Locus 4098

Sequence ID	3L_DroMel_CAF1
Location	11,952,637 – 11,952,743
Length	106
Max. P	0.960036

overview

Window 4

Location	11,952,637 – 11,952,743
Length	106
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.12
Mean single sequence MFE	-26.55
Consensus MFE	-16.30
Energy contribution	-16.42
Covariance contribution	0.12
Combinations/Pair	1.33
Mean z-score	-1.91
Structure conservation index	0.61
SVM decision value	1.51
SVM RNA-class probability	0.960036
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11952637 106 + 23771897
CG--UAACGCGUUUCCAAUAACUAUCCUUUUAUUUCGCUAU---UACAGUCCGGAAACUGCGAUCCUCAGGUCUGCAAUGACCAGUCAGAGUACUUCGUCUCUCCGGACUA
.(--(((.(((.....(((((........))))).)))..)---)))((((((((....((((..(((.((((......)))).....)))....))))...)))))))). ( -27.50)
>DroSec_CAF1 5514 106 + 1
CG--UAACGCCUUUCCAAUAACUAUCCCUUUAUUUCUCUAU---UACAGUCCGGAAACUGCGAUCCUCUGGUCUGCAAUGACCAGUCGGAGUACUUCGUCUCUCCGGACUA
..--.....................................---...((((((((....(((((((.((((((......))))))..))).....))))...)))))))). ( -29.50)
>DroSim_CAF1 5452 106 + 1
CG--UAACGCCUUUCCAAUAACUAUCCCUUUAUUUCGCUAU---UACAGUCCGGAAACUGCGAUCCUCUGGUCUGCAAUGACCAGUCGGAGUACUUCGUCUCUCCGGACUA
.(--(((.((......(((((........)))))..))..)---)))((((((((....(((((((.((((((......))))))..))).....))))...)))))))). ( -29.80)
>DroEre_CAF1 5973 107 + 1
CGACCUACAUGUUUUCAACAACAAUCCCUUCAU-UCCCUAU---UACAGUCCGGAAACUGCGAUCCCCGGGUCUGCACCGGCAAGUUGGAUUUCUACGUCUCUCCGGACUU
.........((((......))))..........-.......---...((((((((...(((((((....)))).)))((((....)))).............)))))))). ( -23.80)
>DroYak_CAF1 3652 108 + 1
CGACCUACAAGUUUUCAACAACAAUCCCCUUAUUUCCGUAU---UACAGUCCGGAAACUGCGAUCCUCAGGUCUGCGUCGACCAGACGGAGUACUACAUCUCUCCGGACUA
.........................................---...((((((((..(((.......)))((((.((((.....)))).)).))........)))))))). ( -23.70)
>DroPer_CAF1 6244 105 + 1
------AGAAAUUUUGGAUGAGUAACAUUAUAUCCCGCUUUAAACGCAGACUGGAGAGUGCGAUCCCGCGUCCUGUGUCGGUAAUCCGGAGUACUGGAUUUCCCCCAAUUA
------.......((((..........................(((((((((((.((......))))).)).)))))).((.(((((((....))))))).)).))))... ( -25.00)
>consensus
CG__UAACACGUUUCCAAUAACUAUCCCUUUAUUUCGCUAU___UACAGUCCGGAAACUGCGAUCCUCAGGUCUGCAACGACCAGUCGGAGUACUUCGUCUCUCCGGACUA
...............................................(((((((....(((((((....)))).)))..........((((........))))))))))). (-16.30 = -16.42 +   0.12)

alignment

secondary structure

dotplot

Window 5

Location	11,952,637 – 11,952,743
Length	106
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.12
Mean single sequence MFE	-30.61
Consensus MFE	-18.54
Energy contribution	-19.27
Covariance contribution	0.73
Combinations/Pair	1.25
Mean z-score	-1.25
Structure conservation index	0.61
SVM decision value	-0.03
SVM RNA-class probability	0.517448
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11952637 106 - 23771897
UAGUCCGGAGAGACGAAGUACUCUGACUGGUCAUUGCAGACCUGAGGAUCGCAGUUUCCGGACUGUA---AUAGCGAAAUAAAAGGAUAGUUAUUGGAAACGCGUUA--CG
.((((((((((..(((....(((.....((((......)))).)))..)))...))))))))))(((---((.((..(((((........)))))(....)))))))--). ( -32.30)
>DroSec_CAF1 5514 106 - 1
UAGUCCGGAGAGACGAAGUACUCCGACUGGUCAUUGCAGACCAGAGGAUCGCAGUUUCCGGACUGUA---AUAGAGAAAUAAAGGGAUAGUUAUUGGAAAGGCGUUA--CG
..((((((((..........))))..((((((......)))))).))))(((..(((((.((((((.---....(....)......))))))...))))).)))...--.. ( -31.80)
>DroSim_CAF1 5452 106 - 1
UAGUCCGGAGAGACGAAGUACUCCGACUGGUCAUUGCAGACCAGAGGAUCGCAGUUUCCGGACUGUA---AUAGCGAAAUAAAGGGAUAGUUAUUGGAAAGGCGUUA--CG
(((((((((((..(((.....(((..((((((......)))))).))))))...)))))))))))((---(((((..............)))))))...........--.. ( -33.84)
>DroEre_CAF1 5973 107 - 1
AAGUCCGGAGAGACGUAGAAAUCCAACUUGCCGGUGCAGACCCGGGGAUCGCAGUUUCCGGACUGUA---AUAGGGA-AUGAAGGGAUUGUUGUUGAAAACAUGUAGGUCG
...........(((.((.((((((..(((.((..(((((..((((..((....))..)))).)))))---...)).)-).)...)))))(((......))).).)).))). ( -29.70)
>DroYak_CAF1 3652 108 - 1
UAGUCCGGAGAGAUGUAGUACUCCGUCUGGUCGACGCAGACCUGAGGAUCGCAGUUUCCGGACUGUA---AUACGGAAAUAAGGGGAUUGUUGUUGAAAACUUGUAGGUCG
(((((((((((..((..((.(((.((((((....).)))))..))).))..)).)))))))))))..---...(((..(((((.................)))))...))) ( -32.13)
>DroPer_CAF1 6244 105 - 1
UAAUUGGGGGAAAUCCAGUACUCCGGAUUACCGACACAGGACGCGGGAUCGCACUCUCCAGUCUGCGUUUAAAGCGGGAUAUAAUGUUACUCAUCCAAAAUUUCU------
...(((((((.(((((........))))).))((((..(((.(((....)))....)))..(((((.......)))))......)))).....))))).......------ ( -23.90)
>consensus
UAGUCCGGAGAGACGAAGUACUCCGACUGGUCAUUGCAGACCAGAGGAUCGCAGUUUCCGGACUGUA___AUAGCGAAAUAAAGGGAUAGUUAUUGAAAACGCGUUA__CG
(((((((((((......((..(((....((((......))))...)))..))..))))))))))).............................................. (-18.54 = -19.27 +   0.73)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:25 2006