Locus 8085

Sequence ID	X_DroMel_CAF1
Location	20,126,707 – 20,126,801
Length	94
Max. P	0.752215

overview

Window 2

Location	20,126,707 – 20,126,801
Length	94
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	87.16
Mean single sequence MFE	-32.40
Consensus MFE	-21.08
Energy contribution	-23.56
Covariance contribution	2.48
Combinations/Pair	1.06
Mean z-score	-2.59
Structure conservation index	0.65
SVM decision value	0.48
SVM RNA-class probability	0.752215
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20126707 94 + 22224390
GAGUUGAAGUUCGAGUUUGCAG-------CUUGCAGUUGCAAAGUCCAAAGGCCGAGAGUGAACCAAUGCGACACUUAAAAGUUAUGGCUUACUCGAACUC
.......(((((((.(((((((-------(.....)))))))).))..........((((((.(((..((...........))..))).))))))))))). ( -27.80)
>DroSec_CAF1 28369 101 + 1
GAGUUCCAGUUCGAGUUUGCAGCUUGCAGCUUGCAGUUGCAAAGUCCAAAGGCCGAGAGUGAAGCAAUGCGACACUUAAAAGUUAUGGCUUACUCGAACUC
((((((.(((..((.(((((((((.((.....))))))))))).))...((((((.(((((..((...))..)))))........))))))))).)))))) ( -34.90)
>DroSim_CAF1 11759 101 + 1
GAGUUCGAGUUCGAGUUUGCAGCUUGCAGCUUGCAGUUGCAAAGUCCAAAGGCCGAGAGUGAAGCAAUGCGACACUUAAAAGUUAUGGCUUACUCGAACUC
((((((((((..((.(((((((((.((.....))))))))))).))...((((((.(((((..((...))..)))))........)))))))))))))))) ( -40.80)
>DroEre_CAF1 22692 94 + 1
AAGUUCGAGUUCGAGCUGGCAG-------CCUGCAGCUGCAAAGUCCAAAGGCCGAGAGUGCAGCAAUGCGACACUCCAAACUUGUGGCUUAAUCGAACUC
......((((((((....((((-------(.....))))).(((.((((((...(.(((((..((...))..))))))...))).))))))..)))))))) ( -33.30)
>DroYak_CAF1 7529 88 + 1
GAGUUCGAGUUC------GCAG-------CUUGCAGUUGCAAAGUCCAAAGGCCGAGAGUGAAGCAAUGCGACACUUAAAAGUUAUGGCUUACUCCAACUC
(((((.((((..------((((-------(.....))))).........((((((.(((((..((...))..)))))........)))))))))).))))) ( -25.20)
>consensus
GAGUUCGAGUUCGAGUUUGCAG_______CUUGCAGUUGCAAAGUCCAAAGGCCGAGAGUGAAGCAAUGCGACACUUAAAAGUUAUGGCUUACUCGAACUC
((((((((((..((.(((((((..............))))))).))...((((((.(((((..((...))..)))))........)))))))))))))))) (-21.08 = -23.56 +   2.48)

alignment

secondary structure

dotplot

Window 3

Location	20,126,707 – 20,126,801
Length	94
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	87.16
Mean single sequence MFE	-29.19
Consensus MFE	-19.64
Energy contribution	-20.48
Covariance contribution	0.84
Combinations/Pair	1.15
Mean z-score	-2.09
Structure conservation index	0.67
SVM decision value	0.22
SVM RNA-class probability	0.639170
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20126707 94 - 22224390
GAGUUCGAGUAAGCCAUAACUUUUAAGUGUCGCAUUGGUUCACUCUCGGCCUUUGGACUUUGCAACUGCAAG-------CUGCAAACUCGAACUUCAACUC
((((((((((.(((..............(((.((..((((.......))))..))))).((((....)))))-------))....))))))))))...... ( -26.80)
>DroSec_CAF1 28369 101 - 1
GAGUUCGAGUAAGCCAUAACUUUUAAGUGUCGCAUUGCUUCACUCUCGGCCUUUGGACUUUGCAACUGCAAGCUGCAAGCUGCAAACUCGAACUGGAACUC
.(((((((((.(((((.........((((..((...))..)))).........))).))(((((.((((.....)).)).))))))))))))))....... ( -27.97)
>DroSim_CAF1 11759 101 - 1
GAGUUCGAGUAAGCCAUAACUUUUAAGUGUCGCAUUGCUUCACUCUCGGCCUUUGGACUUUGCAACUGCAAGCUGCAAGCUGCAAACUCGAACUCGAACUC
((((((((((.(((((.........((((..((...))..)))).........))).))(((((.((((.....)).)).)))))))))))))))...... ( -31.47)
>DroEre_CAF1 22692 94 - 1
GAGUUCGAUUAAGCCACAAGUUUGGAGUGUCGCAUUGCUGCACUCUCGGCCUUUGGACUUUGCAGCUGCAGG-------CUGCCAGCUCGAACUCGAACUU
((((((((..((((((...((..(((((((.((...)).)))))))..))...))).))).(((((.....)-------))))....))))))))...... ( -37.00)
>DroYak_CAF1 7529 88 - 1
GAGUUGGAGUAAGCCAUAACUUUUAAGUGUCGCAUUGCUUCACUCUCGGCCUUUGGACUUUGCAACUGCAAG-------CUGC------GAACUCGAACUC
((((.(((((((((....(((....)))...)).)))))))))))((((..((((.(.(((((....)))))-------.).)------))).)))).... ( -22.70)
>consensus
GAGUUCGAGUAAGCCAUAACUUUUAAGUGUCGCAUUGCUUCACUCUCGGCCUUUGGACUUUGCAACUGCAAG_______CUGCAAACUCGAACUCGAACUC
((((((((((..((......((..(((.((((....(.....)...)))))))..))..((((....))))..........))..))))))))))...... (-19.64 = -20.48 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:06 2006