Locus 5054

Sequence ID	3R_DroMel_CAF1
Location	13,305,816 – 13,306,015
Length	199
Max. P	0.978675

overview

Window 5

Location	13,305,816 – 13,305,910
Length	94
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	76.56
Mean single sequence MFE	-22.51
Consensus MFE	-10.06
Energy contribution	-9.82
Covariance contribution	-0.24
Combinations/Pair	1.10
Mean z-score	-2.41
Structure conservation index	0.45
SVM decision value	1.82
SVM RNA-class probability	0.978675
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13305816 94 + 27905053
--------AACAUU-UUUUAUGCACUUUU-UCAAAUUUUCCAUUAAAAUCGAACUGUGGUCUCGUU-------CUCCGAGUGCAUGCGUGCAAAUAUUUGUAUGUAUAUUG
--------......-......((((((..-.........((((............)))).......-------....))))))((((((((((....)))))))))).... ( -19.45)
>DroSec_CAF1 58286 97 + 1
UAUAUACAAAUAUUAUUUUAUGCAUGUUU-------UUUCCAUUGAAUUCGAACUCUGGUCUGGUU-------CUCCGAAUACAUGCGUGCAAAUAUUUGUAUGUAUAUUG
((((((((((((((....(((((((((..-------.(((....((((..((.(....)))..)))-------)...))).)))))))))..))))))))))))))..... ( -27.00)
>DroSim_CAF1 61964 97 + 1
UAUAUACAAAUAUUAUUUUAUGCAUGUUU-------UUUCCAUUGAAAUCCAACUCUGGUCUGGUU-------CUCCGAGUGCAUGCGUGCAAAUAUUUGUAUGUAUAUUG
((((((((((((((....(((((((((..-------.(((....(((..(((....))).....))-------)...))).)))))))))..))))))))))))))..... ( -26.60)
>DroEre_CAF1 60019 102 + 1
CAUGCAAAAAUAAUAUUUUAUCCACAUGGCUUAUAUUUCCCAUUGUAAUCGAACUUU--UCUGCUU-------CUCCGAGUGCAUGCGUGCAAAUAUUUGUACGUAUAUUG
..(((((....(((((.....((....))...))))).....)))))..........--...((((-------....))))..((((((((((....)))))))))).... ( -15.80)
>DroYak_CAF1 69415 101 + 1
CAUAUAAAAAUAAUAUUUUAUGCACAUGGU--------UCCAUUGAAAUCGAACUUG--UCCGGUUCUCCGUUCUCCGAGUGCAUGCGUGCAAAUAUUUGUACGUAUAUAG
...((((((......))))))((((.(((.--------....(((....)))....(--..(((....)))..).))).))))((((((((((....)))))))))).... ( -23.70)
>consensus
CAUAUAAAAAUAUUAUUUUAUGCACAUUU_______UUUCCAUUGAAAUCGAACUCUGGUCUGGUU_______CUCCGAGUGCAUGCGUGCAAAUAUUUGUAUGUAUAUUG
...................................................................................((((((((((....)))))))))).... (-10.06 =  -9.82 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	13,305,910 – 13,306,015
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	74.22
Mean single sequence MFE	-38.98
Consensus MFE	-24.60
Energy contribution	-25.13
Covariance contribution	0.53
Combinations/Pair	1.15
Mean z-score	-1.76
Structure conservation index	0.63
SVM decision value	1.32
SVM RNA-class probability	0.941702
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13305910 105 - 27905053
GUACGAAUUCUGGGUUUCGGCUUCGACAUCCGUGGGCGAAGGGGAGCCCACAUCUGUGAUCGCCCAGGCCACCAAUACGCGAGGUAGGU--UGCAUCCAGAUA------------AAUA-
........(((((((...(((.((.(((...((((((........))))))...)))))..)))...((.(((....(....)...)))--.)))))))))..------------....- ( -33.90)
>DroVir_CAF1 58117 107 - 1
GUACGAGUUCUGGGUCUCUGCAUCCACAUCAGUGGGUGAGGGUGAGCCCACAUCGGUGGUGGCCCAGGCCACAAAUACACGAGGUAGGCGUUAUAGCGCUUUA------------AAAA-
((((((....(((((((((.(((((((....)))))))))))...)))))..)))...(((((....)))))...))).......((((((....))))))..------------....- ( -40.30)
>DroPse_CAF1 75329 90 - 1
GUACGAGUUCUGGGUAUCCGCGUCCACGUCCGUGGGCGAGGGCGAGCCCACAUCUGUGGUUGCCCAGGCAACCAAUACGCGAGGU-----------------A------------AAUA-
.(((..((.(((((((.((((((((((....))))))..(((....)))......)))).)))))))))........(....)))-----------------)------------....- ( -37.00)
>DroGri_CAF1 58184 119 - 1
GUACGAGUUCUGGGUAUCAGCAUCCACGUCGGUGGGUGAGGGUGAGCCCACAUCUGUGGUGGCCCAGGCCACCAAUACACGAGGUAGGUAUCGCAGCUGCAACUGCAACUCUUUAAAGU-
....(((((...((((((..(((((((....))))))).(((....)))((.(((((((((((....))))))...))).)).)).))))))((((......)))))))))........- ( -44.90)
>DroAna_CAF1 79158 105 - 1
GUACGAGUUCUGGGUAUCGGCCUCCACAUCCGUCGGGGAGGGCGAGCCUACUUCGGUGAUUGCCCAGGCAACCAAUACAAGAGGUAGGC--AGAAU-CAGAUA------------AAUAU
........(((((...(((.(((((.(........)))))).)))(((((((((..((.((((....)))).))......)))))))))--....)-))))..------------..... ( -39.50)
>DroPer_CAF1 69343 90 - 1
GUACGAGUUCUGGGUAUCCGCGUCCACGUCCGUGGGCGAGGGCGAGCCCACAUCUGUGGUUGCCCAGGCCACCAAUACGCGAGGU-----------------A------------AAUA-
.(((..(..(((((((.((((((((((....))))))..(((....)))......)))).)))))))..).......(....)))-----------------)------------....- ( -38.30)
>consensus
GUACGAGUUCUGGGUAUCCGCAUCCACAUCCGUGGGCGAGGGCGAGCCCACAUCUGUGGUUGCCCAGGCCACCAAUACACGAGGUAGG____G_A_____AUA____________AAUA_
(((.((....(((((.((..(((((((....)))))))..))...)))))..))..(((((((....))))))).))).......................................... (-24.60 = -25.13 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:07 2006