Locus 4093

Sequence ID	3R_DroMel_CAF1
Location	11,168,788 – 11,168,908
Length	120
Max. P	0.764388

overview

Window 4

Location	11,168,788 – 11,168,908
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.19
Mean single sequence MFE	-31.55
Consensus MFE	-22.10
Energy contribution	-21.47
Covariance contribution	-0.63
Combinations/Pair	1.24
Mean z-score	-1.52
Structure conservation index	0.70
SVM decision value	-0.01
SVM RNA-class probability	0.528185
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11168788 120 + 27905053
UUUUAUACCCGGUAAUUGCCCAAUACACGGGUAUAUUGUACACGCAACUGUGUUUGUCGCCAGCUGCAGAAAACACUUCCGCCCCUAUAAGUUACUUGUGUGCAUUGUGUAUUGCAAUUG
...(((((((((((.........))).))))))))(((((.((((((..((((((...((.....))...))))))....((...((((((...)))))).)).))))))..)))))... ( -29.30)
>DroSim_CAF1 9361 120 + 1
UUUUAUACCCGGUAAUUGCACAAUACACGGGUAUAUUGUACACGCAACUGUGUUUGUCGCCAGCUGCAGAAAACACUUCCGCCCCUAUAAGUUACUUGUGUGCAUUGUGUAUUGCAAUUG
...........(((((.((((((((((((((((..(((((...((....((((((...((.....))...))))))....))...)))))..)))))))))..))))))))))))..... ( -32.30)
>DroEre_CAF1 9719 120 + 1
UUGUGUACCCGGUAAUUGCACAAUACAUGGGUAUAUUGUGCUCGCAAUUGUGUUUGUUGCCAGCUGAAGAAAACGCUUCCGCCCCUAUAUGUUUCUUAUAUGCAGUGGGUAUUGCAACUA
((((((((((((((((.(((((((...(((((((...)))))))..)))))))..)))))).((.((((......)))).))...((((((.....))))))....))))).)))))... ( -35.30)
>DroYak_CAF1 9679 120 + 1
UUGUGUACCCGGUAAUUGCACAAUACAUGGGUAUAUUGUGUUCGCAACUGUGUUUGUCGCAAGCUGAAGCAAACACUUCCGCCCCUAUAAGAUAUUUUUGUGCAUUGUAUAUUGCACCUA
..(((((....(((..(((((((.....((((...((((....))))..((((((((..(.....)..))))))))....))))(.....)......)))))))...)))..)))))... ( -29.30)
>consensus
UUGUAUACCCGGUAAUUGCACAAUACACGGGUAUAUUGUACACGCAACUGUGUUUGUCGCCAGCUGAAGAAAACACUUCCGCCCCUAUAAGUUACUUGUGUGCAUUGUGUAUUGCAACUA
...(((((((((((.........))).))))))))..((((((((....((((((...((.....))...))))))....))...((((((.....))))))....))))))........ (-22.10 = -21.47 +  -0.63)

alignment

secondary structure

dotplot

Window 5

Location	11,168,788 – 11,168,908
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.19
Mean single sequence MFE	-32.31
Consensus MFE	-23.09
Energy contribution	-23.90
Covariance contribution	0.81
Combinations/Pair	1.07
Mean z-score	-2.01
Structure conservation index	0.71
SVM decision value	0.51
SVM RNA-class probability	0.764388
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11168788 120 - 27905053
CAAUUGCAAUACACAAUGCACACAAGUAACUUAUAGGGGCGGAAGUGUUUUCUGCAGCUGGCGACAAACACAGUUGCGUGUACAAUAUACCCGUGUAUUGGGCAAUUACCGGGUAUAAAA
.........(((((...((((....((..(.....)..))....)))).....(((((((..........))))))))))))...((((((((.(((.........)))))))))))... ( -34.00)
>DroSim_CAF1 9361 120 - 1
CAAUUGCAAUACACAAUGCACACAAGUAACUUAUAGGGGCGGAAGUGUUUUCUGCAGCUGGCGACAAACACAGUUGCGUGUACAAUAUACCCGUGUAUUGUGCAAUUACCGGGUAUAAAA
.........(((((...((((....((..(.....)..))....)))).....(((((((..........))))))))))))...((((((((.(((.........)))))))))))... ( -34.00)
>DroEre_CAF1 9719 120 - 1
UAGUUGCAAUACCCACUGCAUAUAAGAAACAUAUAGGGGCGGAAGCGUUUUCUUCAGCUGGCAACAAACACAAUUGCGAGCACAAUAUACCCAUGUAUUGUGCAAUUACCGGGUACACAA
.........(((((..((((...((((((.......(.((....)).)))))))....((....))........)))).((((((((((....)))))))))).......)))))..... ( -29.91)
>DroYak_CAF1 9679 120 - 1
UAGGUGCAAUAUACAAUGCACAAAAAUAUCUUAUAGGGGCGGAAGUGUUUGCUUCAGCUUGCGACAAACACAGUUGCGAACACAAUAUACCCAUGUAUUGUGCAAUUACCGGGUACACAA
...((((.........(((((((........(((((((((.(((((....))))).))(((((((.......)))))))..........))).)))))))))))........)))).... ( -31.33)
>consensus
CAAUUGCAAUACACAAUGCACACAAGUAACUUAUAGGGGCGGAAGUGUUUUCUGCAGCUGGCGACAAACACAGUUGCGAGCACAAUAUACCCAUGUAUUGUGCAAUUACCGGGUACAAAA
....((((........))))...............(((((.((((......)))).))).(((((.......)))))..((((((((((....)))))))))).....)).......... (-23.09 = -23.90 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:57 2006