Locus 1514

Sequence ID	3L_DroMel_CAF1
Location	4,353,754 – 4,353,844
Length	90
Max. P	0.999879

overview

Window 5

Location	4,353,754 – 4,353,844
Length	90
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	93.06
Mean single sequence MFE	-23.68
Consensus MFE	-21.47
Energy contribution	-21.87
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.72
Structure conservation index	0.91
SVM decision value	4.36
SVM RNA-class probability	0.999879
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4353754 90 + 23771897
UUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACU---UUUAUUUGGGCUGCAACUUCUACUACUGCCCACCUUUUGGCGCCGAGCCAAGC
(((((((((((...((..............(((((..---......))))).(((...........)))..))..)))))))))))....... ( -24.30)
>DroSec_CAF1 4425 87 + 1
UUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACU---UGUUUUCGGGCUGCAACUUCUA---CUGCCCACCUUUUGGCGCCGAGCCAAGC
(((((((((((...(((.........)))........---.......((((...........---..))))....)))))))))))....... ( -24.22)
>DroSim_CAF1 4422 87 + 1
UUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACU---UGUUUUCGGGCUGCAACUUCUA---CUGCCCACCUUUUGGCGCCGAGCCAAGC
(((((((((((...(((.........)))........---.......((((...........---..))))....)))))))))))....... ( -24.22)
>DroEre_CAF1 4474 85 + 1
CUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACU-----UUUUCGGGCUGCAACUUCUA---CUGCCCACCUUUUGGCGCCGAGCCAAGC
.((((((((((...((..............((((...-----.....)))).(((.......---.)))..))..))))))))))........ ( -23.20)
>DroYak_CAF1 4475 90 + 1
UUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACUAUUUUUUUUUGGCCCGCAACUUCUA---GUGCCCACCUUUUGGCGCCGAGCCAAGC
(((((((((((...((..............(((..............)))..(((.......---.)))..))..)))))))))))....... ( -22.44)
>consensus
UUGGCGCCAAAUUUGUAUAAAUUUUCUACUGCCUACU___UGUUUUCGGGCUGCAACUUCUA___CUGCCCACCUUUUGGCGCCGAGCCAAGC
(((((((((((...(((.........)))..................((((................))))....)))))))))))....... (-21.47 = -21.87 +   0.40)

alignment

secondary structure

dotplot

Window 6

Location	4,353,754 – 4,353,844
Length	90
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-26.52
Consensus MFE	-23.15
Energy contribution	-23.11
Covariance contribution	-0.04
Combinations/Pair	1.06
Mean z-score	-2.60
Structure conservation index	0.87
SVM decision value	3.55
SVM RNA-class probability	0.999378
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4353754 90 - 23771897
GCUUGGCUCGGCGCCAAAAGGUGGGCAGUAGUAGAAGUUGCAGCCCAAAUAAA---AGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAA
.........(((((((((...(((((.((((......)))).)))))......---........(((.........)))...))))))))).. ( -28.40)
>DroSec_CAF1 4425 87 - 1
GCUUGGCUCGGCGCCAAAAGGUGGGCAG---UAGAAGUUGCAGCCCGAAAACA---AGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAA
.........(((((((((...(((((.(---(((...)))).)))))......---........(((.........)))...))))))))).. ( -26.50)
>DroSim_CAF1 4422 87 - 1
GCUUGGCUCGGCGCCAAAAGGUGGGCAG---UAGAAGUUGCAGCCCGAAAACA---AGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAA
.........(((((((((...(((((.(---(((...)))).)))))......---........(((.........)))...))))))))).. ( -26.50)
>DroEre_CAF1 4474 85 - 1
GCUUGGCUCGGCGCCAAAAGGUGGGCAG---UAGAAGUUGCAGCCCGAAAA-----AGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAG
.........(((((((((...(((((.(---(((...)))).)))))....-----........(((.........)))...))))))))).. ( -26.50)
>DroYak_CAF1 4475 90 - 1
GCUUGGCUCGGCGCCAAAAGGUGGGCAC---UAGAAGUUGCGGGCCAAAAAAAAAUAGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAA
..(((((((..((((....)))).(((.---.......))))))))))............(((.((...((((((....)))))).))))).. ( -24.70)
>consensus
GCUUGGCUCGGCGCCAAAAGGUGGGCAG___UAGAAGUUGCAGCCCGAAAAAA___AGUAGGCAGUAGAAAAUUUAUACAAAUUUGGCGCCAA
.........(((((((((...(((((................))))).................(((.........)))...))))))))).. (-23.15 = -23.11 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:09:35 2006