Locus 1497

Sequence ID	3R_DroMel_CAF1
Location	4,313,225 – 4,313,423
Length	198
Max. P	0.980923

overview

Window 2

Location	4,313,225 – 4,313,343
Length	118
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	76.75
Mean single sequence MFE	-27.70
Consensus MFE	-19.33
Energy contribution	-19.67
Covariance contribution	0.34
Combinations/Pair	1.09
Mean z-score	-1.55
Structure conservation index	0.70
SVM decision value	0.60
SVM RNA-class probability	0.794675
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4313225 118 - 27905053
CUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGGUGCGCUAUUACAGUAUAAAGCCGAGUAGGGAUUACUCUUUCAAGCAUUCAAAUAUUAA--AUUUUGAUGAUUGGGUAUAU
(((((((((...((((((((((....))).)))))))(((((((((............))).((((((...))))))......)))))).........--.....)))))))))...... ( -28.00)
>DroSec_CAF1 659 117 - 1
CUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGGUGCGCUAUUGCAGUAUAAAGCCGAGUGGCGAUUACCCUUUGAAGCAAUACAUUUUUAG--CUUAUGAUGGUUGAGUAUA-
.((((((((...((((((((((....))).)))))))((((((((((((((........))..)))))))..)))))....((((............)--)))..))))))))......- ( -28.20)
>DroEre_CAF1 687 105 - 1
CUAAUCAUUUCUUUGUAGUAUCCUCAGGUAACUACAAGGGUGCGCUGUUA-------UAGCCGAUUGUCGAUUGCUCUUUCGAGCAUUUAAAUAUAAAUGGUGUUGAUGGUU--------
..((((((((((((((((((((....))).)))))))))).(((((((((-------((..((.....))..(((((....)))))......))).)))))))).)))))))-------- ( -26.90)
>consensus
CUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGGUGCGCUAUUACAGUAUAAAGCCGAGUGGCGAUUACUCUUUCAAGCAUUAAAAUAUUAA__AUUUUGAUGGUUG_GUAUA_
.(((((((((((((((((((((....))).))))))))))((((((............))).(((((.....)))))......)))...................))))))))....... (-19.33 = -19.67 +   0.34)

alignment

secondary structure

dotplot

Window 3

Location	4,313,303 – 4,313,423
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	98.89
Mean single sequence MFE	-35.03
Consensus MFE	-35.25
Energy contribution	-35.03
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-2.57
Structure conservation index	1.01
SVM decision value	1.87
SVM RNA-class probability	0.980923
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4313303 120 - 27905053
AGCUCAUUUCCGCUGCCACAAUUAAAAUGUUAAUCCACCGGAUGCAGGUGGCAGCCAUCGUGGACAAGAACAUGAUUAUGCUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGG
(((........((((((((........(((..((((...))))))).)))))))).((((((........))))))...)))........((((((((((((....))).))))))))). ( -35.80)
>DroSec_CAF1 736 120 - 1
AGCUCAUUUCCGCUGCCACAAUUAAAAUGUUAAUCCACCGGAUGCAGGUGGCAGCCAUCGUGGACAAGAACAUGAUUAUGCUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGG
(((........((((((((........(((..((((...))))))).)))))))).((((((........))))))...)))........((((((((((((....))).))))))))). ( -35.80)
>DroEre_CAF1 752 120 - 1
AGCUCAUUUCCGCUGCUACAAUUAAAAUGUUAAUCCACCGGAUGCAGGUGGCAGCCAUCGUGGACAAGAACAUGAUUAUGCUAAUCAUUUCUUUGUAGUAUCCUCAGGUAACUACAAGGG
(((........((((((((........(((..((((...))))))).)))))))).((((((........))))))...)))........((((((((((((....))).))))))))). ( -33.50)
>consensus
AGCUCAUUUCCGCUGCCACAAUUAAAAUGUUAAUCCACCGGAUGCAGGUGGCAGCCAUCGUGGACAAGAACAUGAUUAUGCUAAUCAUUUCUUUGUAGUAUCCUAAGGUAACUACAAGGG
(((........((((((((........(((..((((...))))))).)))))))).((((((........))))))...)))........((((((((((((....))).))))))))). (-35.25 = -35.03 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:00 2006