Locus 4305

Sequence ID	3R_DroMel_CAF1
Location	11,423,797 – 11,423,947
Length	150
Max. P	0.973006

overview

Window 5

Location	11,423,797 – 11,423,916
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.69
Mean single sequence MFE	-35.84
Consensus MFE	-27.99
Energy contribution	-29.02
Covariance contribution	1.03
Combinations/Pair	1.03
Mean z-score	-2.31
Structure conservation index	0.78
SVM decision value	1.50
SVM RNA-class probability	0.959143
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11423797 119 - 27905053
AUUCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUGCAGCAGGUUUCUUGUUGCCUCAAC
.(((.(...-.).)))(.((((((.((....)).))).))))(((((((((........)))))...)))).....(((....))).........((((((((...))))))))...... ( -35.80)
>DroSec_CAF1 171336 119 - 1
AUUCUGGAA-GCUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUGCAGCAGGUUCCUUGUUGCUUCAAC
.....(((.-((((......((((.((....)).))))))))(((((((((........)))))...)))).....(((....)))....)))..((((((((...))))))))...... ( -38.60)
>DroSim_CAF1 165196 97 - 1
AUUCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUG----------------------AC
.(((.(...-.).)))(.((((((.((....)).))).))))(((((((((........)))))...)))).....(((....)))..........----------------------.. ( -27.30)
>DroEre_CAF1 161037 119 - 1
GUCCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCUGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUGUUGCAGGUUCCUUGUUGGUUCAAC
(((..(...-.)....)))....((((((((((...(((((((((((((((........)))))...)))).....(((....)))............)))))).)))).)))))).... ( -39.40)
>DroYak_CAF1 163617 120 - 1
GUCCUGGAAAAGUGAAGACUGUAAAGCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUGCAGCAGGUUCCUUGUUGCUUCAAC
.....(((...(((..(.(((..((((.....))))..))))(((((((((........)))))...)))).))).(((....)))....)))..((((((((...))))))))...... ( -38.10)
>consensus
AUUCUGGAA_ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGUAUACGCAUUAUCCUUGCAGCAGGUUCCUUGUUGCUUCAAC
.....(((............((((.((....)).))))..(.(((((((((........)))))...)))).)...(((....)))....)))..((((((((...))))))))...... (-27.99 = -29.02 +   1.03)

alignment

secondary structure

dotplot

Window 6

Location	11,423,837 – 11,423,947
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.68
Mean single sequence MFE	-34.74
Consensus MFE	-27.50
Energy contribution	-28.06
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.34
Structure conservation index	0.79
SVM decision value	1.70
SVM RNA-class probability	0.973006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11423837 110 - 27905053
UC---------GUCGCAGGACAAACAGGACUCGCAACUGGAUUCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
..---------(((....)))..........(((..(((..(((.(...-.).)))....((((.((....)).))))))).(((((((((........)))))...)))).....))). ( -30.70)
>DroSec_CAF1 171376 110 - 1
UC---------GUCGCAGGACAAACAGGACUCGAAACAGGAUUCUGGAA-GCUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
..---------(((....)))...(((((..(......)..)))))...-((((..(.((((((.((....)).))).))))(((((((((........)))))...))))...)))).. ( -35.60)
>DroSim_CAF1 165214 110 - 1
UC---------GUCGCAGGACAAACAGGACUCGAAACAGGAUUCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
..---------..(((.((.(((............((((..(((.(...-.).)))..))))...((....)).))))).(.(((((((((........)))))...)))).)...))). ( -34.10)
>DroEre_CAF1 161077 113 - 1
UCGCAGGACACGUCGCAGGACAAACAGGAAUCGA------GUCCUGGAA-ACUGAAGACUGUAAACCGAAAGGCUUGCCUGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
..((((((((.(((.(((......(((((.....------.)))))...-.)))..))))))...((....))....)))))(((((((((........)))))...))))......... ( -39.10)
>DroYak_CAF1 163657 105 - 1
UC---------GUCGCAGGACAAACAGGAUUCGA------GUCCUGGAAAAGUGAAGACUGUAAAGCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
..---------..(((........((((((....------)))))).....(((..(.(((..((((.....))))..))))(((((((((........)))))...)))).))).))). ( -34.20)
>consensus
UC_________GUCGCAGGACAAACAGGACUCGAAAC_GGAUUCUGGAA_ACUGAAGACUGUAAACCGAAAGGCUUGCCAGCGCCUUGUGCAAACACUAGCGCAAAAAGGCACACAGCGU
...........(((.(((......(((((..(......)..))))).....)))..))).((((.((....)).))))..(.(((((((((........)))))...)))).)....... (-27.50 = -28.06 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:25 2006