Locus 6940

Sequence ID	X_DroMel_CAF1
Location	17,380,335 – 17,380,450
Length	115
Max. P	0.981317

overview

Window 2

Location	17,380,335 – 17,380,430
Length	95
Sequences	4
Columns	99
Reading direction	forward
Mean pairwise identity	79.83
Mean single sequence MFE	-28.03
Consensus MFE	-23.90
Energy contribution	-23.28
Covariance contribution	-0.62
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.85
SVM decision value	1.88
SVM RNA-class probability	0.981317
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17380335 95 + 22224390
CGAAUUAAUAUUUGCCAUUCCCUUGGUUACACCUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCC----UCAUCCCCAGCCUGCAACGCGC
.............(((((.((((((((.((.......)).)))))))).)))))......(((((.......)----)))).....((.......)).. ( -26.90)
>DroSec_CAF1 97222 96 + 1
CGAAUUAAUAUUUGCCAUUCCCUUGGCUACACAUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCCCAUCCCAUCCC---CCUGCAACGCGC
((.....((((..(((((.((((((((.((.(....))).)))))))).)))))....)))).....))...............---............ ( -26.60)
>DroEre_CAF1 97963 82 + 1
CGAAUUAAUAUUUGCCAUUCCCUUGGCUACACCUUUGCUCGCCAGGGGCGUGGUUUUCAUAUGAGGACGAUCC-----------------CCAUGCCCC
.............(((((.((((((((.............)))))))).))))).....((((.((.....))-----------------.)))).... ( -24.72)
>DroYak_CAF1 89373 93 + 1
CGAAUUAAUAUUUGCCAUUCCCUUGGCUACACCUUUGUUGGCCGGGGGCGUGGUCUCUAUAUGAGGGCGAUCCU---CGAUUCC---CCUCCAAUCCCC
.......((((..(((((.((((((((((((....)).)))))))))).)))))....))))(((((.((((..---.)))).)---))))........ ( -33.90)
>consensus
CGAAUUAAUAUUUGCCAUUCCCUUGGCUACACCUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCC____CCAUCCC___CCUCCAACCCCC
((.....((((..(((((.((((((((..((....))...)))))))).)))))....)))).....)).............................. (-23.90 = -23.28 +  -0.62)

alignment

secondary structure

dotplot

Window 3

Location	17,380,356 – 17,380,450
Length	94
Sequences	4
Columns	98
Reading direction	forward
Mean pairwise identity	74.69
Mean single sequence MFE	-24.15
Consensus MFE	-13.61
Energy contribution	-13.05
Covariance contribution	-0.56
Combinations/Pair	1.33
Mean z-score	-1.71
Structure conservation index	0.56
SVM decision value	-0.04
SVM RNA-class probability	0.513747
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17380356 94 + 22224390
CUUGGUUACACCUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCC----UCAUCCCCAGCCUGCAACGCGCUUCAUCCCCACUAUCCCCCC
..((((.((.......)).))))(((((((((((.....(((((.......)----))))....))))......)))))))................. ( -21.60)
>DroSec_CAF1 97243 95 + 1
CUUGGCUACACAUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCCCAUCCCAUCCC---CCUGCAACGCGCUUCAUCCCCACUAUCAUCCC
...(((((......)))))((((((((.((((.((((.....)))).(((...))))))).))---))))....))...................... ( -20.20)
>DroEre_CAF1 97984 79 + 1
CUUGGCUACACCUUUGCUCGCCAGGGGCGUGGUUUUCAUAUGAGGACGAUCC-----------------CCAUGCCCCACCAUCACCACUAUCCCC--
..((((.............))))(((((((((...((....))((.....))-----------------)))))))))..................-- ( -23.52)
>DroYak_CAF1 89394 92 + 1
CUUGGCUACACCUUUGUUGGCCGGGGGCGUGGUCUCUAUAUGAGGGCGAUCCU---CGAUUCC---CCUCCAAUCCCCACCAUCCCCACCAUCUCCCC
...(((((((....)).)))))(((((.(((((........(((((.((((..---.)))).)---))))........))))).))).))........ ( -31.29)
>consensus
CUUGGCUACACCUUUGGUCGCCAGGGGCGUGGCUUCUAUAUGAGAACGAUCC____CCAUCCC___CCUCCAACCCCCACCAUCCCCACUAUCCCCCC
...((((((.((((((.....)))))).))))))................................................................ (-13.61 = -13.05 +  -0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:21 2006