Locus 1821

Sequence ID	3L_DroMel_CAF1
Location	5,104,047 – 5,104,166
Length	119
Max. P	0.591565

overview

Window 2

Location	5,104,047 – 5,104,166
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.56
Mean single sequence MFE	-24.23
Consensus MFE	-16.76
Energy contribution	-18.32
Covariance contribution	1.56
Combinations/Pair	1.17
Mean z-score	-1.61
Structure conservation index	0.69
SVM decision value	0.00
SVM RNA-class probability	0.533773
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104047 119 + 23771897
GAUACACGGAACCAUCGCUGUU-UAAAAAUAGCGAGGAAAAUAAAGCGACUGAGAAGCCAGUAGAGAAAACCGAAGAAGCAAGUACAGAGGUUACUCAGUCGAAAGAGGAUAGUUCGGAA
......((((.((.((((((((-....)))))))))).........((((((((.((((..............................)))).))))))))...........))))... ( -30.51)
>DroSec_CAF1 296997 119 + 1
GAUACUCGGAACCAACGCUGUU-UAAAAAUACUAAGGAAAAUAAAGCGACUGAGAAGCCAGUAGAGAAAAACGAAGAAGUAAGUACAGAGCUUACUCAGUCGAAAGAGGAUAGUUCGGAA
.....((.((((....(((...-.....................)))((((((((((((.(((.......((......))...))).).)))).)))))))...........)))).)). ( -22.86)
>DroSim_CAF1 318645 120 + 1
GAUACACGGAACCAACACUAUUUUAAACAUACUAAAGAAAAUAAAGCGACUGAGAAGCCAGUGGAGAAAAACGAAGAAGCAAGUACGGAGGUUACUCAGUCGAAAGAGGAUAGUUCGGAA
...........((...((((((((.......(....).........((((((((.((((..((......................))..)))).))))))))....))))))))..)).. ( -22.15)
>DroYak_CAF1 309339 119 + 1
GAUACACGGAACCAUCGCUGUU-UAAAGAUAGUGAAGAACAUGAAACGACUGACAAGCCAGUGGAGAAAAAUGAAGAAACUAGUACAGAAGUUACUCAGCCGAAAGAGGAUAGCUCGGAA
......(((..((.((((((((-....)))))))).............((((......)))))).......(((.(.((((........)))).)))).)))...(((.....))).... ( -21.40)
>consensus
GAUACACGGAACCAACGCUGUU_UAAAAAUACUAAAGAAAAUAAAGCGACUGAGAAGCCAGUAGAGAAAAACGAAGAAGCAAGUACAGAGGUUACUCAGUCGAAAGAGGAUAGUUCGGAA
......(.((((.(((((((((.....)))))).............((((((((.((((.(((....................)))...)))).))))))))......))).)))).).. (-16.76 = -18.32 +   1.56)

alignment

secondary structure

dotplot

Window 3

Location	5,104,047 – 5,104,166
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.56
Mean single sequence MFE	-22.32
Consensus MFE	-15.96
Energy contribution	-16.02
Covariance contribution	0.06
Combinations/Pair	1.25
Mean z-score	-1.63
Structure conservation index	0.71
SVM decision value	0.12
SVM RNA-class probability	0.591565
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5104047 119 - 23771897
UUCCGAACUAUCCUCUUUCGACUGAGUAACCUCUGUACUUGCUUCUUCGGUUUUCUCUACUGGCUUCUCAGUCGCUUUAUUUUCCUCGCUAUUUUUA-AACAGCGAUGGUUCCGUGUAUC
....((((((((......((((((((...((...(((.......(....).......))).))...)))))))).............(((.((....-)).)))))))))))........ ( -27.84)
>DroSec_CAF1 296997 119 - 1
UUCCGAACUAUCCUCUUUCGACUGAGUAAGCUCUGUACUUACUUCUUCGUUUUUCUCUACUGGCUUCUCAGUCGCUUUAUUUUCCUUAGUAUUUUUA-AACAGCGUUGGUUCCGAGUAUC
(((.((((((.........(((((((.(((((..(((...((......)).......))).))))))))))))(((.....................-...)))..)))))).))).... ( -23.96)
>DroSim_CAF1 318645 120 - 1
UUCCGAACUAUCCUCUUUCGACUGAGUAACCUCCGUACUUGCUUCUUCGUUUUUCUCCACUGGCUUCUCAGUCGCUUUAUUUUCUUUAGUAUGUUUAAAAUAGUGUUGGUUCCGUGUAUC
..(((((((((.......((((((((...((.........((......))...........))...))))))))..........(((((.....)))))))))).))))........... ( -18.55)
>DroYak_CAF1 309339 119 - 1
UUCCGAGCUAUCCUCUUUCGGCUGAGUAACUUCUGUACUAGUUUCUUCAUUUUUCUCCACUGGCUUGUCAGUCGUUUCAUGUUCUUCACUAUCUUUA-AACAGCGAUGGUUCCGUGUAUC
....((((((((......(((((((...((....)).(((((................)))))....))))))).....((((..............-))))..))))))))........ ( -18.93)
>consensus
UUCCGAACUAUCCUCUUUCGACUGAGUAACCUCUGUACUUGCUUCUUCGUUUUUCUCCACUGGCUUCUCAGUCGCUUUAUUUUCCUCACUAUUUUUA_AACAGCGAUGGUUCCGUGUAUC
....((((((((.......(((((((...((..............................))...)))))))(((.........................)))))))))))........ (-15.96 = -16.02 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:17:36 2006