Locus 1760

Sequence ID	3R_DroMel_CAF1
Location	5,074,560 – 5,074,701
Length	141
Max. P	0.558882

overview

Window 1

Location	5,074,560 – 5,074,680
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.67
Mean single sequence MFE	-35.72
Consensus MFE	-29.27
Energy contribution	-28.50
Covariance contribution	-0.77
Combinations/Pair	1.38
Mean z-score	-1.47
Structure conservation index	0.82
SVM decision value	0.05
SVM RNA-class probability	0.558882
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5074560 120 + 27905053
CGAUGGCAAGCUGGACUAUGAUAAGCUCUUCGAGUCGCUGAAUAACCAAUCCUUCCGUCGCCGCUGGAUCAAGUCGGCCACACUCUACCUGGCCGACUGGGCCAGCUACCUGGCCAAUCC
((((((.(((...((((.(((........)))))))..((......))...))))))))).....((((..(((((((((.........))))))))).((((((....)))))).)))) ( -41.40)
>DroVir_CAF1 895 120 + 1
UGAUGGCAAGUUGGAUUAUGACAAAUUGUUCGAGUCUCUGAACAAUCAAUCAUUCCGUCGUCGCUGGAUCAAAUCGGCCACAUUGUAUUUGGCUGACUGGGCCAGUUAUUUGGCCAAUCC
.((((((.....(((..((((...((((((((......))))))))...)))))))))))))...((((....(((((((.........)))))))...((((((....)))))).)))) ( -37.90)
>DroGri_CAF1 1845 120 + 1
CGAUGGUAAAGUGGAUUAUGACAAGCUAUUCGAGUCUCUGAACAAUCAAUCCUUCCGUCGUCGCUGGAUCAAGUCGGCCACAUUAUAUUUGGCUGAUUGGACCAGCUAUUUAGCCAAUCC
((((((......(((((..(((...........)))...((....)))))))..))))))..(((((.((.(((((((((.........))))))))).))))))).............. ( -34.30)
>DroWil_CAF1 1618 120 + 1
CGAUGGCAAAUUGGACUAUGAUAAGCUCUUUGAAUCUCUGAAUAAUCAAUCGUUCCGUCGCCGCUGGAUUAAAUCGGCCACUUUGUAUUUGGCCGAUUGGGCAAGUUAUCUGGCCAAUCC
....(((....((((..(((((......(((........)))......)))))))))..)))...(((((.(((((((((.........))))))))).(((.((....)).)))))))) ( -30.30)
>DroMoj_CAF1 1834 120 + 1
CGAUGGCAAAGUCGAUUACGAUAAACUGUUCGAGUCACUGAAUAAUCAAUCCUUCCGUCGUCGCUGGAUCAAAUCGGCCACUUUGUAUUUGGCUGACUGGGCCAGCUAUAUAGCCAAUCC
.((((((..(((.((((.(((........))))))))))((....)).........))))))(((((..((..(((((((.........))))))).))..))))).............. ( -33.90)
>DroPer_CAF1 891 120 + 1
CGAUGGAAAGCUGGACUACGACAAGCUCUUCGAAUCGCUGAACAACCAAUCCUUCCGCAGGCGCUGGAUCAAGUCGGCAACGCUUUACCUUGCCGACUGGGCCAGCUAUCUCGCCAAUCC
.(((.((((((((........).)))).)))..)))((.(((..........))).)).((((((((..((.((((((((.(.....).))))))))))..)))))......)))..... ( -36.50)
>consensus
CGAUGGCAAACUGGACUAUGACAAGCUCUUCGAGUCUCUGAACAAUCAAUCCUUCCGUCGUCGCUGGAUCAAAUCGGCCACAUUGUAUUUGGCCGACUGGGCCAGCUAUCUGGCCAAUCC
.((((((......((((.(((........)))))))..........................(((((.((.(((((((((.........))))))))).)))))))......))).))). (-29.27 = -28.50 +  -0.77)

alignment

secondary structure

dotplot

Window 2

Location	5,074,600 – 5,074,701
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	83.17
Mean single sequence MFE	-29.87
Consensus MFE	-23.12
Energy contribution	-22.54
Covariance contribution	-0.58
Combinations/Pair	1.38
Mean z-score	-1.37
Structure conservation index	0.77
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5074600 101 + 27905053
AAUAACCAAUCCUUCCGUCGCCGCUGGAUCAAGUCGGCCACACUCUACCUGGCCGACUGGGCCAGCUACCUGGCCAAUCCCGAGGUGUAUCUCAGGUGAGU
.................((((((((((..((.((((((((.........))))))))))..)))))(((((((......)).))))).......))))).. ( -39.70)
>DroPse_CAF1 1049 101 + 1
AACAACCAAUCCUUCCGCAGGCGCUGGAUCAAGUCGGCAACGCUUUACCUGGCCGACUGGGCCAGCUAUCUCGCCAAUCCCGAUGUCUAUCUCAGGUGAGU
..........(((.....))).(((((..((.((((((.............))))))))..)))))...((((((...................)))))). ( -29.13)
>DroGri_CAF1 1885 101 + 1
AACAAUCAAUCCUUCCGUCGUCGCUGGAUCAAGUCGGCCACAUUAUAUUUGGCUGAUUGGACCAGCUAUUUAGCCAAUCCCGAAAAUUAUCUAAGGUGAGU
.....(((..((((........(((((.((.(((((((((.........))))))))).)))))))...............((......)).))))))).. ( -24.70)
>DroWil_CAF1 1658 101 + 1
AAUAAUCAAUCGUUCCGUCGCCGCUGGAUUAAAUCGGCCACUUUGUAUUUGGCCGAUUGGGCAAGUUAUCUGGCCAAUCCUGAUGUGUAUUUGAGGUGAGC
...........(((((.(((.(((.(((((.(((((((((.........))))))))).(((.((....)).))))))))....)))....))).).)))) ( -30.20)
>DroMoj_CAF1 1874 101 + 1
AAUAAUCAAUCCUUCCGUCGUCGCUGGAUCAAAUCGGCCACUUUGUAUUUGGCUGACUGGGCCAGCUAUAUAGCCAAUCCGGAAAACUAUCUCAGGUGAGC
............(((((....)(((((..((..(((((((.........))))))).))..)))))..............))))......(((....))). ( -23.60)
>DroPer_CAF1 931 101 + 1
AACAACCAAUCCUUCCGCAGGCGCUGGAUCAAGUCGGCAACGCUUUACCUUGCCGACUGGGCCAGCUAUCUCGCCAAUCCCGAUGUCUAUCUCAGGUGAGU
..........(((.....))).(((((..((.((((((((.(.....).))))))))))..)))))...((((((...................)))))). ( -31.91)
>consensus
AACAACCAAUCCUUCCGUCGCCGCUGGAUCAAGUCGGCCACACUGUACCUGGCCGACUGGGCCAGCUAUCUAGCCAAUCCCGAUGUCUAUCUCAGGUGAGU
......................(((((.((.(((((((((.........))))))))).)))))))...((.(((...................))).)). (-23.12 = -22.54 +  -0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:39 2006