Locus 2481

Sequence ID	X_DroMel_CAF1
Location	6,596,628 – 6,596,720
Length	92
Max. P	0.988385

overview

Window 1

Location	6,596,628 – 6,596,720
Length	92
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	65.12
Mean single sequence MFE	-33.48
Consensus MFE	-17.06
Energy contribution	-17.05
Covariance contribution	-0.00
Combinations/Pair	1.12
Mean z-score	-2.15
Structure conservation index	0.51
SVM decision value	2.12
SVM RNA-class probability	0.988385
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6596628 92 + 22224390
UC---------CUCCCCACUCGAUUCGAGUUUUGUGUUUCGAG-------UUGAGUUUCGAGUUU------------GCGAUCGAGUUGGAGGCAACCAAGCCUGACCGUUCUUGGUCUA
..---------(((...((((((((((((........))))))-------))))))...)))...------------..(((((((.(((((((......))))..)))..))))))).. ( -33.30)
>DroSim_CAF1 8717 87 + 1
UC--------------CACUCGAUUCGAGUUUUGAGUUUCGAG-------UUGAGUUUCGAGUUU------------GAGUUCGGGUUGGAGGCAGCCAAGCCUGACCGUUCUUGGUCUA
..--------------.((((((((((((........))))))-------)))))).(((((..(------------(.(((.((.((((......)))).)).)))))..))))).... ( -31.00)
>DroEre_CAF1 12156 120 + 1
UCAACCCUCAACUGUCCACUCGAUUCGAGUUCUGAGUCUGAGUCUGGGUCUGGAGUCUCGACUCCGACUCCGAGUUCGAGUUCCAGCGCGAGGCAGCCAAGCCUGACCGUUCUUGGUCCA
...(((...(((.(((.....(((((((..((.(((((.(((((.(((.(....).)))))))).))))).))..)))))))........((((......))))))).)))...)))... ( -41.00)
>DroYak_CAF1 11499 97 + 1
UCAACUCUCGACUGUCCACUUGAUUCGAGUU-----------UCAAAGUUUGGAGUCUCGAUUCU------------AAGCUCUAGCUCGAGGCAGCCAAGCCUGACCGUUCUUGGUCUA
........................(((((((-----------....((((((((((....)))))------------)))))..)))))))(((......))).(((((....))))).. ( -28.60)
>consensus
UC_________CUGUCCACUCGAUUCGAGUUUUGAGUUUCGAG_______UGGAGUCUCGAGUCU____________GAGUUCGAGCUCGAGGCAGCCAAGCCUGACCGUUCUUGGUCUA
.....................((((((((...........................))))))))..........................((((......))))(((((....))))).. (-17.06 = -17.05 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	6,596,628 – 6,596,720
Length	92
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	65.12
Mean single sequence MFE	-30.62
Consensus MFE	-13.60
Energy contribution	-13.85
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.44
SVM decision value	0.56
SVM RNA-class probability	0.781108
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6596628 92 - 22224390
UAGACCAAGAACGGUCAGGCUUGGUUGCCUCCAACUCGAUCGC------------AAACUCGAAACUCAA-------CUCGAAACACAAAACUCGAAUCGAGUGGGGAG---------GA
..(((((((..(.....).))))))).(((((.(((((((((.------------.....))).......-------.((((..........)))).))))))..))))---------). ( -27.90)
>DroSim_CAF1 8717 87 - 1
UAGACCAAGAACGGUCAGGCUUGGCUGCCUCCAACCCGAACUC------------AAACUCGAAACUCAA-------CUCGAAACUCAAAACUCGAAUCGAGUG--------------GA
..((((......)))).(((......)))(((....(((....------------....))).......(-------(((((...((.......)).)))))))--------------)) ( -20.00)
>DroEre_CAF1 12156 120 - 1
UGGACCAAGAACGGUCAGGCUUGGCUGCCUCGCGCUGGAACUCGAACUCGGAGUCGGAGUCGAGACUCCAGACCCAGACUCAGACUCAGAACUCGAAUCGAGUGGACAGUUGAGGGUUGA
..((((......))))...((..((((..((.((((.((..((((..((.(((((.(((((...............))))).))))).))..)))).)).))))))))))..))...... ( -42.96)
>DroYak_CAF1 11499 97 - 1
UAGACCAAGAACGGUCAGGCUUGGCUGCCUCGAGCUAGAGCUU------------AGAAUCGAGACUCCAAACUUUGA-----------AACUCGAAUCAAGUGGACAGUCGAGAGUUGA
..((((......))))...((((((((((.(((((....))))------------.((.(((((..((........))-----------..))))).))..).)).))))))))...... ( -31.60)
>consensus
UAGACCAAGAACGGUCAGGCUUGGCUGCCUCCAACUCGAACUC____________AAACUCGAAACUCAA_______AUCGAAACUCAAAACUCGAAUCGAGUGGACAG_________GA
..((((......))))((((......))))............................................................(((((...)))))................. (-13.60 = -13.85 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:56 2006