Locus 4394

Sequence ID	3L_DroMel_CAF1
Location	12,868,415 – 12,868,507
Length	92
Max. P	0.823667

overview

Window 2

Location	12,868,415 – 12,868,507
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	85.11
Mean single sequence MFE	-28.97
Consensus MFE	-20.99
Energy contribution	-21.36
Covariance contribution	0.37
Combinations/Pair	1.21
Mean z-score	-2.04
Structure conservation index	0.72
SVM decision value	0.69
SVM RNA-class probability	0.823667
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12868415 92 + 23771897
UCUCGAAGUGGAUGAGCUGCUCACUUAGAUGUGGGCGGUGGCGGUUCGAUUGCCCGUACUUUUAAGUGAGUGCAAUAAAGACUGAGUGAGUU
......(((......)))((((((((((....(((((((.(.....).)))))))((((((......))))))........)))))))))). ( -32.50)
>DroSec_CAF1 1689 70 + 1
UCUCGAGGUGGAUGAGCUGCUCACUUAGAUGUGAG----------------------ACUUUUAAGUGAGUGCAAUAAAGACUGAGUGAGUU
.((((.(((......((.(((((((((((.(....----------------------.).))))))))))))).......)))...)))).. ( -18.72)
>DroSim_CAF1 1881 91 + 1
UCUCGAGGUGGAUGAGCUGCUCACUUAGAUGUGGGCGGUGGCGGUUCGAUUGCCCAUAC-UUUAAGUGAGUGCAAUAAAGACUGAGUGAGUU
.((((.(((......((.(((((((((((((((((((((.(.....).)))))))))).-))))))))))))).......)))...)))).. ( -34.52)
>DroEre_CAF1 1902 92 + 1
UCUCGAGGUGGAUGAGCUGCUCACUUAGAUGUGGGCGGUGGCGGUUCGAUUACCCAUACGUUUCAGUGAGUGCAAUAAAGUCCGAGUGGGUU
.((((...(((((..((.(((((((.(((((((.(.(((((((...)).)))))).))))))).)))))))))......)))))..)))).. ( -30.20)
>DroYak_CAF1 1848 92 + 1
UCUCGAGGUGGAUGAGCUGCUCACUUAGAUGUGGGCGGUGGCGGUUCGAUUACCCAUACGUUUGAGUGGGUGCAAUAAAGACUGAGUGCGUU
..(((((.((.....(((((((((......)))))))))..)).)))))..((((((........))))))(((...(....)...)))... ( -28.90)
>consensus
UCUCGAGGUGGAUGAGCUGCUCACUUAGAUGUGGGCGGUGGCGGUUCGAUUACCCAUACGUUUAAGUGAGUGCAAUAAAGACUGAGUGAGUU
.((((.(((......((.(((((((((((.(((.(.(((((........)))))).))).))))))))))))).......)))...)))).. (-20.99 = -21.36 +   0.37)

alignment

secondary structure

dotplot

Window 3

Location	12,868,415 – 12,868,507
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	85.11
Mean single sequence MFE	-17.70
Consensus MFE	-13.48
Energy contribution	-14.65
Covariance contribution	1.17
Combinations/Pair	1.14
Mean z-score	-1.73
Structure conservation index	0.76
SVM decision value	0.35
SVM RNA-class probability	0.698888
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12868415 92 - 23771897
AACUCACUCAGUCUUUAUUGCACUCACUUAAAAGUACGGGCAAUCGAACCGCCACCGCCCACAUCUAAGUGAGCAGCUCAUCCACUUCGAGA
......((((((.......((.((((((((...((..((((...............))))))...))))))))..))......)))..))). ( -18.98)
>DroSec_CAF1 1689 70 - 1
AACUCACUCAGUCUUUAUUGCACUCACUUAAAAGU----------------------CUCACAUCUAAGUGAGCAGCUCAUCCACCUCGAGA
......(((((........((.((((((((.....----------------------........))))))))..))........)).))). ( -12.31)
>DroSim_CAF1 1881 91 - 1
AACUCACUCAGUCUUUAUUGCACUCACUUAAA-GUAUGGGCAAUCGAACCGCCACCGCCCACAUCUAAGUGAGCAGCUCAUCCACCUCGAGA
......(((((........((.((((((((..-((.(((((...............))))).)).))))))))..))........)).))). ( -21.15)
>DroEre_CAF1 1902 92 - 1
AACCCACUCGGACUUUAUUGCACUCACUGAAACGUAUGGGUAAUCGAACCGCCACCGCCCACAUCUAAGUGAGCAGCUCAUCCACCUCGAGA
......(((((........((.((((((.....((.(((((...............))))).))...))))))..)).........))))). ( -19.29)
>DroYak_CAF1 1848 92 - 1
AACGCACUCAGUCUUUAUUGCACCCACUCAAACGUAUGGGUAAUCGAACCGCCACCGCCCACAUCUAAGUGAGCAGCUCAUCCACCUCGAGA
......(((((........(((((((..(....)..)))))...............((.(((......))).)).))........)).))). ( -16.79)
>consensus
AACUCACUCAGUCUUUAUUGCACUCACUUAAAAGUAUGGGCAAUCGAACCGCCACCGCCCACAUCUAAGUGAGCAGCUCAUCCACCUCGAGA
......(((((........((.((((((((...((.(((((...............))))).)).))))))))..))........)).))). (-13.48 = -14.65 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:33 2006