Locus 468

Sequence ID	X_DroMel_CAF1
Location	1,374,733 – 1,374,851
Length	118
Max. P	0.818008

overview

Window 6

Location	1,374,733 – 1,374,851
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.85
Mean single sequence MFE	-35.70
Consensus MFE	-20.88
Energy contribution	-22.82
Covariance contribution	1.94
Combinations/Pair	1.17
Mean z-score	-2.00
Structure conservation index	0.58
SVM decision value	0.42
SVM RNA-class probability	0.729398
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1374733 118 + 22224390
CUGUUGGCCUGGUGUCUAGAAUAGAGAAA--CAUGCAAUUUUGAAGACGGCCGUGGCCAGUUUUCUCGGCCAAAUUGAGUAAAAUUUCGAGUCGUGGUACCAGGCGAACAGAAAUGCCAG
(((((.((((((((.(((((...((((..--....((((((.(((((((((....))).))))))......)))))).......))))...)).))))))))))).)))))......... ( -41.42)
>DroSec_CAF1 6769 118 + 1
CUGUUGGCCUAGUGUCUAGAAUCAGGAAA--CAUGCAAUUUUGAAGACUGCCGUGGCCAGUUUUCUCGGCCAAAUUGAGUAAAAUAUCCAGUCGAGGUACCAGGCGAACAGAAAUGUCAG
(((((.((((.((..((.......(....--).............(((((...(((((((....)).)))))....((........))))))).))..)).)))).)))))......... ( -35.70)
>DroSim_CAF1 7501 118 + 1
CUGUUGGCCUAGUGUCUAGAAUCAGGAAA--CAUGCAAUUUUGAAGACGGCCGUGGCCAGUUUUCUCGGCCAAAUUGAGUAAAAUAUCCAGUCGAGGUACCAGGCGAACAGAAAUGUCAG
(((((.((((.((..((.......(....--).............((((((....))).((((((((((.....))))).))))).....))).))..)).)))).)))))......... ( -35.20)
>DroEre_CAF1 5549 116 + 1
AUGAUCGCCUGGUGCAACAAUUAAUGAAAACUAUGAAAAUCGGA---CGUUUGAUCCGAGUUUUCUUGGGUAAAUUGAG-AGAUUCUGGGUUUCAGAUAACAGGCGAACAGAAAUGUCAG
....(((((((......(..(((((.....(((.((((((((((---.......))))).))))).)))....))))).-.)..((((.....))))...)))))))(((....)))... ( -30.50)
>consensus
CUGUUGGCCUAGUGUCUAGAAUAAGGAAA__CAUGCAAUUUUGAAGACGGCCGUGGCCAGUUUUCUCGGCCAAAUUGAGUAAAAUAUCCAGUCGAGGUACCAGGCGAACAGAAAUGUCAG
(((((.(((((((((((.((....(((.......((.............))..(((((((....)).)))))..............)))..)).))))))))))).)))))......... (-20.88 = -22.82 +   1.94)

alignment

secondary structure

dotplot

Window 7

Location	1,374,733 – 1,374,851
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.85
Mean single sequence MFE	-30.70
Consensus MFE	-18.79
Energy contribution	-20.23
Covariance contribution	1.44
Combinations/Pair	1.14
Mean z-score	-2.01
Structure conservation index	0.61
SVM decision value	0.67
SVM RNA-class probability	0.818008
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1374733 118 - 22224390
CUGGCAUUUCUGUUCGCCUGGUACCACGACUCGAAAUUUUACUCAAUUUGGCCGAGAAAACUGGCCACGGCCGUCUUCAAAAUUGCAUG--UUUCUCUAUUCUAGACACCAGGCCAACAG
.........(((((.(((((((..........(((((......((((((....((((....((((....))))))))..))))))...)--))))((((...)))).))))))).))))) ( -30.70)
>DroSec_CAF1 6769 118 - 1
CUGACAUUUCUGUUCGCCUGGUACCUCGACUGGAUAUUUUACUCAAUUUGGCCGAGAAAACUGGCCACGGCAGUCUUCAAAAUUGCAUG--UUUCCUGAUUCUAGACACUAGGCCAACAG
.........(((((.(((((((..((.((..(((..............((((((.......))))))..(((((.......)))))...--..)))....)).))..))))))).))))) ( -32.20)
>DroSim_CAF1 7501 118 - 1
CUGACAUUUCUGUUCGCCUGGUACCUCGACUGGAUAUUUUACUCAAUUUGGCCGAGAAAACUGGCCACGGCCGUCUUCAAAAUUGCAUG--UUUCCUGAUUCUAGACACUAGGCCAACAG
.........(((((.(((((((..((((.(..(((..........)))..).))))......(((....)))(((((((((((.....)--)))..)))....))))))))))).))))) ( -32.60)
>DroEre_CAF1 5549 116 - 1
CUGACAUUUCUGUUCGCCUGUUAUCUGAAACCCAGAAUCU-CUCAAUUUACCCAAGAAAACUCGGAUCAAACG---UCCGAUUUUCAUAGUUUUCAUUAAUUGUUGCACCAGGCGAUCAU
..........((.(((((((...((((.....))))....-..............(((((.((((((.....)---))))))))))((((((......)))))).....))))))).)). ( -27.30)
>consensus
CUGACAUUUCUGUUCGCCUGGUACCUCGACUCGAUAUUUUACUCAAUUUGGCCGAGAAAACUGGCCACGGCCGUCUUCAAAAUUGCAUG__UUUCCUGAUUCUAGACACCAGGCCAACAG
.........(((((.(((((((..........................((((((.......)))))).....((((...........................))))))))))).))))) (-18.79 = -20.23 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:16 2006