Locus 4387

Sequence ID	3R_DroMel_CAF1
Location	11,601,438 – 11,601,530
Length	92
Max. P	0.963334

overview

Window 7

Location	11,601,438 – 11,601,530
Length	92
Sequences	5
Columns	95
Reading direction	forward
Mean pairwise identity	78.75
Mean single sequence MFE	-17.46
Consensus MFE	-9.58
Energy contribution	-10.34
Covariance contribution	0.76
Combinations/Pair	1.21
Mean z-score	-1.88
Structure conservation index	0.55
SVM decision value	0.25
SVM RNA-class probability	0.654069
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11601438 92 + 27905053
AUGCUUUUA---UUAGUCACUAUUAAAGCAGUGACGUUAAAUGUCGUGAUUUUUAACAAACAUGUGUAACUCUCAAUAAUGGUAUUAAAAGGAAA
(((((.(((---((.((((((........))))))((((.((((.((........))..))))...))))....))))).))))).......... ( -16.60)
>DroSec_CAF1 131243 92 + 1
AUGCUUUUA---UUAGUCACUAUUAAAGCAGUGACGUUAAAUGUCGUGAUUUUUAUCAAACUCAUGUAUCUCUUAAUACUGGUAUUAAAAGUAAA
.((((((((---.((((((((........))))))(((((..(.(((((.(((....))).)))))...)..))))).....)).)))))))).. ( -18.40)
>DroSim_CAF1 139421 87 + 1
UUGCUUUUA---UUAGUCACUAUUAAAGCAGUGACGUUAAAU-----GAUUUUUAUCAAACUGAUGUAUCUCUUAAUACUGGUAUUAAAAGUAAA
(((((((((---.((((((((........))))))(((((..-----(((...((((.....)))).)))..))))).....)).))))))))). ( -19.90)
>DroEre_CAF1 140308 72 + 1
GUGCUUUUA---UUAGUCACUAUUAAAGCAGUGAA-------------------AUC-AACAUGUGUACCUCCUAAUACUGGUACUACAGCUAAA
(((((..((---(((((((((........))))).-------------------...-.((....)).....))))))..))))).......... ( -13.30)
>DroYak_CAF1 132618 95 + 1
GUGCUUUUAUUAUUAGUCACUAUUAAACCAGUGACGCUAAAUGUCGUGAUUUUUAUCAAACAUGUGCACCUCUAAAUACUGGUAUUAAGACUAAA
(((((..((((....((((((........))))))((...((((..((((....)))).))))..)).......))))..))))).......... ( -19.10)
>consensus
AUGCUUUUA___UUAGUCACUAUUAAAGCAGUGACGUUAAAUGUCGUGAUUUUUAUCAAACAUGUGUACCUCUUAAUACUGGUAUUAAAAGUAAA
.((((((((......((((((........))))))..............................(((((..........))))))))))))).. ( -9.58 = -10.34 +   0.76)

alignment

secondary structure

dotplot

Window 8

Location	11,601,438 – 11,601,530
Length	92
Sequences	5
Columns	95
Reading direction	reverse
Mean pairwise identity	78.75
Mean single sequence MFE	-17.70
Consensus MFE	-11.22
Energy contribution	-11.98
Covariance contribution	0.76
Combinations/Pair	1.19
Mean z-score	-2.27
Structure conservation index	0.63
SVM decision value	1.55
SVM RNA-class probability	0.963334
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11601438 92 - 27905053
UUUCCUUUUAAUACCAUUAUUGAGAGUUACACAUGUUUGUUAAAAAUCACGACAUUUAACGUCACUGCUUUAAUAGUGACUAA---UAAAAGCAU
....(((((((((....)))))))))......((((((((((((..........))))))(((((((......)))))))...---...)))))) ( -17.90)
>DroSec_CAF1 131243 92 - 1
UUUACUUUUAAUACCAGUAUUAAGAGAUACAUGAGUUUGAUAAAAAUCACGACAUUUAACGUCACUGCUUUAAUAGUGACUAA---UAAAAGCAU
....(((((((((....)))))))))........(((((((....)))).))).......(((((((......)))))))...---......... ( -17.90)
>DroSim_CAF1 139421 87 - 1
UUUACUUUUAAUACCAGUAUUAAGAGAUACAUCAGUUUGAUAAAAAUC-----AUUUAACGUCACUGCUUUAAUAGUGACUAA---UAAAAGCAA
....(((((((((....)))))))))........(((((((....)))-----.......(((((((......)))))))...---...)))).. ( -17.10)
>DroEre_CAF1 140308 72 - 1
UUUAGCUGUAGUACCAGUAUUAGGAGGUACACAUGUU-GAU-------------------UUCACUGCUUUAAUAGUGACUAA---UAAAAGCAC
.((((((((.(((((..........)))))))).)))-)).-------------------.((((((......))))))....---......... ( -15.30)
>DroYak_CAF1 132618 95 - 1
UUUAGUCUUAAUACCAGUAUUUAGAGGUGCACAUGUUUGAUAAAAAUCACGACAUUUAGCGUCACUGGUUUAAUAGUGACUAAUAAUAAAAGCAC
.....(((.((((....)))).))).((((..(((((((((....)))).))))).....(((((((......)))))))...........)))) ( -20.30)
>consensus
UUUACUUUUAAUACCAGUAUUAAGAGAUACACAUGUUUGAUAAAAAUCACGACAUUUAACGUCACUGCUUUAAUAGUGACUAA___UAAAAGCAC
....(((((((((....)))))))))..................................(((((((......)))))))............... (-11.22 = -11.98 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:52 2006