Locus 3044

Sequence ID 2R_DroMel_CAF1
Location 10,499,167 – 10,499,299
Length 132
Max. P 0.990135
window5014 window5015

overview

Window 4

Location 10,499,167 – 10,499,270
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.50
Mean single sequence MFE -35.07
Consensus MFE -32.97
Energy contribution -33.47
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.40
Structure conservation index 0.94
SVM decision value 2.20
SVM RNA-class probability 0.990135
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10499167 103 + 20766785
U---CAAAAA------A----AAAAAAAUCUC----AAGUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
.---......------.----...........----..((((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..)))))..... ( -36.00)
>DroVir_CAF1 17328 112 + 1
UCAAUUUAAU----AAA----AAAAAAAUCCCAAUCACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
..........----...----..................(((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..))))...... ( -32.10)
>DroGri_CAF1 14238 114 + 1
UCAAUUUGCCACACAAA----AAAAGAAGCUCAA--AGUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCACUCGGCCACGCUAC
.......((((.((...----.............--.))))))(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).. ( -34.13)
>DroSim_CAF1 12480 110 + 1
U---CAAAAA----AAAAAAAAAAAAAAUCUCA---AAGUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
.---......----...................---..((((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..)))))..... ( -36.00)
>DroEre_CAF1 12705 98 + 1
G---G-----------A----AAAAAAAUCGC----AUGUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
.---.-----------.----.........((----..((((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..)))))))... ( -36.20)
>DroYak_CAF1 12733 98 + 1
A---A-----------A----AAAAAAAUCCU----AAGUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
.---.-----------.----...........----..((((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..)))))..... ( -36.00)
>consensus
U___C__AA_______A____AAAAAAAUCUC____AAGUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUAC
......................................((((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).))))..)))))..... (-32.97 = -33.47 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,499,190 – 10,499,299
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.53
Mean single sequence MFE -39.35
Consensus MFE -32.85
Energy contribution -32.85
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.83
SVM decision value -0.02
SVM RNA-class probability 0.522336
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10499190 109 + 20766785
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCCAUAAUC-AU--C-GCUGGUCAUAA-------GCGCUUC
((((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).)))).(((((.((...........-..--.-)))))))....-------..))).. ( -36.44)
>DroVir_CAF1 17360 111 + 1
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCCCGUGUCCGAGUG--UCGCUCAAAU-------AUAUUGC
.(.(((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).(((((((.((((......)))).)))))))--.)))))....-------....... ( -42.70)
>DroGri_CAF1 14272 109 + 1
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCACUCGGCCACGCUACCAAACAGCCGAUCGAGCCACCAAAAU-------AC----C
(((.(((.((((.......))))))).((..(((.(.(((((.......)))))).)))..))....(((((..............)))))....)))........-------..----. ( -33.94)
>DroEre_CAF1 12723 116 + 1
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCCAUAAUU-GC--G-UUCGGUCAGAACGCUUUUGCGCUUA
((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))..(((..-((--(-(((.....))))))..)))...... ( -42.40)
>DroMoj_CAF1 16995 110 + 1
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUGUGGCUGGCCG---CGUUCAAAU-------ACAUUUC
.(((((((((((.......)))))...((..(((.(.(((((.......)))))).)))..)).)))).(((((.(((((...)))))))))))---)........-------....... ( -44.20)
>DroAna_CAF1 13815 111 + 1
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCACUGAGU-UC-CAAGGCGACAAAAA-------ACACUUC
((..(((.((((.......)))))))..))((((...(((((.......)))))((((((.((..((((((...........))))))-))-.)))))).......-------...)))) ( -36.40)
>consensus
GGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAAUAAGC_GA_CG_GCCGCUCAAAA_______ACACUUC
((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))....................................... (-32.85 = -32.85 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:55 2006