Locus 7487

Sequence ID	2L_DroMel_CAF1
Location	20,792,281 – 20,792,429
Length	148
Max. P	0.779314

overview

Window 5

Location	20,792,281 – 20,792,392
Length	111
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	94.59
Mean single sequence MFE	-23.58
Consensus MFE	-18.84
Energy contribution	-19.08
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.61
Structure conservation index	0.80
SVM decision value	0.24
SVM RNA-class probability	0.648437
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20792281 111 + 22407834
AUGGAGUUAUCAAAUAAUACAAAAU-UCAAUUGAAGUUUUUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCU
...(((((..............)))-))......((((((((((......(((((((((((....)))))))))-------))..........((.....)).......)))))))))) ( -23.54)
>DroSec_CAF1 15476 111 + 1
AUGGAGUUAUCAAAUAAUGCAAAAU-UCAAUUGAAGUUUUUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCU
...(((((..((.....))...)))-))......((((((((((......(((((((((((....)))))))))-------))..........((.....)).......)))))))))) ( -23.70)
>DroSim_CAF1 19009 111 + 1
AUGGAGUUAUCAAAUAAUACAAAAU-UCAAUUGAAGUUUUUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCU
...(((((..............)))-))......((((((((((......(((((((((((....)))))))))-------))..........((.....)).......)))))))))) ( -23.54)
>DroEre_CAF1 18788 111 + 1
GUGGAGUUAUCAAAUAAUACGAAAUUUCAAUUGAAGUU-UUUACGAGUGCGGCUAGGCAAAUGAUUUCGCUUGG-------UCAUGGAAGAUAUCAAAGUGGAAAAAGAGUGAAAGGCU
....((((.(((........((((((((....))))))-))......(((......)))..)))((((((((..-------((((.((.....))...)))).....)))))))))))) ( -18.60)
>DroYak_CAF1 16267 119 + 1
AUGGAGUUAUCAAAUAAUAAAAAAUUUCAAUUGAAGUUUUUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGGUCAUUGGUCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCU
.(((((((..............))))))).....((((((((((......(((((((((((....))))))))))).((..((((.((.....))...))))..))...)))))))))) ( -28.54)
>consensus
AUGGAGUUAUCAAAUAAUACAAAAU_UCAAUUGAAGUUUUUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG_______UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCU
..................................((((((((((........(((((((((....))))))))).......((((.((.....))...)))).......)))))))))) (-18.84 = -19.08 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	20,792,319 – 20,792,429
Length	110
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	91.61
Mean single sequence MFE	-30.88
Consensus MFE	-22.48
Energy contribution	-22.72
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.32
Structure conservation index	0.73
SVM decision value	0.55
SVM RNA-class probability	0.779314
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20792319 110 + 22407834
UUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCUUGGAAUGCUCUUUAGUGCUUAGCGCUUUUAAUUGUGU
.(((.(((((((((((((((((....)))))))))-------)).............(((((...(((((((..............)))))))..))))).)))))).)))...... ( -31.24)
>DroSec_CAF1 15514 110 + 1
UUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCUUGGAAUGCUCUUUAGCGCUUAGCGCUUUUAAUUGUGU
.(((.(((((((((((((((((....)))))))))-------)).............(((((...(((((((..............)))))))..))))).)))))).)))...... ( -33.64)
>DroSim_CAF1 19047 110 + 1
UUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG-------UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCUUGGAAUGCUCUUUAGCGCUUAGCGCUUUUAAUUGUGU
.(((.(((((((((((((((((....)))))))))-------)).............(((((...(((((((..............)))))))..))))).)))))).)))...... ( -33.64)
>DroEre_CAF1 18826 103 + 1
UUUACGAGUGCGGCUAGGCAAAUGAUUUCGCUUGG-------UCAUGGAAGAUAUCAAAGUGGAAAAAGAGUGAAAGGCUCGGAAUGCUCUUUA-------CCGCUUUUAAUUGUGU
..(((((....((((((((.((....)).))))))-------))............(((((((..(((((((..............))))))).-------)))))))...))))). ( -25.24)
>DroYak_CAF1 16306 109 + 1
UUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGGUCAUUGGUCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCUCG-AAUGCUCUUUA-------GCGCUUUUAAUUGUGU
.(((.(((((((((((((((((....))))))))))).....((((.((.....))...))))..(((((((..........-...))))))).-------)))))).)))...... ( -30.62)
>consensus
UUUACGAGUGCGGCUAGGCAAAUGAUUUUGCUUGG_______UCAUGGAAGAUAUCAAAGUGAAAAAAGAGUGAAAGGCUUGGAAUGCUCUUUAG_GCUUAGCGCUUUUAAUUGUGU
.(((.((((((..(((((((((....))))))))).......((((.((.....))...))))..(((((((..............)))))))........)))))).)))...... (-22.48 = -22.72 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:03 2006