Locus 1165

Sequence ID	3L_DroMel_CAF1
Location	3,359,974 – 3,360,094
Length	120
Max. P	0.907677

overview

Window 4

Location	3,359,974 – 3,360,094
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.08
Mean single sequence MFE	-34.14
Consensus MFE	-27.48
Energy contribution	-27.08
Covariance contribution	-0.40
Combinations/Pair	1.22
Mean z-score	-1.87
Structure conservation index	0.80
SVM decision value	1.05
SVM RNA-class probability	0.907677
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3359974 120 + 23771897
GGCGGCUAUCGAGGCUUUUCAACGUGACUUUAAGGCCACGGAAAUUGAGCUACAAGACUUUGAAAAAGUUCUGACCAAGCAGAAAUCCUCGCUCACUCAAAGCCAAAUAGAUGGCUACUA
((..((((((..((((((....((((.((....)).)))).....(((((..((..((((.....))))..))........((.....)))))))...)))))).....))))))..)). ( -32.50)
>DroSec_CAF1 27158 120 + 1
AGCGGCUAUCGAGGCUUUUCAGCGUGACUUUGAAGCCACGGAAAUUGAGUUGCAAGACUUUGAAAAAGUUCUGGUUAAGCAGAAAUCCUCGCUCACUCAAAGCCAAAUAGAUGGUUACUA
((..((((((..((((((..((.....))..))))))..((...((((((.((.((..(((....)))(((((......)))))...)).))..))))))..)).....))))))..)). ( -33.00)
>DroSim_CAF1 24847 120 + 1
AGCGGCUAUCGAGGCUUUUCAGCGUGACUUUGAGGCCACGGAAAUUGAGCUACAAGACUUUGAAAAAGUUCUGGUUAAGCAGAAAUCCUCGCUCACUCAAAGCCAAAUAGAUGGCUACUA
((..((((((((((..((((..((((.((....)).))))........(((.((..((((.....))))..))....))).)))).))))(((.......)))......))))))..)). ( -32.90)
>DroEre_CAF1 25723 120 + 1
GGCGGCUAUCGAGGCUUUUCAGCGUGAUUUUGAGGCCACAGAAAUUGAUCUACAAGAUUUUGAAAAAGUUUUGGCCAAGCAGAAAUCCUCACUCACUCAAAGCCAAAUAGAUGGCUACUA
((..((((((..((((((...(.(((((((((.((((..(((......)))..(((((((.....)))))))))))...)))))....)))).)....)))))).....))))))..)). ( -31.80)
>DroYak_CAF1 25711 120 + 1
GGCGGCCAUUGAGGCUUUUCAGCGUGAUUUUGAGGCCACUGAAAUUGAGCUGAAGGACUUUGAAAAAGUUCUGGCCAAGCAGAAAUCCUCACUCACUCAAAGCCAAAUAGAUGGCUACUA
((..((((((..((((((...(.((((...(((((...(((...(((.(((..(((((((.....))))))))))))).)))....))))).)))).))))))).....))))))..)). ( -40.50)
>consensus
GGCGGCUAUCGAGGCUUUUCAGCGUGACUUUGAGGCCACGGAAAUUGAGCUACAAGACUUUGAAAAAGUUCUGGCCAAGCAGAAAUCCUCGCUCACUCAAAGCCAAAUAGAUGGCUACUA
((..((((((..((((((...(.((((...(((((...((((..(((.....)))...))))......(((((......)))))..))))).)))).))))))).....))))))..)). (-27.48 = -27.08 +  -0.40)

alignment

secondary structure

dotplot

Window 5

Location	3,359,974 – 3,360,094
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.08
Mean single sequence MFE	-33.16
Consensus MFE	-27.36
Energy contribution	-27.40
Covariance contribution	0.04
Combinations/Pair	1.19
Mean z-score	-1.52
Structure conservation index	0.83
SVM decision value	0.54
SVM RNA-class probability	0.773116
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3359974 120 - 23771897
UAGUAGCCAUCUAUUUGGCUUUGAGUGAGCGAGGAUUUCUGCUUGGUCAGAACUUUUUCAAAGUCUUGUAGCUCAAUUUCCGUGGCCUUAAAGUCACGUUGAAAAGCCUCGAUAGCCGCC
..(..((.(((.....((((((((((..((((((..(((((......)))))(((.....))))))))).))))..((..((((((......))))))..))))))))..))).))..). ( -32.90)
>DroSec_CAF1 27158 120 - 1
UAGUAACCAUCUAUUUGGCUUUGAGUGAGCGAGGAUUUCUGCUUAACCAGAACUUUUUCAAAGUCUUGCAACUCAAUUUCCGUGGCUUCAAAGUCACGCUGAAAAGCCUCGAUAGCCGCU
..........(((((.((((((((((..((((((..(((((......)))))(((.....))))))))).))))))(((((((((((....)))))))..))))))))..)))))..... ( -33.00)
>DroSim_CAF1 24847 120 - 1
UAGUAGCCAUCUAUUUGGCUUUGAGUGAGCGAGGAUUUCUGCUUAACCAGAACUUUUUCAAAGUCUUGUAGCUCAAUUUCCGUGGCCUCAAAGUCACGCUGAAAAGCCUCGAUAGCCGCU
.((..((.(((....((((((((((...(((..((((...(((..((.(((.(((.....)))))).)))))..))))..)))...)))))))))).(((....)))...))).))..)) ( -35.80)
>DroEre_CAF1 25723 120 - 1
UAGUAGCCAUCUAUUUGGCUUUGAGUGAGUGAGGAUUUCUGCUUGGCCAAAACUUUUUCAAAAUCUUGUAGAUCAAUUUCUGUGGCCUCAAAAUCACGCUGAAAAGCCUCGAUAGCCGCC
.(((((....))))).(((((((((...((((((....))....(((((.........(((....)))((((......)))))))))......))))(((....)))))))).))))... ( -28.10)
>DroYak_CAF1 25711 120 - 1
UAGUAGCCAUCUAUUUGGCUUUGAGUGAGUGAGGAUUUCUGCUUGGCCAGAACUUUUUCAAAGUCCUUCAGCUCAAUUUCAGUGGCCUCAAAAUCACGCUGAAAAGCCUCAAUGGCCGCC
..(..(((((......((((((((((....(((((((((((......)))))..........))))))..))))))((((((((............))))))))))))...)))))..). ( -36.00)
>consensus
UAGUAGCCAUCUAUUUGGCUUUGAGUGAGCGAGGAUUUCUGCUUGGCCAGAACUUUUUCAAAGUCUUGUAGCUCAAUUUCCGUGGCCUCAAAGUCACGCUGAAAAGCCUCGAUAGCCGCC
................((((((((((((((.((((((((((......)))))..........)))))...)))))......(((((......)))))(((....)))))))).))))... (-27.36 = -27.40 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:50 2006