
GC---CAACCAUUUUAGCUUUGACC--------AAGUUACGCACUGCAAACUAAAAACUAAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAGUA
((---(.....((((((.((((...--------.(((.....))).)))))))))).................((((((........))))))...(((......))).)))........ ( -21.60)
>DroYak_CAF1 29774 101 + 1
GC---CAACCAUUUUAGCUUUGACC--------AAGUUACGCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAGA-
((---(.....((((((.((((.((--------..(.....)..))))))))-------))))..........((((((........))))))...(((......))).))).......- ( -22.50)
>DroAna_CAF1 28308 101 + 1
GU---CAAUCACUUCAGCUGCGCCCGAAUGGCUGAGUGGCGAAUGGCGGCCC-------AAAAAUGCACAAUUGCAAGUGCAGUGGCA-------GGCCCGAUAUGGAUUGGA-AUAAA-
.(---(((((...((.(((.(((((..........).))))...)))((((.-------.....(((((........)))))......-------)))).))....)))))).-.....- ( -30.60)
>consensus
GC___CAACCAUUUUAGCUUUGACC________AAGUUACGCACGGCAAACU_______AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAAA_
................((((.....................................................((((((........))))))...(((......)))))))........ ( -7.30 =  -8.58 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,283,930 – 6,284,041
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.49
Mean single sequence MFE -22.22
Consensus MFE -9.10
Energy contribution -10.58
Covariance contribution 1.48
Combinations/Pair 1.12
Mean z-score -2.36
Structure conservation index 0.41
SVM decision value 2.27
SVM RNA-class probability 0.991396
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6283930 111 + 20766785
GCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAAA--CAAAAAAAAAAAACAUACACAUACAUAAGUGUGUGUAUA
.....((.....-------..............((((((........))))))...(((......)))..)).......--..............((((((((((....)))))))))). ( -24.50)
>DroSec_CAF1 26541 92 + 1
GCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAUA--CAACAA------ACAUAUA------UA------UGUAU-
............-------..............((((((........))))))...(((......)))..(((((((((--......------...))))------))------)))..- ( -16.40)
>DroEre_CAF1 27476 111 + 1
GCACUGCAAACUAAAAACUAAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAGUAUAAACAUAU-ACAGCAU------ACAUA--UGUGUGUAUA
((.((((..........................((((((........))))))(((....)))...)))))).....(((((....)))-)).((((------((...--.))))))... ( -24.30)
>DroYak_CAF1 29803 107 + 1
GCACGGCAAACU-------AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAGA--CAAUAUAU-ACAAUAUAUACA-ACAUA--UGUGUGUAUA
.....((.....-------..............((((((........))))))...(((......)))..))(((((..--...)))))-...(((((((((-.....--))))))))). ( -20.00)
>DroAna_CAF1 28345 103 + 1
GAAUGGCGGCCC-------AAAAAUGCACAAUUGCAAGUGCAGUGGCA-------GGCCCGAUAUGGAUUGGA-AUAAA--CAAUAUAGUAUAGUAUAGUACUAUAUGGUGCUCUGUAUG
..((((.(((((-------.....(((...(((((....))))).)))-------...(((((....))))).-.....--..(((((((((......))))))))))).)))))))... ( -25.90)
>consensus
GCACGGCAAACU_______AAAAAUAUACAUUCGCAAUUGCAAUCGAAAUUGCAUCGCCCGAUAUGGCAGGCAUAUAAA__CAACAUAU_ACAACAUAUA___ACAUA__UGUGUGUAUA
.......................(((((((...((((((........))))))...(((......)))............................................))))))). ( -9.10 = -10.58 +   1.48)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:09 2006