Locus 1297

Sequence ID	2L_DroMel_CAF1
Location	3,427,514 – 3,427,618
Length	104
Max. P	0.850817

overview

Window 3

Location	3,427,514 – 3,427,618
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	87.25
Mean single sequence MFE	-35.87
Consensus MFE	-26.28
Energy contribution	-26.44
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-1.95
Structure conservation index	0.73
SVM decision value	0.52
SVM RNA-class probability	0.766551
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3427514 104 + 22407834
UGGCAGUUGGGUGGAAAAGUCGGUGUACCCAGCGAUGGAACUGAACCGAUGCGAUCCGAACUGACAUUAAGCUCAAGGACGACAUCUUCCACUCAGUGCUGUGC
.((((.((((((((((...(((((....(((....))).)))))...((((((.(((....(((........))).))))).)))))))))))))))))).... ( -34.60)
>DroSec_CAF1 16477 104 + 1
UGGCAGUUGGGUGGAAAAGUCUGUGUACCCAGCGAUGGAACUGAACCGAUGCGAUCCGAACUGGCAUUAAGCCCAAGGACGACAUCUUCCACCCAGUGCUGUGC
.((((.((((((((((...((.((....(((....))).)).))...((((((.(((.....(((.....)))...))))).)))))))))))))))))).... ( -37.90)
>DroSim_CAF1 16593 104 + 1
UGGCAGUUGGGUGGAAAAGUCUGUGUACCCAGCGAUGGAACUGAACCGAUGCGAUCCGAACUGGCAUUAAGCCCAAGGACGACAUCUUCCACCCAGUGCUGUGC
.((((.((((((((((...((.((....(((....))).)).))...((((((.(((.....(((.....)))...))))).)))))))))))))))))).... ( -37.90)
>DroEre_CAF1 16908 99 + 1
UGGCAGUGGGGUGGAAAAGUCUGUGUACCCAGCGAUGGUACUGAACCG-----AUCCGAACUGACAUUAAGCUCAAGGACGACUGCUUCCACCCACUGCUGUGC
.(((((((((.(((((.((((...(((((.......)))))......(-----.(((....(((........))).))))))))..)))))))))))))).... ( -37.00)
>DroYak_CAF1 17973 85 + 1
UGGCAGUUGGGUGGAAAAGUCUGUGUGCCCAGCGAUGGA-------------------AACUGACAUUAAGCUCAAGGACGACAUCUUCCACCCACUGCUGUGC
.((((((.((((((((..((((.((.((........(..-------------------..).........)).)).))))......)))))))))))))).... ( -31.93)
>consensus
UGGCAGUUGGGUGGAAAAGUCUGUGUACCCAGCGAUGGAACUGAACCGAUGCGAUCCGAACUGACAUUAAGCUCAAGGACGACAUCUUCCACCCAGUGCUGUGC
..((((((((((((((..(((.......(((....)))................(((....(((........))).))).)))...)))))))))..))))).. (-26.28 = -26.44 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	3,427,514 – 3,427,618
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	87.25
Mean single sequence MFE	-36.92
Consensus MFE	-25.09
Energy contribution	-26.10
Covariance contribution	1.01
Combinations/Pair	1.03
Mean z-score	-2.60
Structure conservation index	0.68
SVM decision value	0.79
SVM RNA-class probability	0.850817
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3427514 104 - 22407834
GCACAGCACUGAGUGGAAGAUGUCGUCCUUGAGCUUAAUGUCAGUUCGGAUCGCAUCGGUUCAGUUCCAUCGCUGGGUACACCGACUUUUCCACCCAACUGCCA
.....(((.((.(((((((((((.((((..(((((.......))))))))).)))))((((((((......)))))....))).....)))))).))..))).. ( -31.60)
>DroSec_CAF1 16477 104 - 1
GCACAGCACUGGGUGGAAGAUGUCGUCCUUGGGCUUAAUGCCAGUUCGGAUCGCAUCGGUUCAGUUCCAUCGCUGGGUACACAGACUUUUCCACCCAACUGCCA
.....(((.((((((((((((((.((((...(((.....))).....)))).))))).(..((((......))))..)..........)))))))))..))).. ( -39.70)
>DroSim_CAF1 16593 104 - 1
GCACAGCACUGGGUGGAAGAUGUCGUCCUUGGGCUUAAUGCCAGUUCGGAUCGCAUCGGUUCAGUUCCAUCGCUGGGUACACAGACUUUUCCACCCAACUGCCA
.....(((.((((((((((((((.((((...(((.....))).....)))).))))).(..((((......))))..)..........)))))))))..))).. ( -39.70)
>DroEre_CAF1 16908 99 - 1
GCACAGCAGUGGGUGGAAGCAGUCGUCCUUGAGCUUAAUGUCAGUUCGGAU-----CGGUUCAGUACCAUCGCUGGGUACACAGACUUUUCCACCCCACUGCCA
.....((((((((((((((.((((((((..(((((.......)))))))))-----.......(((((.......)))))...)))))))))).)))))))).. ( -41.10)
>DroYak_CAF1 17973 85 - 1
GCACAGCAGUGGGUGGAAGAUGUCGUCCUUGAGCUUAAUGUCAGUU-------------------UCCAUCGCUGGGCACACAGACUUUUCCACCCAACUGCCA
.....(((((((((((((((.(((.....(((.(.....))))((.-------------------((((....)))).))...))))))))))))).))))).. ( -32.50)
>consensus
GCACAGCACUGGGUGGAAGAUGUCGUCCUUGAGCUUAAUGUCAGUUCGGAUCGCAUCGGUUCAGUUCCAUCGCUGGGUACACAGACUUUUCCACCCAACUGCCA
.....(((.(((((((((((.(((......(((((.......)))))(((((.....)))))....(((....))).......))))))))))))))..))).. (-25.09 = -26.10 +   1.01)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:00 2006