Locus 2446

Sequence ID	3R_DroMel_CAF1
Location	6,775,584 – 6,775,771
Length	187
Max. P	0.984561

overview

Window 1

Location	6,775,584 – 6,775,691
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.48
Mean single sequence MFE	-24.26
Consensus MFE	-19.96
Energy contribution	-20.68
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.42
Structure conservation index	0.82
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6775584 107 - 27905053
UGCGGAAGACAUCUUCAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGAAAAUGGAUUGUGCUAAUUCAUGUCAGGAUCUGAAUCCCCCUUUUC-------------CCAUCCCUUAAC
...((.(((((.(((..(((((...)))))..))).))))).))....((..((((((((...)))))))).)).((((..(((........)))-------------..))))...... ( -23.60)
>DroSec_CAF1 39764 107 - 1
UAAGGAAGACAUCUACAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGAAAAUGGAUUGUGCUAAUUCAUGUCAGAAUCUGAAACCCCAUUUUC-------------CCAUCCCUGAAC
..(((.(((((.((...(((((...)))))...)).))))).)))...((((((((......(..((((......))))..).....))))))))-------------............ ( -24.60)
>DroSim_CAF1 43771 107 - 1
UAUGGAAGACAUCUACAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGAAAAUGGAUUGUGCUAAUUCAUGUCAGAAUCUGAAACCCCAUUUUC-------------CCAUCCCUGAAC
.((((.(((((.((...(((((...)))))...)).))))).......((((((((......(..((((......))))..).....))))))))-------------))))........ ( -23.40)
>DroEre_CAF1 24893 120 - 1
UAUGGAAGACAUCUUCAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGAAAAUGAAUUGUGCUAAUUCACGUCAGAAUCUUAAAUCUCCUUUUCGCCCUCCAAAAACCCAUUCCUUAAC
..(((((((((.(((..(((((...)))))..))).))))).....((((...(((...(((......))).)))...)))).................))))................. ( -21.40)
>DroYak_CAF1 37111 120 - 1
UAUGGAAGACAGCUUCAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGCAAAUGGAUUGUGCUAAUUCAUGUCAGAAUCUGAAACUCCAUUUUCGCCCUUCUAAAACCCAUCCCUUAGC
.((((.(((((((((..(((((...)))))..))))))))).......(((((((((.(...(..((((......))))..)..).)))))))..))...........))))........ ( -28.30)
>consensus
UAUGGAAGACAUCUUCAUUGAGCAGCUCAAGAAAGUUGUCUGCCUAAAGAAAAUGGAUUGUGCUAAUUCAUGUCAGAAUCUGAAACCCCAUUUUC_____________CCAUCCCUUAAC
...((.(((((.(((..(((((...)))))..))).))))).))....((((((((......(..((((......))))..).....))))))))......................... (-19.96 = -20.68 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	6,775,611 – 6,775,731
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.74
Mean single sequence MFE	-25.24
Consensus MFE	-20.86
Energy contribution	-21.46
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.83
SVM decision value	0.35
SVM RNA-class probability	0.701688
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6775611 120 + 27905053
GAUCCUGACAUGAAUUAGCACAAUCCAUUUUCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCGCAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGAC
..............((((((.....(((((((.((..((((.(((.....)))..))))..)).))))))).(((((((....))).))))......................)))))). ( -24.60)
>DroSec_CAF1 39791 120 + 1
GAUUCUGACAUGAAUUAGCACAAUCCAUUUUCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGUAGAUGUCUUCCUUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGAC
(((((......))))).......(((((((.....(((.(((((.((...(((((...)))))...)).))))).)))...))))).))(((((.(((((......))))).)))))... ( -24.10)
>DroSim_CAF1 43798 120 + 1
GAUUCUGACAUGAAUUAGCACAAUCCAUUUUCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGUAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGAC
(((((......))))).......(((((((......((.(((((.((...(((((...)))))...)).))))).))....))))).))(((((.(((((......))))).)))))... ( -21.80)
>DroEre_CAF1 24933 110 + 1
GAUUCUGACGUGAAUUAGCACAAUUCAUUUUCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUA----------AACUUGCUGAC
...(((.(((((((((.....)))))))........((.(((((.((((.(((((...))))).)))).))))).))......)).)))(((((.....----------...)))))... ( -26.10)
>DroYak_CAF1 37151 119 + 1
GAUUCUGACAUGAAUUAGCACAAUCCAUUUGCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGAAGCUGUCUUCCAUAUAAGUGAGAAGUAACUUUA-AAUACAUUAAACGUGCUGCC
(((((......)))))(((((......((..(((..((.(((((.((((.(((((...))))).)))).))))).))....)))..))..(((......-..))).......)))))... ( -29.60)
>consensus
GAUUCUGACAUGAAUUAGCACAAUCCAUUUUCUUUAGGCAGACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGAC
(((((......)))))((((................((.(((((.((((.(((((...))))).)))).))))).))....((((........))))................))))... (-20.86 = -21.46 +   0.60)

alignment

secondary structure

dotplot

Window 3

Location	6,775,651 – 6,775,771
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.41
Mean single sequence MFE	-23.99
Consensus MFE	-20.87
Energy contribution	-21.67
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.87
SVM decision value	1.98
SVM RNA-class probability	0.984561
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6775651 120 + 27905053
GACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCGCAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGACAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAUAAUAUU
((((.((((.(((((...))))).)))).))))..........((((((((((((((.............(((((((.........)))))))....))))).)).)).)))))...... ( -23.63)
>DroSec_CAF1 39831 119 + 1
GACAACUUUCUUGAGCUGCUCAAUGUAGAUGUCUUCCUUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGACAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAUAAUAU-
((((.((...(((((...)))))...)).))))..........((((((((((((((.............(((((((.........)))))))....))))).)).)).))))).....- ( -20.43)
>DroSim_CAF1 43838 120 + 1
GACAACUUUCUUGAGCUGCUCAAUGUAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGACAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAAAAUAUU
..........(((((((((.....))))(((.((((((((((.((....(((((.(((((......))))).))))).)).))))))).))).))).............)))))...... ( -24.40)
>DroEre_CAF1 24973 110 + 1
GACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUA----------AACUUGCUGACAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAUAAUAUU
((((.((((.(((((...))))).)))).))))..........((((((((((((((..----------.(((((((.........)))))))....))))).)).)).)))))...... ( -27.00)
>DroYak_CAF1 37191 119 + 1
GACAACUUUCUUGAGCUGCUCAAUGAAGCUGUCUUCCAUAUAAGUGAGAAGUAACUUUA-AAUACAUUAAACGUGCUGCCAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAUAAUAUU
((((.((((.(((((...))))).)))).))))..........(((((.((((..((((-(.....)))))..))))((((....))))....................)))))...... ( -24.50)
>consensus
GACAACUUUCUUGAGCUGCUCAAUGAAGAUGUCUUCCAUAUAAGUGAGAAGUAACUUUAAAAUACAUUAAACUUGCUGACAUAUAUGGCAAGUCAUUAAGUUCACAUUACUCAUAAUAUU
((((.((((.(((((...))))).)))).))))..........((((((((((((((.............(((((((.........)))))))....))))).)).)).)))))...... (-20.87 = -21.67 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:18 2006