Locus 8350

Sequence ID	3L_DroMel_CAF1
Location	21,899,712 – 21,899,861
Length	149
Max. P	0.883542

overview

Window 2

Location	21,899,712 – 21,899,822
Length	110
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	96.21
Mean single sequence MFE	-28.97
Consensus MFE	-27.36
Energy contribution	-27.68
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.94
SVM decision value	0.93
SVM RNA-class probability	0.883542
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21899712 110 - 23771897
GCGGUAUUUGCGGAGCCUCGAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAACACAACUGCACACAAGAUAAACCUCAAAAUUCAUUUCAUG
(((((...((((((((((((((((........))))))....))))))).)))....((((....)))).....)))))............................... ( -29.80)
>DroSec_CAF1 20454 110 - 1
GCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAGCACAACUGCACACAAGAUAAACCUCAAAAUUCAUUUCAAG
(((((...((((((((((((((((........))))))....)))))))........((((....)))))))..)))))............................... ( -30.90)
>DroSim_CAF1 21102 110 - 1
GCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAGCACAACUGCACACAAGAUAAACCUCAAAAUUCAUUUCAAG
(((((...((((((((((((((((........))))))....)))))))........((((....)))))))..)))))............................... ( -30.90)
>DroYak_CAF1 25812 110 - 1
GCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGACUCCAGCAUUAAUUUGGCAACCGAACACAACUGCACAAAAGAUAAACCUCAAACUUCAUUUCAAG
(((((...((((((((((((((((........))))))...))).)))).)))....(((((...)))))....)))))............................... ( -24.30)
>consensus
GCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAACACAACUGCACACAAGAUAAACCUCAAAAUUCAUUUCAAG
(((((...((((((((((((((((........))))))....))))))).)))....((((....)))).....)))))............................... (-27.36 = -27.68 +   0.31)

alignment

secondary structure

dotplot

Window 3

Location	21,899,752 – 21,899,861
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	87.71
Mean single sequence MFE	-32.40
Consensus MFE	-23.98
Energy contribution	-25.74
Covariance contribution	1.76
Combinations/Pair	1.10
Mean z-score	-1.94
Structure conservation index	0.74
SVM decision value	0.54
SVM RNA-class probability	0.773375
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21899752 109 - 23771897
AUUGCAGUGCAUACCAAGUGGGUAUUUCAGAAAUCCAAUGCGGUAUUUGCGGAGCCUCGAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAA
.....((((((((((...(((((.........)))))....)))))...((((((((((((((........))))))....)))))))))))))..((((....)))). ( -35.60)
>DroSec_CAF1 20494 109 - 1
AUUGCAGUGCAUACCAAGUGGGUAUUUGAGAAAUCCAAUGCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAG
.....(((((....((((((.(((((.((....)).)))))..))))))((((((((((((((........))))))....)))))))))))))..((((....)))). ( -36.00)
>DroSim_CAF1 21142 109 - 1
AUUGCAGUGCAUACCAAGUGGGUAUUUCAGAAAUCCAAUGCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAG
.....((((((((((...(((((.........)))))....)))))...((((((((((((((........))))))....)))))))))))))..((((....)))). ( -35.90)
>DroEre_CAF1 21071 93 - 1
AUUGCUGUGCAUAACAAGUGGGUAUUUGAAAACCCCAAUGCGGUAUCUGCGGAGCCUCAAGAGCACGAAA-UGCU---------CUCC------CAUUUGGCAACAGAA
....((((((....((((((((................((.(((.((....))))).))((((((.....-))))---------))))------)))))))).)))).. ( -26.00)
>DroYak_CAF1 25852 109 - 1
AUUGCAGUGCAUACCAAGUGGGUUAUUGAGAUAUCCAAUGCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGACUCCAGCAUUAAUUUGGCAACCGAA
.((((((((((((((...(((((.........)))))....)))))....(((((((((((((........))))))...))).)))).)))))......))))..... ( -28.50)
>consensus
AUUGCAGUGCAUACCAAGUGGGUAUUUGAGAAAUCCAAUGCGGUAUUUGCGGAGCCUCAAGAGCACGAAAAUUCUUGGCAAGGGCUCCGGCAUUAAUUUGGCAACAGAA
...((((...(((((...(((((.........)))))....)))))))))(((((((((((((........))))))....)))))))........((((....)))). (-23.98 = -25.74 +   1.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:14 2006