Locus 3568

Sequence ID	3R_DroMel_CAF1
Location	9,668,827 – 9,668,987
Length	160
Max. P	0.998817

overview

Window 3

Location	9,668,827 – 9,668,947
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.39
Mean single sequence MFE	-26.21
Consensus MFE	-25.42
Energy contribution	-25.42
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.23
Structure conservation index	0.97
SVM decision value	0.84
SVM RNA-class probability	0.862921
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9668827 120 - 27905053
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAGCCAGCCAACCAACCAACUAGAGAUCCACUUAGGUAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).))))))))...................(((.(((.....))).)))....(((((....))))).. ( -25.90)
>DroSec_CAF1 60635 116 - 1
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG----CCAACCAACCAACUAGAGAUCCACUUAGGCAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).))))))))...(----((.........................)))....(((((....))))).. ( -26.51)
>DroSim_CAF1 63541 116 - 1
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG----CCAACCAACCAACUAGAGAUCCACUUAGGCAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).))))))))...(----((.........................)))....(((((....))))).. ( -26.51)
>DroEre_CAF1 61461 112 - 1
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAA--------CCAUCCAACUAGAGAUCCACUUAGGCAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).))))))))....--------...........((((((.............)))))).......... ( -25.42)
>DroYak_CAF1 65416 112 - 1
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG--------CCAUCCAACUAGAGAUCCACUUAGGCAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).))))))))...(--------((.....................)))....(((((....))))).. ( -26.70)
>consensus
UAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG____CCAACCAACCAACUAGAGAUCCACUUAGGCAAAAGAUCUUCGCAGAUUAU
....((((((((.((((((((........)))).....((.......)))))).)))))))).......................((((((.............)))))).......... (-25.42 = -25.42 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	9,668,867 – 9,668,987
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.39
Mean single sequence MFE	-37.64
Consensus MFE	-34.30
Energy contribution	-34.50
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.19
Structure conservation index	0.91
SVM decision value	3.24
SVM RNA-class probability	0.998817
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9668867 120 - 27905053
GAACGAUCGGAGCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAGCCAGCCAACCAACC
....((((((......))))))(((((..(((((((...)))))((((((((.((((((((........)))).....((.......)))))).)))))))))))))))........... ( -38.20)
>DroSec_CAF1 60675 116 - 1
GAACGAUCGGAGCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG----CCAACCAACC
....((((((......))))))(((((..(((((((...)))))((((((((.((((((((........)))).....((.......)))))).))))))))))))----)))....... ( -38.20)
>DroSim_CAF1 63581 116 - 1
GAACGAUCGGAGCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG----CCAACCAACC
....((((((......))))))(((((..(((((((...)))))((((((((.((((((((........)))).....((.......)))))).))))))))))))----)))....... ( -38.20)
>DroEre_CAF1 61501 112 - 1
GAACGAUCGGAGCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAA--------CCAUCC
.......((((((.(.......).))))))((((((...))))))(((((((.((((((((........)))).....((.......)))))).))))))).....--------...... ( -35.60)
>DroYak_CAF1 65456 112 - 1
GAACGAUCGGACCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG--------CCAUCC
....((((((......))))))(((((..(((((((...)))))((((((((.((((((((........)))).....((.......)))))).))))))))))))--------)))... ( -38.00)
>consensus
GAACGAUCGGAGCGAAUCGAUCUGGCUCCGGGUUAGACACUAACUGGGCUCAUCAUGGAGCGUUAACAAGCUCAUUUUUCUAAACUUGACGUGCUGAGUCCACCAG____CCAACCAACC
.......((((((.(.......).))))))((((((...))))))(((((((.((((((((........)))).....((.......)))))).)))))))................... (-34.30 = -34.50 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:27 2006