Locus 3896

Sequence ID	2L_DroMel_CAF1
Location	11,398,779 – 11,398,944
Length	165
Max. P	0.558719

overview

Window 9

Location	11,398,779 – 11,398,881
Length	102
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.06
Mean single sequence MFE	-26.43
Consensus MFE	-19.94
Energy contribution	-19.80
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-0.78
Structure conservation index	0.75
SVM decision value	0.05
SVM RNA-class probability	0.558719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11398779 102 - 22407834
ACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACAGAGCACUAGACGAUUCCC---UUCAUUUAGGCCCCCCCUUCCAACGAGAGACA
...(((...(((......((((.((((...)))).)......((((........))))..)))((.....---.))......)))..)))......(....)... ( -25.70)
>DroSec_CAF1 115608 101 - 1
ACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCCC---CCGAUCCG-AACCCCUUUCCCUACUAGAGCCA
....(((((((.......((((.((((...)))).)......((((........))))..))).......---)).....(-((.....))).......))))). ( -26.94)
>DroSim_CAF1 123035 84 - 1
ACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACUGCACUAGACGAUUCCC---CCGAUCCG-AACC-----------------CA
...(((.((((.......(((((((((...))))........(((((......)))))............---))))))))-).))-----------------). ( -26.81)
>DroEre_CAF1 123610 86 - 1
ACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACGGCACUAGACGAUUCCC---CCGAUCCG----------------GAGAGUCG
.(((((.((((.......((((.((((...)))).)......((((........))))..))).......---))))))))----------------)....... ( -27.94)
>DroYak_CAF1 119796 88 - 1
ACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCCCACUCCGCUAC-----------------GAAAGUCA
.(((((((((((......))))).))).)))((((.......((((........))))..((....)).....)))).((-----------------....)).. ( -25.10)
>DroAna_CAF1 104408 96 - 1
ACUGGGCCCGGCAUUCGAGUCGGCGCCACAGACGGCAAUAAUGUGCAGCACCCAGCACUAGACCAGAUCC---CCGAACUU-CCCC-----CAAAGCUGGCGAAA
.(((((((((((......))))).))).))).((((......((((........)))).......((...---.......)-)...-----....))))...... ( -26.10)
>consensus
ACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAUAAUGUGCAACACACAGCACUAGACGAUUCCC___CCGAUCCG___CC___________GAGAGACA
.(((((((((((......))))).))).)))...........((((........))))............................................... (-19.94 = -19.80 +  -0.14)

alignment

secondary structure

dotplot

Window 0

Location	11,398,842 – 11,398,944
Length	102
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.58
Mean single sequence MFE	-35.25
Consensus MFE	-25.80
Energy contribution	-26.72
Covariance contribution	0.92
Combinations/Pair	1.12
Mean z-score	-1.26
Structure conservation index	0.73
SVM decision value	0.01
SVM RNA-class probability	0.540663
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11398842 102 - 22407834
UUUACCA---------UCCCACCCCACCA-AGUUCGCG-------AUCCUCGAUCCUGGGUUCCUGAUCUCGGGAUUGUAACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAU
.......---------.............-.((.(((.-------.....((((((((((........))))))))))...(((((((((((......))))).))).))))))))... ( -32.70)
>DroSec_CAF1 115670 102 - 1
UUUACCA---------UCCCACCUCCCCA-AGUUCGCG-------AUCCUCGAUCCUGGGUUCCUGAUCGCGGGAUUGUAACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAU
.......---------..((.(((.....-((((.(((-------((((((((((..((...)).))))).)))))))))))).((((((((......))))).)))..))).)).... ( -35.10)
>DroSim_CAF1 123080 102 - 1
UUUACCA---------UCCCACCUUCCCA-AGUUCGCG-------AUCCUCGAUCCUGGGUUCCUGAUCGCGGGAUUGUAACUGGGCUCGGCAUUUAAGUCGGCGCCACAGGCGGCAAU
.......---------..((.(((.....-((((.(((-------((((((((((..((...)).))))).)))))))))))).((((((((......))))).)))..))).)).... ( -35.10)
>DroEre_CAF1 123657 102 - 1
CUCGCCA---------UCCCACCUCCCCA-AGUGCGCG-------AUCCUCGAUCCUGGGUGCCUGAUCUCGGGAUUGUAACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAU
...(((.---------...(((.......-.))).((.-------.....((((((((((........))))))))))...(((((((((((......))))).))).))))))))... ( -36.70)
>DroYak_CAF1 119845 119 - 1
CUUGCCACUUGCCACUUCCCACCUCGCCAAAGUACUCGAUUCUCGAUACUCGAUCCUGGGUUCCUGAUCUCGGGAUUGUAACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAU
.(((((....(((((((....((..(((..((((.(((.....)))))))((((((((((........))))))))))......)))..)).....)))).)))(((...)))))))). ( -41.60)
>DroAna_CAF1 104465 101 - 1
UUUACCU-------CUACCCGCA-GUCUG-GCUUUUCG-------GCUCUCGAUCCUGGCUA--UGUUCUUGGCUUUGUAACUGGGCCCGGCAUUCGAGUCGGCGCCACAGACGGCAAU
.......-------......((.-(((((-.....(((-------((((..(((((.((((.--.((((........).)))..)))).)).))).))))))).....))))).))... ( -30.30)
>consensus
UUUACCA_________UCCCACCUCCCCA_AGUUCGCG_______AUCCUCGAUCCUGGGUUCCUGAUCUCGGGAUUGUAACUGGGCUCGGCAUUCAAGUCGGCGCCACAGGCGGCAAU
..................................(((.............((((((((((........))))))))))...(((((((((((......))))).))).))))))..... (-25.80 = -26.72 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:00 2006