Locus 7907

Sequence ID	3L_DroMel_CAF1
Location	21,048,835 – 21,048,995
Length	160
Max. P	0.985293

overview

Window 4

Location	21,048,835 – 21,048,955
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.44
Mean single sequence MFE	-47.20
Consensus MFE	-43.24
Energy contribution	-43.42
Covariance contribution	0.19
Combinations/Pair	1.06
Mean z-score	-2.65
Structure conservation index	0.92
SVM decision value	2.00
SVM RNA-class probability	0.985293
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21048835 120 + 23771897
GCAGCGAGUGCAGGUCCGAAGGGCACCUGGAGGUCAGAGCUAAUUGAUUGGGAAAACCAUCUCUCGAUCCAAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCA
(((.....)))((((((....)).))))((.(.((((((((....((((((((........))))))))...)).)))))).).))......(.(((((((.((....)).)))))))). ( -42.90)
>DroSec_CAF1 103991 120 + 1
GCGGCGAGUGCAGGUCCGAAGGGCACCUGGAGGUCAGAGCUAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCA
..(((.....(((((((....)).)))))..(.((((((((....((((((((........))))))))...)).)))))).))))......(.(((((((.((....)).)))))))). ( -47.10)
>DroSim_CAF1 10228 120 + 1
GCGGCGAGUGCAGGUCCGAAGGGCACCUGGAGGUCAGAGCUAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCA
..(((.....(((((((....)).)))))..(.((((((((....((((((((........))))))))...)).)))))).))))......(.(((((((.((....)).)))))))). ( -47.10)
>DroEre_CAF1 25984 120 + 1
GCAGCGAGCGCAGGUCCGAAGGGCACUUGGAGGUCAGAGCUAAUUGAUUGGGAAAACCAUUUCUCGAUCCGACGUCUCUGGCCGCCAUUAACAAGCUGGGAGCACAUGUGGUCCCAGCCA
.....(.((.(((((((....)).)))))..((((((((......((((((((((....))))))))))......)))))))))))........(((((((.((....)).))))))).. ( -51.70)
>consensus
GCAGCGAGUGCAGGUCCGAAGGGCACCUGGAGGUCAGAGCUAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCA
..(((.....(((((((....)).)))))..(.((((((((....((((((((........))))))))...)).)))))).))))........(((((((.((....)).))))))).. (-43.24 = -43.42 +   0.19)

alignment

secondary structure

dotplot

Window 5

Location	21,048,875 – 21,048,995
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.81
Mean single sequence MFE	-33.65
Consensus MFE	-30.45
Energy contribution	-30.33
Covariance contribution	-0.13
Combinations/Pair	1.03
Mean z-score	-1.91
Structure conservation index	0.90
SVM decision value	1.21
SVM RNA-class probability	0.931190
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21048875 120 + 23771897
UAAUUGAUUGGGAAAACCAUCUCUCGAUCCAAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCAUGGCUAAUCUGGUUAAUUCCACUAAUCCACUAAGUGGCCA
.....((((((((........))))))))....(((....)))((((((...(.(((((((.((....)).)))))))).(((......(((......))).....)))...)))))).. ( -32.10)
>DroSec_CAF1 104031 112 + 1
UAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCAUGGCUAAUCUGGUUAAUUCCA--------CUAAGUGGCCA
.....((((((((........))))))))...........((((((((....(.(((((((.((....)).))))))))))))).....(((......)))--------.......))). ( -31.20)
>DroSim_CAF1 10268 112 + 1
UAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCAUGGCUAAUCUGGUUAAUUCCA--------CUAAGUGGCCA
.....((((((((........))))))))...........((((((((....(.(((((((.((....)).))))))))))))).....(((......)))--------.......))). ( -31.20)
>DroEre_CAF1 26024 112 + 1
UAAUUGAUUGGGAAAACCAUUUCUCGAUCCGACGUCUCUGGCCGCCAUUAACAAGCUGGGAGCACAUGUGGUCCCAGCCAUGGCUAAUCUGGUUAAUUCCC--------CUAAGUGGCCA
.....((((((((((....))))))))))..........(((((((((......(((((((.((....)).))))))).)))))......((......)).--------......)))). ( -40.10)
>consensus
UAAUUGAUUGGGAAAACCAUCUCUCGAUCCGAAGUCUCUGGGCGCCAUUAACGAGCUUGGAACACAUAUGAUCCGAGCCAUGGCUAAUCUGGUUAAUUCCA________CUAAGUGGCCA
.....((((((((........))))))))....(((....)))((((((.....(((((((.((....)).)))))))..(((((.....))))).................)))))).. (-30.45 = -30.33 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:22 2006