Locus 7317

Sequence ID	2L_DroMel_CAF1
Location	20,466,326 – 20,466,446
Length	120
Max. P	0.999965

overview

Window 2

Location	20,466,326 – 20,466,446
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.63
Mean single sequence MFE	-35.20
Consensus MFE	-32.32
Energy contribution	-32.56
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-3.30
Structure conservation index	0.92
SVM decision value	4.96
SVM RNA-class probability	0.999965
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20466326 120 + 22407834
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACCAAACGGUGGUGCCGCGUCACCGGCACCACCACCAACACCAUCGCAUUCGCAAUCGCCAAGUUGAA
(((....((((............(((.....)))....(((((....))..........((((((((((......))))))))))..........)))...))))....)))........ ( -35.30)
>DroSec_CAF1 19286 120 + 1
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACCAAACGGUGGUGCCGCGUCACCGGCACCACCACCAACACCAUCGCAUUCGCAAUCGCCAAGUUGAA
(((....((((............(((.....)))....(((((....))..........((((((((((......))))))))))..........)))...))))....)))........ ( -35.30)
>DroSim_CAF1 21257 120 + 1
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACCAAACGGUGGUGCCGCGUCACCGGCACCACCACCAACACCAUUGCAUUCGCAAUCGCCAAGUUGAA
(((....((((...........(((((..............((....))..........((((((((((......))))))))))...........)))))))))....)))........ ( -34.80)
>DroEre_CAF1 21838 111 + 1
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACAAAACGGUGGUGCCGCGUCACCGGCACCAC---------CAUCGCAUUCGCAAUCGCCAAGUUGAA
(((....((((............(((.....)))....(((((....))..........((((((((((......)))))))))---------).)))...))))....)))........ ( -35.30)
>DroYak_CAF1 18950 111 + 1
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACAAAACGGUGGUGCCGCGUCACCGGCACCAC---------CAUCGCAUUCGCAAUCGCCAAGUUGAA
(((....((((............(((.....)))....(((((....))..........((((((((((......)))))))))---------).)))...))))....)))........ ( -35.30)
>consensus
GGCACAAGCGACCAUAUUUCAAAUGCACACCGCACCACCGAGCCACCGCACCACCAAACGGUGGUGCCGCGUCACCGGCACCACCACCAACACCAUCGCAUUCGCAAUCGCCAAGUUGAA
(((....((((............(((.....)))....(((((....))..........((((((((((......))))))))))..........)))...))))....)))........ (-32.32 = -32.56 +   0.24)

alignment

secondary structure

dotplot

Window 3

Location	20,466,326 – 20,466,446
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.63
Mean single sequence MFE	-47.76
Consensus MFE	-43.02
Energy contribution	-42.86
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.90
SVM decision value	2.68
SVM RNA-class probability	0.996317
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20466326 120 - 22407834
UUCAACUUGGCGAUUGCGAAUGCGAUGGUGUUGGUGGUGGUGCCGGUGACGCGGCACCACCGUUUGGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
...............(((...(((((.(((((...(((((..(((.((((((.((((((((....)))))))).)))..))).)))..)......))))...))))).)))))...))). ( -47.30)
>DroSec_CAF1 19286 120 - 1
UUCAACUUGGCGAUUGCGAAUGCGAUGGUGUUGGUGGUGGUGCCGGUGACGCGGCACCACCGUUUGGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
...............(((...(((((.(((((...(((((..(((.((((((.((((((((....)))))))).)))..))).)))..)......))))...))))).)))))...))). ( -47.30)
>DroSim_CAF1 21257 120 - 1
UUCAACUUGGCGAUUGCGAAUGCAAUGGUGUUGGUGGUGGUGCCGGUGACGCGGCACCACCGUUUGGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
....((..(((((((.((((((((((.(..(((.(((....((((....)((.((((((((....)))))))).)))))))).)))..).)).))))))))......))))))).))... ( -47.40)
>DroEre_CAF1 21838 111 - 1
UUCAACUUGGCGAUUGCGAAUGCGAUG---------GUGGUGCCGGUGACGCGGCACCACCGUUUUGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
....(((.(((.((((((.(((.((((---------(((((((((......))))))))))))).)))..)))))).))).)))((..(((((..(((.......)))..))).))..)) ( -48.40)
>DroYak_CAF1 18950 111 - 1
UUCAACUUGGCGAUUGCGAAUGCGAUG---------GUGGUGCCGGUGACGCGGCACCACCGUUUUGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
....(((.(((.((((((.(((.((((---------(((((((((......))))))))))))).)))..)))))).))).)))((..(((((..(((.......)))..))).))..)) ( -48.40)
>consensus
UUCAACUUGGCGAUUGCGAAUGCGAUGGUGUUGGUGGUGGUGCCGGUGACGCGGCACCACCGUUUGGUGGUGCGGUGGCUCGGUGGUGCGGUGUGCAUUUGAAAUAUGGUCGCUUGUGCC
....((..(((((((.((((((((.............(.(..(((.((((((.(((((((......))))))).)))..))).)))..).)..))))))))......))))))).))... (-43.02 = -42.86 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:18 2006