Locus 4999

Sequence ID	3R_DroMel_CAF1
Location	13,169,641 – 13,169,739
Length	98
Max. P	0.999511

overview

Window 3

Location	13,169,641 – 13,169,739
Length	98
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	89.16
Mean single sequence MFE	-30.12
Consensus MFE	-24.62
Energy contribution	-26.30
Covariance contribution	1.68
Combinations/Pair	1.04
Mean z-score	-2.46
Structure conservation index	0.82
SVM decision value	2.24
SVM RNA-class probability	0.990995
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13169641 98 + 27905053
UGUGGCCUUGGAUUUUCUUUUU----GAAAACGCCUGGAAAAGGCCGAAAAACAUCCAAAACGACUGCACUGAUUGCAAACGAGGGAAUGUUCCCAUUGAAA
.((.(..((((((((((.....----))))).((((.....)))).........)))))..).))((((.....))))..(((((((....)))).)))... ( -23.60)
>DroSec_CAF1 199143 98 + 1
UGUGGCCUUGCAUUUUCUUUUU----GAAAAUGCCUGGAAAAGGCCGCAAAACAUCCAGAACGACUGCACUGAUUGCAAUCGAGGGAAUGUCCCCAUUGAAA
(((((((((((((((((.....----))))))))......))))))))).......(((..(((.((((.....)))).))).(((......))).)))... ( -34.10)
>DroSim_CAF1 184480 98 + 1
UGUGGCCUUGCUUUUUCUUUUU----GAAAAUGCCUGGAAAAGGCCGCAAAACAUCCAGAACGACUGCACUGAUUGCAAUCGAGGGAAUGUCCCCAUCGAAA
(((((((((((.(((((.....----))))).))......))))))))).........((.(((.((((.....)))).))).(((......))).)).... ( -30.00)
>DroEre_CAF1 190016 98 + 1
UGUGGCCUUGCACUUCCGUUUA----GAAAUUGGCAGGAAAAGGCCGCAAAACACCCAGAACGACUGCACUGAUUGCAAUCGAGGGAAUGUCCCCAUUGAAA
(((((((((...((.(((....----.....))).))...))))))))).......(((..(((.((((.....)))).))).(((......))).)))... ( -30.80)
>DroYak_CAF1 198043 102 + 1
UGUGGCCUUGCAUUUCCGUGAAAUGCGAAAAUGUGUAGAAAAGGCCGCAAAACAACCAGAACGACUGCACUGAUUGCAAUCGAGGGAAUGUCCCCAUUGAAA
(((((((((((((((.(((.....))).))))))......)))))))))...(((......(((.((((.....)))).))).(((......))).)))... ( -32.10)
>consensus
UGUGGCCUUGCAUUUUCUUUUU____GAAAAUGCCUGGAAAAGGCCGCAAAACAUCCAGAACGACUGCACUGAUUGCAAUCGAGGGAAUGUCCCCAUUGAAA
(((((((((((((((((.........))))))))......)))))))))............(((.((((.....)))).))).(((......)))....... (-24.62 = -26.30 +   1.68)

alignment

secondary structure

dotplot

Window 4

Location	13,169,641 – 13,169,739
Length	98
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	89.16
Mean single sequence MFE	-31.64
Consensus MFE	-28.02
Energy contribution	-28.78
Covariance contribution	0.76
Combinations/Pair	1.13
Mean z-score	-2.73
Structure conservation index	0.89
SVM decision value	3.67
SVM RNA-class probability	0.999511
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13169641 98 - 27905053
UUUCAAUGGGAACAUUCCCUCGUUUGCAAUCAGUGCAGUCGUUUUGGAUGUUUUUCGGCCUUUUCCAGGCGUUUUC----AAAAAGAAAAUCCAAGGCCACA
.......((((((((((...((.(((((.....))))).))....)))))))))).((((((.....((.((((((----.....))))))))))))))... ( -27.30)
>DroSec_CAF1 199143 98 - 1
UUUCAAUGGGGACAUUCCCUCGAUUGCAAUCAGUGCAGUCGUUCUGGAUGUUUUGCGGCCUUUUCCAGGCAUUUUC----AAAAAGAAAAUGCAAGGCCACA
........(((((((((...((((((((.....))))))))....)))))))))(.((((((......((((((((----.....)))))))))))))).). ( -36.00)
>DroSim_CAF1 184480 98 - 1
UUUCGAUGGGGACAUUCCCUCGAUUGCAAUCAGUGCAGUCGUUCUGGAUGUUUUGCGGCCUUUUCCAGGCAUUUUC----AAAAAGAAAAAGCAAGGCCACA
........(((((((((...((((((((.....))))))))....)))))))))(.((((((......((.(((((----.....))))).)))))))).). ( -31.70)
>DroEre_CAF1 190016 98 - 1
UUUCAAUGGGGACAUUCCCUCGAUUGCAAUCAGUGCAGUCGUUCUGGGUGUUUUGCGGCCUUUUCCUGCCAAUUUC----UAAACGGAAGUGCAAGGCCACA
....((((....))))(((.((((((((.....))))))))....))).((((((((((........))).(((((----(....))))))))))))).... ( -32.70)
>DroYak_CAF1 198043 102 - 1
UUUCAAUGGGGACAUUCCCUCGAUUGCAAUCAGUGCAGUCGUUCUGGUUGUUUUGCGGCCUUUUCUACACAUUUUCGCAUUUCACGGAAAUGCAAGGCCACA
...((((((((.....))))((((((((.....)))))))).....))))...((.((((((.......((((((((.......)))))))).)))))).)) ( -30.50)
>consensus
UUUCAAUGGGGACAUUCCCUCGAUUGCAAUCAGUGCAGUCGUUCUGGAUGUUUUGCGGCCUUUUCCAGGCAUUUUC____AAAAAGAAAAUGCAAGGCCACA
........(((((((((...((((((((.....))))))))....)))))))))..((((((......((((((((.........))))))))))))))... (-28.02 = -28.78 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:57 2006