Locus 5555

Sequence ID	3L_DroMel_CAF1
Location	15,242,186 – 15,242,328
Length	142
Max. P	0.981423

overview

Window 1

Location	15,242,186 – 15,242,276
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	99.11
Mean single sequence MFE	-22.37
Consensus MFE	-22.11
Energy contribution	-22.11
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.26
Structure conservation index	0.99
SVM decision value	0.29
SVM RNA-class probability	0.669050
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15242186 90 - 23771897
GCCGGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGACUUUGUUCAGCAUCCUU
(((((((((((((....))))))).)).((((((...))))))....................)))).(((((......)))))...... ( -22.40)
>DroSec_CAF1 131516 90 - 1
GCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGACUUUGUUCAGCAUCCUU
(((...(((((((....))))))).((((........(((((.....)))))........))))))).(((((......)))))...... ( -22.09)
>DroSim_CAF1 139320 90 - 1
GCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGACUUUGUUCAGCAUCCUU
(((...(((((((....))))))).((((........(((((.....)))))........))))))).(((((......)))))...... ( -22.09)
>DroEre_CAF1 131634 90 - 1
GCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGAAUUUGUUCAGCAUCCUU
(((...(((((((....))))))).((((........(((((.....)))))........))))))).((((((....))))))...... ( -23.19)
>DroYak_CAF1 137434 90 - 1
GCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGACUUUGUUCAGCAUCCUU
(((...(((((((....))))))).((((........(((((.....)))))........))))))).(((((......)))))...... ( -22.09)
>consensus
GCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUUUGUACAUUAAGUUUUCCCAUCCGCGGCAGUUGACUUUGUUCAGCAUCCUU
(((...(((((((....))))))).((((........(((((.....)))))........))))))).(((((......)))))...... (-22.11 = -22.11 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	15,242,236 – 15,242,328
Length	92
Sequences	3
Columns	92
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-19.51
Consensus MFE	-17.64
Energy contribution	-17.20
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-3.27
Structure conservation index	0.90
SVM decision value	1.89
SVM RNA-class probability	0.981423
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15242236 92 + 23771897
AAUAUAAUUUGCCGCACACACAAACACUUAUGUGGCCGGCACCCCUCGGACCCUCCGAAGGCCCCAAGCCCCAAGCCCCAUUCCUCCAUUCC
..........((((((..............)))))).(((.....((((.....)))).(((.....)))....)))............... ( -19.94)
>DroSec_CAF1 131566 85 + 1
AAUAUAAUUUGCCGCACACACAAACACUUAUGUGGCUGGCACCCCUUGGACCCUCCGAAGGCCCCA-------AGCCCCAUUCCCCCAUUCC
.........((((((.((((.((....)).)))))).))))...(((((..(((....)))..)))-------))................. ( -19.20)
>DroSim_CAF1 139370 85 + 1
AAUAUAAUUUGCCGCACACACAAACACUUAUGUGGCUGGCACCCCUUGGACCCUCCAAAGGCCCCA-------AGUCCCAUUCCCCCAUUCC
.........((((((.((((.((....)).)))))).))))...(((((..(((....)))..)))-------))................. ( -19.40)
>consensus
AAUAUAAUUUGCCGCACACACAAACACUUAUGUGGCUGGCACCCCUUGGACCCUCCGAAGGCCCCA_______AGCCCCAUUCCCCCAUUCC
.........((((((.((((.((....)).)))))).)))).((.((((.....)))).))............................... (-17.64 = -17.20 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	15,242,236 – 15,242,328
Length	92
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-29.10
Consensus MFE	-24.49
Energy contribution	-24.60
Covariance contribution	0.11
Combinations/Pair	1.05
Mean z-score	-2.04
Structure conservation index	0.84
SVM decision value	0.24
SVM RNA-class probability	0.650017
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15242236 92 - 23771897
GGAAUGGAGGAAUGGGGCUUGGGGCUUGGGGCCUUCGGAGGGUCCGAGGGGUGCCGGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUU
(((.((((((..(.((((.....)))).)..)))))).....)))..((..(((((..(((((((....)))))))..)))))..))..... ( -32.20)
>DroSec_CAF1 131566 85 - 1
GGAAUGGGGGAAUGGGGCU-------UGGGGCCUUCGGAGGGUCCAAGGGGUGCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUU
.................((-------((((.(((....))).))))))...((((.(((((((((....))))))).))))))......... ( -27.40)
>DroSim_CAF1 139370 85 - 1
GGAAUGGGGGAAUGGGACU-------UGGGGCCUUUGGAGGGUCCAAGGGGUGCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUU
.................((-------((((.(((....))).))))))...((((.(((((((((....))))))).))))))......... ( -27.70)
>consensus
GGAAUGGGGGAAUGGGGCU_______UGGGGCCUUCGGAGGGUCCAAGGGGUGCCAGCCACAUAAGUGUUUGUGUGUGCGGCAAAUUAUAUU
...............................(((((((.....))))))).((((.(((((((((....))))))).))))))......... (-24.49 = -24.60 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:13 2006