Locus 2836

Sequence ID	3R_DroMel_CAF1
Location	7,606,062 – 7,606,209
Length	147
Max. P	0.918654

overview

Window 7

Location	7,606,062 – 7,606,169
Length	107
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.33
Mean single sequence MFE	-29.57
Consensus MFE	-26.05
Energy contribution	-27.17
Covariance contribution	1.11
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.88
SVM decision value	-0.04
SVM RNA-class probability	0.512447
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7606062 107 - 27905053
CACAGGCGCUUAUGCAAGUGCACGUGUAUAUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUCUCCUGCGCAUUUAUUU-UGUUACUUAAU------------
(((..((((((....))))))..)))..((((((......))))))(((((....((((((..((.(((......)))))..))))))....))))-)..........------------ ( -28.80)
>DroSec_CAF1 1484 120 - 1
CACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUCUCCUGCGACUUUAUUUUUGCUAUUAAAGACAUCAGUUAUU
....((((..........(((((.(.(((((((......))))))).......).)))))((((...)))).)))).((((...((((........))))......)))).......... ( -27.40)
>DroSim_CAF1 1486 120 - 1
CACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUCUCCUGCGCCUUUAUUUUUGCUACUAAAGACAUCAGUUAUU
(((..(((....)))..)))...((((((((((......))))))((((((.(((((((((..((.(((......)))))..))))))))).))))))..........))))........ ( -32.50)
>consensus
CACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUCUCCUGCGCCUUUAUUUUUGCUACUAAAGACAUCAGUUAUU
(((..((((((....))))))..)))(((((((......)))))))(((((.(((((((((..((.(((......)))))..))))))))).)))))....................... (-26.05 = -27.17 +   1.11)

alignment

secondary structure

dotplot

Window 8

Location	7,606,089 – 7,606,209
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-28.50
Consensus MFE	-27.79
Energy contribution	-27.57
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.15
Structure conservation index	0.97
SVM decision value	1.12
SVM RNA-class probability	0.918654
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7606089 120 + 27905053
GACCGGCAAGUCGAUUCGACUGCACCUUAAUUUUUAUGUGUUAAUUCACAUAUACACGUGCACUUGCAUAAGCGCCUGUGUGUGCAUGUCUGUAUGUCUUUUCUCAUUCUUGUUUUUUCC
.....(((.((((...)))))))..............(((..((...(((((((.((((((((..(((((......))))))))))))).)))))))...))..)))............. ( -28.50)
>DroSec_CAF1 1524 120 + 1
GACCGGCAAGUCGAUUCGACUGCACCUUAAUUUUUAUGUGUUAAUUCACACAUACACGUGCACUUGCAUAAACGCCUGUGUGUGCAUGUCUGUAUGUCUUUUCUCAUUCUUGUUUUUUCC
....((((((..((...(((((((..........(((((((......))))))).((((((((..(((((......))))))))))))).)))).)))...)).....))))))...... ( -28.80)
>DroSim_CAF1 1526 120 + 1
GACCGGCAAGUCGAUUCGACUGCACCUUAAUUUUUAUGUGUUAAUUCACACAUACACGUGCACUUGCAUAAACGCCUGUGUGUGCAUGUCUGUAUGUCUUUCCUCAUUCUUGUUUUUUCC
....((((((..((...(((((((..........(((((((......))))))).((((((((..(((((......))))))))))))).)))).))).....))...))))))...... ( -28.20)
>consensus
GACCGGCAAGUCGAUUCGACUGCACCUUAAUUUUUAUGUGUUAAUUCACACAUACACGUGCACUUGCAUAAACGCCUGUGUGUGCAUGUCUGUAUGUCUUUUCUCAUUCUUGUUUUUUCC
....((((((..((...(((((((..........(((((((......))))))).((((((((..(((((......))))))))))))).)))).))).....))...))))))...... (-27.79 = -27.57 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	7,606,089 – 7,606,209
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-29.00
Consensus MFE	-27.31
Energy contribution	-26.87
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-2.01
Structure conservation index	0.94
SVM decision value	0.65
SVM RNA-class probability	0.811507
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7606089 120 - 27905053
GGAAAAAACAAGAAUGAGAAAAGACAUACAGACAUGCACACACAGGCGCUUAUGCAAGUGCACGUGUAUAUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUC
........((((.(((........)))...(((.(((((((((..((((((....))))))..)))).((((((......)))))).........)))))))).......))))...... ( -30.40)
>DroSec_CAF1 1524 120 - 1
GGAAAAAACAAGAAUGAGAAAAGACAUACAGACAUGCACACACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUC
......................(((...((.((((((((.(((..(((....)))..)))...)))))))).))....................((((.(((((...))))))))).))) ( -28.30)
>DroSim_CAF1 1526 120 - 1
GGAAAAAACAAGAAUGAGGAAAGACAUACAGACAUGCACACACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUC
......................(((...((.((((((((.(((..(((....)))..)))...)))))))).))....................((((.(((((...))))))))).))) ( -28.30)
>consensus
GGAAAAAACAAGAAUGAGAAAAGACAUACAGACAUGCACACACAGGCGUUUAUGCAAGUGCACGUGUAUGUGUGAAUUAACACAUAAAAAUUAAGGUGCAGUCGAAUCGACUUGCCGGUC
........((((.(((........)))...(((.(((((((((..((((((....))))))..)))).((((((......)))))).........)))))))).......))))...... (-27.31 = -26.87 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:45:56 2006