Locus 5031

Sequence ID	2L_DroMel_CAF1
Location	14,425,755 – 14,425,853
Length	98
Max. P	0.820479

overview

Window 2

Location	14,425,755 – 14,425,853
Length	98
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	82.74
Mean single sequence MFE	-17.14
Consensus MFE	-13.34
Energy contribution	-13.74
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.68
Structure conservation index	0.78
SVM decision value	0.35
SVM RNA-class probability	0.701272
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425755 98 + 22407834
CUUGUCUGCUCUCCUCAAUCCCAAUUCCAAUCCCA-UCCC-AUCCCAAUCCC--AGUCCCGUUUCCCGAUCCCGAUCGGGAUCCCAACUUUCGGUGGACUGU
...................................-....-..........(--(((((.(..(((((((....)))))))..)..((.....)))))))). ( -19.90)
>DroSec_CAF1 16268 81 + 1
CUUGUCUGCUCUCCUCAAUCCCAAUCCCAAUCCCA-UC--------------------CCGUUUCCCGAUCCCGAUCGGGAUCCCAACUUUCGGUGGACUGU
...(((..(..........................-..--------------------..(..(((((((....)))))))..)...(....))..)))... ( -16.20)
>DroSim_CAF1 17940 81 + 1
CUUGUCUGCUCUCCUCAAUCCCAAUCCCAAUCCCA-UC--------------------CCGUUUCCCGAUCCCGAUCGGGAUCCCAACUUUCGGUGGACUGU
...(((..(..........................-..--------------------..(..(((((((....)))))))..)...(....))..)))... ( -16.20)
>DroEre_CAF1 17525 102 + 1
CUUGUCUGCUCUCCUCAAUCCCAGUCGCAAUCCCAAUCCCAGUCCCGUUUCCCGAUUCCCGAUUCCCGAUCCCGAUCGGUAUCCCUACUUUCGGUGGACUGU
...(.(((.............))).).............((((((......((((.....(((..(((((....))))).))).......)))).)))))). ( -19.02)
>DroYak_CAF1 17757 100 + 1
CUUGUCUGCUCUCCUCAAUCCCAGUUCCAAUCCCAAUCCCAAUGCCAAUCCC--AGUCCCGUUUCCCGAUCCCGAUCGGUAUCCCUACUUUCGGUGGACUGC
...................................................(--(((((......(((((....)))))....((.......)).)))))). ( -14.40)
>consensus
CUUGUCUGCUCUCCUCAAUCCCAAUCCCAAUCCCA_UCCC__U_CC__U_CC__A_UCCCGUUUCCCGAUCCCGAUCGGGAUCCCAACUUUCGGUGGACUGU
...(((..(...................................................(..(((((((....)))))))..)...(....))..)))... (-13.34 = -13.74 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	14,425,755 – 14,425,853
Length	98
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	82.74
Mean single sequence MFE	-26.82
Consensus MFE	-18.64
Energy contribution	-19.24
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.00
Structure conservation index	0.70
SVM decision value	0.68
SVM RNA-class probability	0.820479
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425755 98 - 22407834
ACAGUCCACCGAAAGUUGGGAUCCCGAUCGGGAUCGGGAAACGGGACU--GGGAUUGGGAU-GGGA-UGGGAUUGGAAUUGGGAUUGAGGAGAGCAGACAAG
.((((((.((((...)))).(((((((((.((.((.(....).)).))--.).))))))))-....-..))))))........................... ( -28.10)
>DroSec_CAF1 16268 81 - 1
ACAGUCCACCGAAAGUUGGGAUCCCGAUCGGGAUCGGGAAACGG--------------------GA-UGGGAUUGGGAUUGGGAUUGAGGAGAGCAGACAAG
.((((((.((((...))))((((((((((..(.((.(....).)--------------------).-)..)))))))))).))))))............... ( -28.20)
>DroSim_CAF1 17940 81 - 1
ACAGUCCACCGAAAGUUGGGAUCCCGAUCGGGAUCGGGAAACGG--------------------GA-UGGGAUUGGGAUUGGGAUUGAGGAGAGCAGACAAG
.((((((.((((...))))((((((((((..(.((.(....).)--------------------).-)..)))))))))).))))))............... ( -28.20)
>DroEre_CAF1 17525 102 - 1
ACAGUCCACCGAAAGUAGGGAUACCGAUCGGGAUCGGGAAUCGGGAAUCGGGAAACGGGACUGGGAUUGGGAUUGCGACUGGGAUUGAGGAGAGCAGACAAG
.((((((.((((.....((....(((((....)))))...)).....))))......))))))...(((...((((..((........))...)))).))). ( -26.00)
>DroYak_CAF1 17757 100 - 1
GCAGUCCACCGAAAGUAGGGAUACCGAUCGGGAUCGGGAAACGGGACU--GGGAUUGGCAUUGGGAUUGGGAUUGGAACUGGGAUUGAGGAGAGCAGACAAG
.((((((.((.......))....((((((..((((.(....)....(.--.(........)..)))))..)))))).....))))))............... ( -23.60)
>consensus
ACAGUCCACCGAAAGUUGGGAUCCCGAUCGGGAUCGGGAAACGGGA_U__GG_A__GG_A__GGGA_UGGGAUUGGGAUUGGGAUUGAGGAGAGCAGACAAG
.((((((.((((.......((((((....)))))).(....)..............................)))).....))))))............... (-18.64 = -19.24 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:01 2006