Locus 7215

Sequence ID	3L_DroMel_CAF1
Location	19,356,504 – 19,356,692
Length	188
Max. P	0.891769

overview

Window 3

Location	19,356,504 – 19,356,616
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.33
Mean single sequence MFE	-30.44
Consensus MFE	-18.91
Energy contribution	-21.35
Covariance contribution	2.44
Combinations/Pair	1.07
Mean z-score	-2.45
Structure conservation index	0.62
SVM decision value	0.02
SVM RNA-class probability	0.542732
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19356504 112 - 23771897
UUUUCCUGGCCAUCCUUUUGGCCCGAGGGACGACU--------AUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCUUAUCUCUGAUUAUUAUCCUUCUAGCUCAGGAGCUCAGGAA
..((((((((((......)))))(((((((((...--------...))....((....))...)))))))((((((...........(((....)))..........))))))..))))) ( -30.20)
>DroSec_CAF1 6492 120 - 1
UUUUCCUGACCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCUUAUCUCUGAUUAUUAUCCUUCUAGCUCAGAAGCUCAGGAA
..(((((((..........((((((((......))))))))((..((((..................)))).............((((((((.........))).))))).))))))))) ( -32.67)
>DroSim_CAF1 6559 120 - 1
UUUUCCUGGCCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCUUAUCUCUGAUUAUUAACCUUCUAGCUCAGGAGCUCAGGAA
..((((((((..((((...((((((((......))))))))((..((((..................))))......((........))..............))..)))))).)))))) ( -33.77)
>DroYak_CAF1 10342 112 - 1
UUUUCCUGGCCAUCCUUUUGGCUUAAGGGGCGACUGGAGCUGCAUCCGAUUAUCCUACGACUUUCCUUCGUCUCCUGCCUUAUCUCUGAUUAUUAUCCUUCUAGCU--------CAGGAA
..((((((((((......))))....((((((..((((......))))..........(((........)))...)))))).........................--------)))))) ( -25.10)
>consensus
UUUUCCUGGCCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCUUAUCUCUGAUUAUUAUCCUUCUAGCUCAGGAGCUCAGGAA
..((((((((((......))))..((((((..(..(((((((.....((...((....))...))...)))))))....)..))))))..........................)))))) (-18.91 = -21.35 +   2.44)

alignment

secondary structure

dotplot

Window 4

Location	19,356,544 – 19,356,656
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.42
Mean single sequence MFE	-37.40
Consensus MFE	-29.84
Energy contribution	-30.90
Covariance contribution	1.06
Combinations/Pair	1.15
Mean z-score	-2.17
Structure conservation index	0.80
SVM decision value	0.97
SVM RNA-class probability	0.891769
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19356544 112 - 23771897
GCAUGUGGCUAAGGAAUGGCUUACAAGCCGGUUCCUUGUUUUUUCCUGGCCAUCCUUUUGGCCCGAGGGACGACU--------AUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCU
....(..((((((((((((((....)))))((((((((.........(((((......)))))))))))))....--------...................)))))).)))..)..... ( -34.10)
>DroSec_CAF1 6532 120 - 1
GCAUGUGGCUAAGGAAUGGCUUACAAGCCGCUUCCCUGUUUUUUCCUGACCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCU
....(..(((((((((.((((....))))((..((((..((.((((((.(((......)))...)))))).))..))))..))...................)))))).)))..)..... ( -36.20)
>DroSim_CAF1 6599 120 - 1
GCAUGUGGCUAAGGAAUGGCUUACAAGCCGCUUCCCUGUUUUUUCCUGGCCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCU
....(..(((((((((.((((....))))((..((((..((.((((((((((......)))))..))))).))..))))..))...................)))))).)))..)..... ( -40.20)
>DroYak_CAF1 10374 120 - 1
GCAUGUGGCUGAGGAAUGGCUUACAAGCCGUUUCUCUGUUUUUUCCUGGCCAUCCUUUUGGCUUAAGGGGCGACUGGAGCUGCAUCCGAUUAUCCUACGACUUUCCUUCGUCUCCUGCCU
(((((..((((((((((((((....))))))))))).(((..((((((((((......)))))..))))).)))...)))..))..............(((........)))...))).. ( -39.10)
>consensus
GCAUGUGGCUAAGGAAUGGCUUACAAGCCGCUUCCCUGUUUUUUCCUGGCCAUCCUUUUGGCCCCAGGGACGACUGGGGCUGCAUCCGAUUAUCUUACGACUUUCCUUCGGCUCCUUUCU
....(..(((((((((.((((....))))((..(((((.((.((((((((((......)))))..))))).)).)))))..))...................)))))).)))..)..... (-29.84 = -30.90 +   1.06)

alignment

secondary structure

dotplot

Window 5

Location	19,356,581 – 19,356,692
Length	111
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	89.44
Mean single sequence MFE	-40.30
Consensus MFE	-31.47
Energy contribution	-33.03
Covariance contribution	1.56
Combinations/Pair	1.07
Mean z-score	-2.42
Structure conservation index	0.78
SVM decision value	0.43
SVM RNA-class probability	0.734575
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19356581 111 + 23771897
-----AGUCGUCCCUCGGGCCAAAAGGAUGGCCAGGAAAAAACAAGGAACCGGCUUGUAAGCCAUUCCUUAGCCACAUGCCUACAAACAGGA----AAAACCAAGGCCAGAAAGCAGUCC
-----....((...((.((((...(((.((((.(((((.......(....)((((....)))).)))))..))))....))).......((.----....))..)))).))..))..... ( -28.70)
>DroSec_CAF1 6572 120 + 1
GCCCCAGUCGUCCCUGGGGCCAAAAGGAUGGUCAGGAAAAAACAGGGAAGCGGCUUGUAAGCCAUUCCUUAGCCACAUGCCUGCAAACAGGGCCAACCAACCAAGGCCAGAAAGCGGGCC
(((((((......)))))))........((((..(.......)((((((..((((....)))).)))))).))))...((((((......((((..........)))).....)))))). ( -45.10)
>DroSim_CAF1 6639 120 + 1
GCCCCAGUCGUCCCUGGGGCCAAAAGGAUGGCCAGGAAAAAACAGGGAAGCGGCUUGUAAGCCAUUCCUUAGCCACAUGCCUGCAAACAGGGCCAACCAACCAAGGCCAGAAAGCGGGCC
(((((((......)))))))........((((..(.......)((((((..((((....)))).)))))).))))...((((((......((((..........)))).....)))))). ( -47.10)
>consensus
GCCCCAGUCGUCCCUGGGGCCAAAAGGAUGGCCAGGAAAAAACAGGGAAGCGGCUUGUAAGCCAUUCCUUAGCCACAUGCCUGCAAACAGGGCCAACCAACCAAGGCCAGAAAGCGGGCC
(((((((......)))))))........(((((.((.......((((((..((((....)))).)))))).........((((....)))).........))..)))))........... (-31.47 = -33.03 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:41:10 2006