Locus 4219

Sequence ID	2R_DroMel_CAF1
Location	13,859,569 – 13,859,669
Length	100
Max. P	0.981096

overview

Window 5

Location	13,859,569 – 13,859,669
Length	100
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.76
Mean single sequence MFE	-21.92
Consensus MFE	-14.57
Energy contribution	-14.90
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.57
Structure conservation index	0.66
SVM decision value	1.88
SVM RNA-class probability	0.981096
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13859569 100 + 20766785
AAGA---AGCCAGAAG----ACGGAGCAGGGAGAAAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUCGACAUAAGUAGAUGUCGGGCC
....---.(((....(----(((..((..((.....(((((((((......))))))))).)).(((((((((.(........))))))))))))...)))).))). ( -28.20)
>DroVir_CAF1 198177 87 + 1
----------CAAGCC----AAGCAGC------ACAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUCGACAUAAGUAGAUGCCGUCGC
----------...((.----..((.((------((........((((((.........))))))(((((((((.(........))))))))))...).))).)).)) ( -20.00)
>DroPse_CAF1 156084 101 + 1
AAGAAGAGGAUAGAAGGAGCAUGGAGAAGAGAG-AAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUAGACAUAAGUAGU-----GGCC
.................................-..(((((((((......)))))))))(((((((((((..((........)).))))))....))-----))). ( -18.50)
>DroGri_CAF1 188391 94 + 1
GCCA---AGCCAAGCC----AAGCAGC------ACAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUCGACAUAAGUAGAUGCCGUACA
....---.........----..((.((------((........((((((.........))))))(((((((((.(........))))))))))...).))).))... ( -20.30)
>DroEre_CAF1 160480 99 + 1
AAGA---AGCCAGAAG----AUGGAGCAGGGAGAA-AAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUCGACAUAAGUAGAUGUCGGGCC
....---.(((....(----(((..((..((....-(((((((((......))))))))).)).(((((((((.(........))))))))))))...)))).))). ( -26.40)
>DroPer_CAF1 156696 101 + 1
AAGAAGAGGAUAGAAGGAGCAUGGAGAAGAGAG-AAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUAGACAUAAGUAGC-----GACC
...............(..((.(((.........-..(((((((((......))))))))).)))(((((((..((........)).)))))))...))-----..). ( -18.10)
>consensus
AAGA___AGCCAGAAG____AUGGAGCAG_GAGAAAAAAAUGUUGGCAAUACAAUAUUUUGCCAUUAUGUCGAACAAUAACAAGUCGACAUAAGUAGAUG_CGGGCC
...........................................((((((.........))))))(((((((((.(........)))))))))).............. (-14.57 = -14.90 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	13,859,569 – 13,859,669
Length	100
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.76
Mean single sequence MFE	-20.55
Consensus MFE	-14.17
Energy contribution	-14.50
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.41
Structure conservation index	0.69
SVM decision value	1.77
SVM RNA-class probability	0.976628
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13859569 100 - 20766785
GGCCCGACAUCUACUUAUGUCGACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUUUCUCCCUGCUCCGU----CUUCUGGCU---UCUU
((((.(((......((((((((((........).)))))))))((((((.........)))))).....................))----)....))))---.... ( -23.20)
>DroVir_CAF1 198177 87 - 1
GCGACGGCAUCUACUUAUGUCGACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUGU------GCUGCUU----GGCUUG----------
.(((((((((....((((((((((........).)))))))))((((((.........))))))........))------)))).))----).....---------- ( -24.30)
>DroPse_CAF1 156084 101 - 1
GGCC-----ACUACUUAUGUCUACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUU-CUCUCUUCUCCAUGCUCCUUCUAUCCUCUUCUU
(((.-----.....(((((((.((........))..)))))))((((((.........)))))).........-.............)))................. ( -13.90)
>DroGri_CAF1 188391 94 - 1
UGUACGGCAUCUACUUAUGUCGACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUGU------GCUGCUU----GGCUUGGCU---UGGC
.....(((((....((((((((((........).)))))))))((((((.........))))))........))------)))(((.----(((...)))---.))) ( -24.40)
>DroEre_CAF1 160480 99 - 1
GGCCCGACAUCUACUUAUGUCGACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUU-UUCUCCCUGCUCCAU----CUUCUGGCU---UCUU
((((.((.......((((((((((........).)))))))))((((((.........)))))).......-...............----..)).))))---.... ( -22.10)
>DroPer_CAF1 156696 101 - 1
GGUC-----GCUACUUAUGUCUACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUU-CUCUCUUCUCCAUGCUCCUUCUAUCCUCUUCUU
((..-----((...(((((((.((........))..)))))))((((((.........)))))).........-.............)).))............... ( -15.40)
>consensus
GGCCCG_CAUCUACUUAUGUCGACUUGUUAUUGUUCGACAUAAUGGCAAAAUAUUGUAUUGCCAACAUUUUUUUCUC_CUGCUCCAU____CUUCUGGCU___UCUU
..............((((((((((........).)))))))))((((((.........))))))........................................... (-14.17 = -14.50 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:32 2006