Locus 3556

Sequence ID	3L_DroMel_CAF1
Location	10,417,615 – 10,417,745
Length	130
Max. P	0.930444

overview

Window 6

Location	10,417,615 – 10,417,714
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	90.81
Mean single sequence MFE	-26.00
Consensus MFE	-21.26
Energy contribution	-23.46
Covariance contribution	2.20
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.82
SVM decision value	1.21
SVM RNA-class probability	0.930444
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10417615 99 - 23771897
GCGGCAACAUCAGCAUCUUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
(((((((.....((((.....(((.((((((((((((....)))).)))))))).)))..)))).....))))))).(((((......)))))...... ( -28.90)
>DroPse_CAF1 314381 80 - 1
GCG-------------------GCAGCUGGUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
(.(-------------------((.((((.(((((((....)))).))).)))).......((((.(....).))))..............))).)... ( -18.30)
>DroSec_CAF1 288645 99 - 1
GCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
(((((((.....((((.....(((.((((((((((((....)))).)))))))).)))..)))).....))))))).(((((......)))))...... ( -28.90)
>DroSim_CAF1 304388 99 - 1
GCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
(((((((.....((((.....(((.((((((((((((....)))).)))))))).)))..)))).....))))))).(((((......)))))...... ( -28.90)
>DroYak_CAF1 301644 99 - 1
GCAGCAAUAUCAGCAUCUUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
...((((.....((((.....(((.((((((((((((....)))).)))))))).)))..)))).....)))).((.(((((......))))).))... ( -25.00)
>consensus
GCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAAAUGCGUCUUUUGUCGUAGUUAAAGUUUAUUGGCCACAUU
(((((((.....((((.....(((.((((((((((((....)))).)))))))).)))..)))).....))))))).(((((......)))))...... (-21.26 = -23.46 +   2.20)

alignment

secondary structure

dotplot

Window 7

Location	10,417,654 – 10,417,745
Length	91
Sequences	4
Columns	91
Reading direction	reverse
Mean pairwise identity	90.48
Mean single sequence MFE	-26.72
Consensus MFE	-20.79
Energy contribution	-22.48
Covariance contribution	1.69
Combinations/Pair	1.07
Mean z-score	-2.38
Structure conservation index	0.78
SVM decision value	1.02
SVM RNA-class probability	0.902043
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10417654 91 - 23771897
AGCAACAGGCCAACUAGAGAUAUCUGCGGCAGCGGCAACAUCAGCAUCUUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAA
.((.(((((((((.((((....((((.(((((((....)....((((....)))).)))))))))))))))))))))...)).))...... ( -28.30)
>DroSec_CAF1 288684 91 - 1
AGCAACAGACCAACUAGCGAUAUCUGCGGCAGCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAA
.((.(((((((((.(((....(((((.(((((((....)....((((....)))).)))))))))))))))))))))...)).))...... ( -28.70)
>DroSim_CAF1 304427 91 - 1
AGCAACAGGCCAACUAGCGAUAUCUGCGGCAGCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAA
.((.(((((((((.(((....(((((.(((((((....)....((((....)))).)))))))))))))))))))))...)).))...... ( -28.10)
>DroYak_CAF1 301683 80 - 1
AGCAACAGGCCAACAAGCGA-----------GCAGCAAUAUCAGCAUCUUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAA
.((.(((((((((.((((((-----------(((((.......((((....)))).))))))).).))).)))))))...)).))...... ( -21.80)
>consensus
AGCAACAGGCCAACUAGCGAUAUCUGCGGCAGCGGCAACAUCAGCAUCCUAGUGCAGCUGCUUAGAUUUAUUGGUCUUAAGUAGCAGCAAA
.((.(((((((((........(((((.(((((((....)....((((....)))).)))))))))))...)))))))...)).))...... (-20.79 = -22.48 +   1.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:55 2006