Locus 2779

Sequence ID	3R_DroMel_CAF1
Location	7,437,714 – 7,437,816
Length	102
Max. P	0.891950

overview

Window 5

Location	7,437,714 – 7,437,816
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	68.92
Mean single sequence MFE	-23.34
Consensus MFE	-11.18
Energy contribution	-12.46
Covariance contribution	1.28
Combinations/Pair	1.08
Mean z-score	-1.89
Structure conservation index	0.48
SVM decision value	0.97
SVM RNA-class probability	0.891950
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7437714 102 + 27905053
AUCCGAAUCCAAAUCCCA------------AUCGCAUCUCGCGCCUCAUCUGUGGCAUGCCAACGGAACAUUAACGCGAGAUGAAAUAUAUAUA------UAUAUAUAGAGUAGACUCUG
..................------------....(((((((((.....(((((((....)).))))).......)))))))))..((((((...------.))))))((((....)))). ( -26.30)
>DroSec_CAF1 20501 96 + 1
AUCCGAAUCACAAUCCCA------------AUCGCAUCUCGCGCCUCAUCUUUGGCAUGCCAACGGAACAUUAACGCGAAAUGAAAUAUA------------UAUAUAGAGUAGACUCUG
..................------------....(((.(((((.....(((((((....)))).))).......))))).))).......------------....(((((....))))) ( -17.10)
>DroSim_CAF1 19113 96 + 1
AUCCGAAUCACAAUCCCA------------AUCGAAUCUCGCGCCUCAUCUUUGGCAUGCCAACGGAACAUUAACGCGAGAUGAAAUAUA------------UACAUAGAGUAGACUCUG
..................------------.....((((((((.....(((((((....)))).))).......))))))))........------------....(((((....))))) ( -20.40)
>DroYak_CAF1 21150 110 + 1
AUCGGAAUCACAAUCCCAAUCCCAAUCCUCAUCUCAUCUCGCGCCC----------GAGCCAACGGAACAUUAGCGCGAGAUGAAAAAUAUAUAUGUAUGUAUAUAUGGAGUAAACUCGG
...(((.......))).....((..........(((((((((((((----------(......))).......)))))))))))...((((((((....)))))))).(((....))))) ( -29.81)
>DroAna_CAF1 18658 97 + 1
GUUGGAGAUAGAAGCCCAAUCUUUAUCC-----ACAUCUAACGCUUCAUCUUUGGCAUGCCAACGGCACAUUAACGCGAGAUGAUAUAUAUAA-----------GCCAGAGUA-------
((((((((((((.........)))))).-----...)))))).......(((((((.((((...)))).((((.(....).))))........-----------)))))))..------- ( -23.10)
>consensus
AUCCGAAUCACAAUCCCA____________AUCGCAUCUCGCGCCUCAUCUUUGGCAUGCCAACGGAACAUUAACGCGAGAUGAAAUAUAUA__________UAUAUAGAGUAGACUCUG
..................................(((((((((((........)))...((...)).........))))))))..................................... (-11.18 = -12.46 +   1.28)

alignment

secondary structure

dotplot

Window 6

Location	7,437,714 – 7,437,816
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	68.92
Mean single sequence MFE	-28.01
Consensus MFE	-16.84
Energy contribution	-19.80
Covariance contribution	2.96
Combinations/Pair	1.21
Mean z-score	-1.34
Structure conservation index	0.60
SVM decision value	0.05
SVM RNA-class probability	0.558137
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7437714 102 - 27905053
CAGAGUCUACUCUAUAUAUA------UAUAUAUAUUUCAUCUCGCGUUAAUGUUCCGUUGGCAUGCCACAGAUGAGGCGCGAGAUGCGAU------------UGGGAUUUGGAUUCGGAU
..((((((((((((((((..------..))))))((.(((((((((((((((...)))))))..(((........))))))))))).)).------------.)))...))))))).... ( -31.50)
>DroSec_CAF1 20501 96 - 1
CAGAGUCUACUCUAUAUA------------UAUAUUUCAUUUCGCGUUAAUGUUCCGUUGGCAUGCCAAAGAUGAGGCGCGAGAUGCGAU------------UGGGAUUGUGAUUCGGAU
..(((((((.(((.....------------...(((.(((((((((((((((...)))))))..(((........))))))))))).)))------------..))).)).))))).... ( -26.00)
>DroSim_CAF1 19113 96 - 1
CAGAGUCUACUCUAUGUA------------UAUAUUUCAUCUCGCGUUAAUGUUCCGUUGGCAUGCCAAAGAUGAGGCGCGAGAUUCGAU------------UGGGAUUGUGAUUCGGAU
..(((((.((...((.(.------------...(((..((((((((((((((...)))))))..(((........))))))))))..)))------------..).)).))))))).... ( -25.20)
>DroYak_CAF1 21150 110 - 1
CCGAGUUUACUCCAUAUAUACAUACAUAUAUAUUUUUCAUCUCGCGCUAAUGUUCCGUUGGCUC----------GGGCGCGAGAUGAGAUGAGGAUUGGGAUUGGGAUUGUGAUUCCGAU
((.((((..(((.(((((((......))))))).((((((((((((((...(((.....)))..----------.)))))))))))))).))))))).))((((((((....)))))))) ( -38.60)
>DroAna_CAF1 18658 97 - 1
-------UACUCUGGC-----------UUAUAUAUAUCAUCUCGCGUUAAUGUGCCGUUGGCAUGCCAAAGAUGAAGCGUUAGAUGU-----GGAUAAAGAUUGGGCUUCUAUCUCCAAC
-------......(((-----------(((........(((.(((((((((((..((((((....)))...)))..))))).)))))-----))))......))))))............ ( -18.74)
>consensus
CAGAGUCUACUCUAUAUA__________UAUAUAUUUCAUCUCGCGUUAAUGUUCCGUUGGCAUGCCAAAGAUGAGGCGCGAGAUGCGAU____________UGGGAUUGUGAUUCGGAU
..(((((...((((((((((........)))))))..(((((((((((((((...)))))))..(((........)))))))))))..................)))....))))).... (-16.84 = -19.80 +   2.96)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:34 2006