Locus 859

Sequence ID	X_DroMel_CAF1
Location	2,442,040 – 2,442,196
Length	156
Max. P	0.914806

overview

Window 5

Location	2,442,040 – 2,442,156
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.24
Mean single sequence MFE	-38.27
Consensus MFE	-24.24
Energy contribution	-24.93
Covariance contribution	0.69
Combinations/Pair	1.14
Mean z-score	-2.28
Structure conservation index	0.63
SVM decision value	1.10
SVM RNA-class probability	0.914806
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2442040 116 + 22224390
AAAAGCAAGGAAUCGAGUAAAC----ACGUUCCACCACCGCUGUGGCAAUCCGUGGCUGGUGCGCAACGGCCACACUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCUUAAGCAU
....((..((((.((.(....)----.))))))..((((((..(((....)))..)).)))).))...((.((((((((...(((((.......)))))..)))))))).))........ ( -35.80)
>DroSec_CAF1 2942 111 + 1
-----CGGGGAACCGAGUAAAC----ACGUUCCACCACCGCUGUGGCAAUCCGCUGAUGGUGCGCAGCGGUCACAUUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUAUGCAU
-----.(((((((.(.(....)----.)))))).))(((((.((((....)))).).))))..((((((((((((((((...(((((.......)))))..))))))))))))).))).. ( -41.20)
>DroSim_CAF1 5095 111 + 1
-----CGGGCAACCGAGUAAAC----ACGUUCCACCACCGCUGUGGCAAUCCGCUGAUGGUGCGCAACGGUCACAUUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUUAGCAU
-----(((....))).......----.........((((((.((((....)))).).))))).((((((((((((((((...(((((.......)))))..)))))))))))))).)).. ( -41.50)
>DroYak_CAF1 3466 113 + 1
-----CAAUUAGCGCAUUAUAUAUCAAUAUUCCACCACCGCUGUGGCAAUCCGUUGCUUGUGCGCAACGGUCACACUGACG--CUGGGCACUUUGUAUUUAUUAGUGUGGCCGUAAUCAU
-----......((((((.......((((......((((....))))......))))...)))))).(((((((((((((..--....((.....)).....)))))))))))))...... ( -34.60)
>consensus
_____CAAGGAACCGAGUAAAC____ACGUUCCACCACCGCUGUGGCAAUCCGCUGAUGGUGCGCAACGGUCACACUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUAAGCAU
...................................((((((.((((....)))).).)))))....(((((((((((((...(((((.......)))))..)))))))))))))...... (-24.24 = -24.93 +   0.69)

alignment

secondary structure

dotplot

Window 6

Location	2,442,076 – 2,442,196
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-37.75
Consensus MFE	-32.00
Energy contribution	-33.50
Covariance contribution	1.50
Combinations/Pair	1.12
Mean z-score	-1.98
Structure conservation index	0.85
SVM decision value	0.99
SVM RNA-class probability	0.896831
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2442076 120 + 22224390
CUGUGGCAAUCCGUGGCUGGUGCGCAACGGCCACACUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCUUAAGCAUUAUUAUUUUCACGUGUGGCACGCAAACGAGCCAAAAAACC
.............(((((.((..((....((((((((((((((((((..(((.....))).))))))))....(((......)))...))).)))))))..))..)).)))))....... ( -34.60)
>DroSec_CAF1 2973 120 + 1
CUGUGGCAAUCCGCUGAUGGUGCGCAGCGGUCACAUUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUAUGCAUUAUUAUUUUCACGUGUGGCACGCAAACGAGCCAAAAAACC
..((((....))))((((((((((..(((((((((((((...(((((.......)))))..))))))))))))).)))))))))).......((.((((.((....)).))))....)). ( -41.20)
>DroSim_CAF1 5126 120 + 1
CUGUGGCAAUCCGCUGAUGGUGCGCAACGGUCACAUUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUUAGCAUUAUUAUUUUCACGUGUGGCACGCAAACGAGCCAAAAAACC
..((((....))))(((((((((..((((((((((((((...(((((.......)))))..)))))))))))))).))))))))).......((.((((.((....)).))))....)). ( -42.60)
>DroYak_CAF1 3501 118 + 1
CUGUGGCAAUCCGUUGCUUGUGCGCAACGGUCACACUGACG--CUGGGCACUUUGUAUUUAUUAGUGUGGCCGUAAUCAUUAUUAUUUUCACGUGUGGCACGCAAACGAGUCAAAAAACC
...((((....((((((..((((...(((((((((((((..--....((.....)).....)))))))))))))...............((....)))))))).)))).))))....... ( -32.60)
>consensus
CUGUGGCAAUCCGCUGAUGGUGCGCAACGGUCACACUGACGCGCUGACCAAUUUUUAGUUAUUAGUGUGACCGUAAGCAUUAUUAUUUUCACGUGUGGCACGCAAACGAGCCAAAAAACC
..(((((.....))(((((((((...(((((((((((((...(((((.......)))))..)))))))))))))..)))))))))....)))((.((((.((....)).))))....)). (-32.00 = -33.50 +   1.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:29 2006