Locus 721

Sequence ID	X_DroMel_CAF1
Location	1,983,394 – 1,983,554
Length	160
Max. P	0.996140

overview

Window 9

Location	1,983,394 – 1,983,514
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.03
Mean single sequence MFE	-30.16
Consensus MFE	-20.99
Energy contribution	-22.30
Covariance contribution	1.31
Combinations/Pair	1.14
Mean z-score	-1.59
Structure conservation index	0.70
SVM decision value	0.12
SVM RNA-class probability	0.592369
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1983394 120 + 22224390
AAAAUAGGAAACGAUUCUGAAAGCUUUGGGGUGGCCUCUGUCUGCAUCUUCUCCUCAGCCAUGGCUUCAUCCAGCCUGUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCACCUGUC
...(((((...((....))......(((((((((.(..((....))...........((((((((......................))))))))).)))))))))........))))). ( -33.95)
>DroSec_CAF1 16841 120 + 1
AAAAUAGGAAAUGAUUCUGAAAGCUUUGGGGUGGCCUCCGUCUGCAUCUUUUCCUCAGCCAUGGCUUCAUCCAGUCUGUCCACCAAUGCCAUGGCAUCCACCCCAACUAUACCGCCUGUC
...(((((.........(....)..(((((((((.....(....)............((((((((......................))))))))..)))))))))........))))). ( -32.15)
>DroEre_CAF1 6527 120 + 1
UGAAUUGGCAAAGCCUCGGAUAUUGUCUGAAAUGAUUCUGUCUGCAUUUUUUCCUCGGCCAUAGCUUCAUCCAGUCUAUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCGCCUGUC
.....(((((......((((((..(((......)))..))))))............((..((((((......)).))))...))..))))).((((................)))).... ( -22.29)
>DroYak_CAF1 17274 120 + 1
AAAACAGAAAACGAUUCUAAAAGCUUCGGGGUGGUCUCCGUCUGCAUCUUCUCCUCAGCCAUGGCUUCGUCCAGUUUGUCCACCAAUGCCAUGGCGUCUACCCCAACUAUACCGCCUGUU
..(((((.....((..(.....)..))(((((((.(...(....)............((((((((......................))))))))).)))))))...........))))) ( -32.25)
>consensus
AAAAUAGGAAACGAUUCUGAAAGCUUCGGGGUGGCCUCCGUCUGCAUCUUCUCCUCAGCCAUGGCUUCAUCCAGUCUGUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCGCCUGUC
....(((((.....)))))........(((((((.....(....)............((((((((......................))))))))..)))))))................ (-20.99 = -22.30 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	1,983,434 – 1,983,554
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-29.10
Consensus MFE	-27.11
Energy contribution	-27.68
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.90
Structure conservation index	0.93
SVM decision value	2.66
SVM RNA-class probability	0.996140
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1983434 120 + 22224390
UCUGCAUCUUCUCCUCAGCCAUGGCUUCAUCCAGCCUGUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCACCUGUCCCCAGGCCGUUCGUCUCUCCUGAUCCAACUCCACCGAUGC
...(((((.........((((((((......................))))))))...................((((....))))..(((.(..((....))..))))......))))) ( -25.65)
>DroSec_CAF1 16881 120 + 1
UCUGCAUCUUUUCCUCAGCCAUGGCUUCAUCCAGUCUGUCCACCAAUGCCAUGGCAUCCACCCCAACUAUACCGCCUGUCCCCAGGCCGUUGGUCUCUCCUGAUCCAACUCCACCGAUGC
...(((((.........((((((((......................))))))))..................(((((....))))).(((((((......)).)))))......))))) ( -35.55)
>DroEre_CAF1 6567 120 + 1
UCUGCAUUUUUUCCUCGGCCAUAGCUUCAUCCAGUCUAUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCGCCUGUCCCCAGGCCGUUGGUCUCUCCUGCUCCACCUCCUCCGAUGC
...(((((.........(((((.((......................)).))))).......(((((......(((((....))))).)))))......................))))) ( -22.75)
>DroYak_CAF1 17314 120 + 1
UCUGCAUCUUCUCCUCAGCCAUGGCUUCGUCCAGUUUGUCCACCAAUGCCAUGGCGUCUACCCCAACUAUACCGCCUGUUCCCAGGCCGUUGGUCUCUGCUGUUCCACCUCCUCCGAUGC
...(((((.........((((((((......................))))))))((..(..(((((......(((((....))))).)))))..)..))...............))))) ( -32.45)
>consensus
UCUGCAUCUUCUCCUCAGCCAUGGCUUCAUCCAGUCUGUCCACCAAUGCCAUGGCGUCCACCCCAACUAUACCGCCUGUCCCCAGGCCGUUGGUCUCUCCUGAUCCAACUCCACCGAUGC
...(((((.........((((((((......................))))))))..........((((.((.(((((....))))).)))))).....................))))) (-27.11 = -27.68 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	1,983,434 – 1,983,554
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.22
Mean single sequence MFE	-41.52
Consensus MFE	-38.04
Energy contribution	-37.98
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-3.09
Structure conservation index	0.92
SVM decision value	2.61
SVM RNA-class probability	0.995733
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1983434 120 - 22224390
GCAUCGGUGGAGUUGGAUCAGGAGAGACGAACGGCCUGGGGACAGGUGGUAUAGUUGGGGUGGACGCCAUGGCAUUGGUGGACAGGCUGGAUGAAGCCAUGGCUGAGGAGAAGAUGCAGA
(((((.......(((..((....))..)))((.(((((....))))).)).(((((....((..(((((......)))))..))((((......))))..))))).......)))))... ( -43.10)
>DroSec_CAF1 16881 120 - 1
GCAUCGGUGGAGUUGGAUCAGGAGAGACCAACGGCCUGGGGACAGGCGGUAUAGUUGGGGUGGAUGCCAUGGCAUUGGUGGACAGACUGGAUGAAGCCAUGGCUGAGGAAAAGAUGCAGA
(((((......(((((.((......))))))).(((((....)))))..................((((((((.(..((......))..).....)))))))).........)))))... ( -43.50)
>DroEre_CAF1 6567 120 - 1
GCAUCGGAGGAGGUGGAGCAGGAGAGACCAACGGCCUGGGGACAGGCGGUAUAGUUGGGGUGGACGCCAUGGCAUUGGUGGAUAGACUGGAUGAAGCUAUGGCCGAGGAAAAAAUGCAGA
((((.......(((.((((.((.....)).((.(((((....))))).))....(..(..((..(((((......)))))..))..)..).....))).).))).........))))... ( -37.99)
>DroYak_CAF1 17314 120 - 1
GCAUCGGAGGAGGUGGAACAGCAGAGACCAACGGCCUGGGAACAGGCGGUAUAGUUGGGGUAGACGCCAUGGCAUUGGUGGACAAACUGGACGAAGCCAUGGCUGAGGAGAAGAUGCAGA
(((((......................(((((.(((((....)))))......))))).......((((((((.(((..(......)....))).)))))))).........)))))... ( -41.50)
>consensus
GCAUCGGAGGAGGUGGAUCAGGAGAGACCAACGGCCUGGGGACAGGCGGUAUAGUUGGGGUGGACGCCAUGGCAUUGGUGGACAGACUGGAUGAAGCCAUGGCUGAGGAAAAGAUGCAGA
(((((......................(((((.(((((....)))))......))))).......((((((((.(..((......))..).....)))))))).........)))))... (-38.04 = -37.98 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:03 2006