Locus 5232

Sequence ID	2R_DroMel_CAF1
Location	17,040,611 – 17,040,711
Length	100
Max. P	0.961859

overview

Window 6

Location	17,040,611 – 17,040,711
Length	100
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	92.50
Mean single sequence MFE	-21.73
Consensus MFE	-18.63
Energy contribution	-17.82
Covariance contribution	-0.81
Combinations/Pair	1.24
Mean z-score	-1.47
Structure conservation index	0.86
SVM decision value	0.09
SVM RNA-class probability	0.580672
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17040611 100 + 20766785
UUGCACCAGUUUCUUACCUAGAAACAGUGUUUUUAUUGCCUCUACAAUUGGAUUCCUAGAAAUUAUGAAAUUUCAAUUGGCUGAGUCACUGCAGCAGCAA
..((((..((((((.....)))))).)))).....((((.....(((((((((((..(....)...)))..))))))))((((........)))).)))) ( -22.20)
>DroSim_CAF1 142146 100 + 1
UUGCUCCAGUUUCUUACCUAGAAACAGUGUUUUUAUUGCCUCUACAAUUGGAUUCCUAGAAAUUAUGAAAUUUCAAUUGGCUGACUCACUGCAGCAGCAA
.((((.(.((((((.....))))))((((..((....(((((((....))))......((((((....))))))....))).))..))))...).)))). ( -21.30)
>DroEre_CAF1 138121 99 + 1
UUGCUCCAGUUUCUUACGUAGGAAUAGUGUUUUUAUUGCCUCCACAAUUGGAUUCCAAGAAAUUAUGAAAUUUCAAUUGGCUUACUCACUGCGGUGGC-A
.((((((.((((((.....))))))((((........(((((((....))))......((((((....))))))....))).....))))..)).)))-) ( -21.42)
>DroYak_CAF1 147447 100 + 1
UUGCUCCAGUUUCUUACCUGGAAACAGUGUUUUUAUUGCCUCCACAAUUGGAUUCCAAGAAAUUAUGAAAUUUCAAUUGACUGACUCACUGCGGCAGCAA
(((((.((((........((((..(((((....)))))..))))(((((((((((.((....))..)))..))))))))........)))).)))))... ( -22.00)
>consensus
UUGCUCCAGUUUCUUACCUAGAAACAGUGUUUUUAUUGCCUCCACAAUUGGAUUCCAAGAAAUUAUGAAAUUUCAAUUGGCUGACUCACUGCAGCAGCAA
(((((.(.((((((.....))))))((((........(((((((....))))......((((((....))))))....))).....))))).)))))... (-18.63 = -17.82 +  -0.81)

alignment

secondary structure

dotplot

Window 7

Location	17,040,611 – 17,040,711
Length	100
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-25.69
Consensus MFE	-22.13
Energy contribution	-22.57
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.39
Structure conservation index	0.86
SVM decision value	1.53
SVM RNA-class probability	0.961859
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17040611 100 - 20766785
UUGCUGCUGCAGUGACUCAGCCAAUUGAAAUUUCAUAAUUUCUAGGAAUCCAAUUGUAGAGGCAAUAAAAACACUGUUUCUAGGUAAGAAACUGGUGCAA
(((((.(((((((.......((....((((((....))))))..))......))))))).)))))......((((((((((.....)))))).))))... ( -26.12)
>DroSim_CAF1 142146 100 - 1
UUGCUGCUGCAGUGAGUCAGCCAAUUGAAAUUUCAUAAUUUCUAGGAAUCCAAUUGUAGAGGCAAUAAAAACACUGUUUCUAGGUAAGAAACUGGAGCAA
....((((.((((...((.(((....((((((....))))))..............((((((((..........)))))))))))..)).)))).)))). ( -24.40)
>DroEre_CAF1 138121 99 - 1
U-GCCACCGCAGUGAGUAAGCCAAUUGAAAUUUCAUAAUUUCUUGGAAUCCAAUUGUGGAGGCAAUAAAAACACUAUUCCUACGUAAGAAACUGGAGCAA
(-(((.(((((((.......((((..((((((....))))))))))......))))))).))))............((((..(....).....))))... ( -24.82)
>DroYak_CAF1 147447 100 - 1
UUGCUGCCGCAGUGAGUCAGUCAAUUGAAAUUUCAUAAUUUCUUGGAAUCCAAUUGUGGAGGCAAUAAAAACACUGUUUCCAGGUAAGAAACUGGAGCAA
(((((.(((((((.......((((..((((((....))))))))))......))))))).))))).........((((.((((........)))))))). ( -27.42)
>consensus
UUGCUGCCGCAGUGAGUCAGCCAAUUGAAAUUUCAUAAUUUCUAGGAAUCCAAUUGUAGAGGCAAUAAAAACACUGUUUCUAGGUAAGAAACUGGAGCAA
(((((.(((((((.......(((...((((((....)))))).)))......))))))).))))).........((((.((((........)))))))). (-22.13 = -22.57 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:43 2006