Locus 7218

Sequence ID	2L_DroMel_CAF1
Location	20,254,028 – 20,254,348
Length	320
Max. P	0.966862

overview

Window 4

Location	20,254,028 – 20,254,148
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-37.67
Consensus MFE	-36.17
Energy contribution	-37.67
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.70
Structure conservation index	0.96
SVM decision value	1.60
SVM RNA-class probability	0.966862
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254028 120 + 22407834
CGCUUCAUUCCUCUGCACAUUUCAUUGGUCAAUUGACUGUGAAAACCUGUGAAAACAAAAACACAUCCGUGGGAGGGACAGCAGAAGGACCGAGGUCCUGGCCAACAAGCCAUGGAAAAU
..((((..((((((((...((((((.((((....)))))))))).(((((....)).....(((....)))..)))....)))).))))..))))(((((((......)))).))).... ( -37.50)
>DroSec_CAF1 15575 120 + 1
CGCUUCAUUCCUCUGCACAUUUCAUUGGUCAAUUGACUGUGAAAACCUGUGAAAACAAAAACACAACCGUGGGAGGGACAGCAGAAGGACCGAGGUCCUGGCCAACAAGCCAUGGAAAAU
..((((..((((((((...((((((.((((....)))))))))).(((((....)).....(((....)))..)))....)))).))))..))))(((((((......)))).))).... ( -37.50)
>DroSim_CAF1 13994 120 + 1
CGCUUCAUUCCUCUGCACAUUUCAUUGGUCAAUUGACUGUGAAAACCUGUGAAAACAAAAACACGACCGUGGGAGGGACAGCAGAAGGACCGAGGUCCUGGCCAACAAGCCAUGGAAAAU
..((((..((((((((...((((((.((((....)))))))))).(((((....)).....(((....)))..)))....)))).))))..))))(((((((......)))).))).... ( -38.00)
>consensus
CGCUUCAUUCCUCUGCACAUUUCAUUGGUCAAUUGACUGUGAAAACCUGUGAAAACAAAAACACAACCGUGGGAGGGACAGCAGAAGGACCGAGGUCCUGGCCAACAAGCCAUGGAAAAU
..((((..((((((((...((((((.((((....)))))))))).(((((....)).....(((....)))..)))....)))).))))..))))(((((((......)))).))).... (-36.17 = -37.67 +   1.50)

alignment

secondary structure

dotplot

Window 5

Location	20,254,148 – 20,254,268
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-32.11
Consensus MFE	-32.21
Energy contribution	-31.99
Covariance contribution	-0.22
Combinations/Pair	1.02
Mean z-score	-1.32
Structure conservation index	1.00
SVM decision value	-0.01
SVM RNA-class probability	0.528267
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254148 120 - 22407834
UAAUGCUAAUGAUAUUUGCCUUAAAGAAUGGCAGCCGGAGUCGGGUUACAGGUAACAUCCAGUUAGCAGCUGCUGCCGGGGACUUUAGUUGAUGAAAAACUCUUUAGAAAUGCAUUAGUA
...((((((((.(((((...(((((((..((((((.(((.....((((....)))).)))(((.....)))))))))(....).................)))))))))))))))))))) ( -32.30)
>DroSec_CAF1 15695 120 - 1
UAAUGCUAAUGAUAUUUGCCUUAAAGAAUGGCAGCCGGAGUCGGGUUACAGGUAACAUCCAGUUAGCAGCUGCUGCCGGGGACUUUAGUUGAUGAAAAACUCUUUAGAAAUGCAUUAGUA
...((((((((.(((((...(((((((..((((((.(((.....((((....)))).)))(((.....)))))))))(....).................)))))))))))))))))))) ( -32.30)
>DroSim_CAF1 14114 120 - 1
UAAUGCUAAUGAUAUUUGCCUUAAAGAAUGGCAGCCGAAGUCGGGUUACAGGUAACAUCCAGUUAGCAGCUGCUGCCGGGGACUUUAGUUGAUGAAAAACUCUUUAGAAAUGCAUUAGUA
...((((((((.(((((...(((((((....((((..(((((..((((....)))).(((.((.(((....))))).))))))))..)))).........)))))))))))))))))))) ( -31.72)
>consensus
UAAUGCUAAUGAUAUUUGCCUUAAAGAAUGGCAGCCGGAGUCGGGUUACAGGUAACAUCCAGUUAGCAGCUGCUGCCGGGGACUUUAGUUGAUGAAAAACUCUUUAGAAAUGCAUUAGUA
...((((((((.(((((...(((((((....((((..(((((..((((....)))).(((.((.(((....))))).))))))))..)))).........)))))))))))))))))))) (-32.21 = -31.99 +  -0.22)

alignment

secondary structure

dotplot

Window 6

Location	20,254,228 – 20,254,348
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-29.73
Consensus MFE	-28.13
Energy contribution	-28.47
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.95
SVM decision value	0.16
SVM RNA-class probability	0.613365
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20254228 120 + 22407834
CUCCGGCUGCCAUUCUUUAAGGCAAAUAUCAUUAGCAUUAUGAUGCCACUCCGCCCAACGACCACGCCACUUCCUCAGCCAUCCAGAUGGGUCCCAUCCUCGUCGCUCUUCGCAGUGGCC
....(((((((.........))))..((((((.......)))))).......)))..........((((((..............((((((......)).))))((.....)))))))). ( -28.60)
>DroSec_CAF1 15775 120 + 1
CUCCGGCUGCCAUUCUUUAAGGCAAAUAUCAUUAGCAUUAUGAUGCCACUCCGCCCACCGACCACGCCACUUCCUCAGCCAUCCAGCUGGGUCCCAUCCUCGUCGCUCUUCGCAGUGGCC
....(((((((.........))))..((((((.......)))))).......)))..........((((((..((((((......)))))).............((.....)))))))). ( -30.30)
>DroSim_CAF1 14194 120 + 1
CUUCGGCUGCCAUUCUUUAAGGCAAAUAUCAUUAGCAUUAUGAUGCCACUCCGCCCACCGACCACGCCACUUCCUCAGCCAUCCAGCUGGGUCCCAUCCUCGUCGCUCUUCGCAGUGGCC
....(((((((.........))))..((((((.......)))))).......)))..........((((((..((((((......)))))).............((.....)))))))). ( -30.30)
>consensus
CUCCGGCUGCCAUUCUUUAAGGCAAAUAUCAUUAGCAUUAUGAUGCCACUCCGCCCACCGACCACGCCACUUCCUCAGCCAUCCAGCUGGGUCCCAUCCUCGUCGCUCUUCGCAGUGGCC
....(((((((.........))))..((((((.......)))))).......)))..........((((((..((((((......)))))).............((.....)))))))). (-28.13 = -28.47 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:38 2006