Locus 8243

Sequence ID	3L_DroMel_CAF1
Location	21,654,171 – 21,654,275
Length	104
Max. P	0.882554

overview

Window 8

Location	21,654,171 – 21,654,275
Length	104
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	94.08
Mean single sequence MFE	-21.48
Consensus MFE	-17.53
Energy contribution	-17.65
Covariance contribution	0.12
Combinations/Pair	1.09
Mean z-score	-1.78
Structure conservation index	0.82
SVM decision value	0.92
SVM RNA-class probability	0.882554
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21654171 104 + 23771897
GGCCAAUCCCCAUACCACAAGCCCCAAAAUGAUUCUGUUGCUGAUUCUCGAUCCUAUU------CCCGGGCCCAUUGUCCAUGUCUCUUAAUAUUUUUGACAUAUUGGCC
(((((((.........((((((((......((.((.......)).))..((......)------)..))))...))))..(((((.............)))))))))))) ( -20.82)
>DroSec_CAF1 31155 104 + 1
GGCCAAUCCCCACACCACAAGCCCCAAACCGAUUCUGUUGCCGAUUCUCGAUCCUAUU------CCCGGGCCCAUUGGCCAUGUCUCUUAAUAUUUUUGACAUAUUGGCC
(((((((.......(((...((((......((.((.......)).))..((......)------)..))))....)))..(((((.............)))))))))))) ( -22.02)
>DroSim_CAF1 35607 104 + 1
GGCCAAUCCCCACACCACAAGCCCCAAACCGAUUCUGUUGCCGAUUCUCGAUCCUAUU------CCCGGGCCCAUUGGCCAUGUCUCUUAAUAUUUUUGACAUAUUGGCC
(((((((.......(((...((((......((.((.......)).))..((......)------)..))))....)))..(((((.............)))))))))))) ( -22.02)
>DroEre_CAF1 30476 104 + 1
GGCCAAUCCCCACACCACAAACCCAAAACCGAUUCUGUUGCCGAUUCUCGAUCCUAUU------CCCGGGCCCAUUGGCCAUGUCUCUUAAUAUUUUUGACAUAUUGGUC
(((((((.(((...................((.((.......)).))..((......)------)..)))...)))))))(((((.............)))))....... ( -19.72)
>DroYak_CAF1 39573 109 + 1
GGCCAAUCCCCACACCACAAACCCAAAACCGAUUCUGUUGCCGAUUCUCGAUCCUAUUCUCGAUCCCGGGCCCAUUGGCCAUGUCUCUUAAUAUUUUUGACAUAUUGG-C
(((((((.(((...................((.((.......)).))..((((........))))..)))...)))))))(((((.............))))).....-. ( -22.82)
>consensus
GGCCAAUCCCCACACCACAAGCCCCAAACCGAUUCUGUUGCCGAUUCUCGAUCCUAUU______CCCGGGCCCAUUGGCCAUGUCUCUUAAUAUUUUUGACAUAUUGGCC
(((((((................................((((((.((((................))))...)))))).(((((.............)))))))))))) (-17.53 = -17.65 +   0.12)

alignment

secondary structure

dotplot

Window 9

Location	21,654,171 – 21,654,275
Length	104
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	94.08
Mean single sequence MFE	-32.95
Consensus MFE	-24.90
Energy contribution	-25.86
Covariance contribution	0.96
Combinations/Pair	1.03
Mean z-score	-2.43
Structure conservation index	0.76
SVM decision value	0.80
SVM RNA-class probability	0.854946
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21654171 104 - 23771897
GGCCAAUAUGUCAAAAAUAUUAAGAGACAUGGACAAUGGGCCCGGG------AAUAGGAUCGAGAAUCAGCAACAGAAUCAUUUUGGGGCUUGUGGUAUGGGGAUUGGCC
((((((((((((.............)))))..((.(..(((((.((------(((.((.((..............)).))))))).)))))..).))......))))))) ( -29.96)
>DroSec_CAF1 31155 104 - 1
GGCCAAUAUGUCAAAAAUAUUAAGAGACAUGGCCAAUGGGCCCGGG------AAUAGGAUCGAGAAUCGGCAACAGAAUCGGUUUGGGGCUUGUGGUGUGGGGAUUGGCC
((((((((((((.............))))).(((.(..(((((.(.------.....((((((...(((....).)).))))))).)))))..))))......))))))) ( -34.22)
>DroSim_CAF1 35607 104 - 1
GGCCAAUAUGUCAAAAAUAUUAAGAGACAUGGCCAAUGGGCCCGGG------AAUAGGAUCGAGAAUCGGCAACAGAAUCGGUUUGGGGCUUGUGGUGUGGGGAUUGGCC
((((((((((((.............))))).(((.(..(((((.(.------.....((((((...(((....).)).))))))).)))))..))))......))))))) ( -34.22)
>DroEre_CAF1 30476 104 - 1
GACCAAUAUGUCAAAAAUAUUAAGAGACAUGGCCAAUGGGCCCGGG------AAUAGGAUCGAGAAUCGGCAACAGAAUCGGUUUUGGGUUUGUGGUGUGGGGAUUGGCC
.......(((((.............)))))(((((((...((((.(------....(((((.((((((((........)))))))).)))))....).)))).))))))) ( -30.32)
>DroYak_CAF1 39573 109 - 1
G-CCAAUAUGUCAAAAAUAUUAAGAGACAUGGCCAAUGGGCCCGGGAUCGAGAAUAGGAUCGAGAAUCGGCAACAGAAUCGGUUUUGGGUUUGUGGUGUGGGGAUUGGCC
(-((((((((((.............))))).((((.(..((((((((((((......(.(((.....)))).......))))))))))))..)))))......)))))). ( -36.04)
>consensus
GGCCAAUAUGUCAAAAAUAUUAAGAGACAUGGCCAAUGGGCCCGGG______AAUAGGAUCGAGAAUCGGCAACAGAAUCGGUUUGGGGCUUGUGGUGUGGGGAUUGGCC
((((((((((((.............))))).(((.(..(((((.............(((((((...(((....).)).))))))).)))))..))))......))))))) (-24.90 = -25.86 +   0.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:17 2006