Locus 4633

Sequence ID	2R_DroMel_CAF1
Location	15,160,470 – 15,160,570
Length	100
Max. P	0.871298

overview

Window 2

Location	15,160,470 – 15,160,570
Length	100
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	74.90
Mean single sequence MFE	-24.67
Consensus MFE	-9.62
Energy contribution	-11.28
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.32
Structure conservation index	0.39
SVM decision value	0.87
SVM RNA-class probability	0.871298
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15160470 100 + 20766785
ACG--UGUGC-GUGCUUUGUCUGGCCAGAGAGGACAACGAG-----GAGAGGUUGCCACAUGUGGCAAAUUAACUUUAAAUUAAGCAAUUAAUUUAAUUAGAGCACGG
...--....(-((((((((....((((.(..((.((((...-----.....))))))...).)))).........(((((((((....))))))))).))))))))). ( -30.90)
>DroVir_CAF1 213556 89 + 1
ACG--UGAGC-----AAUG---GG-CCA---ACAAAACGAG-----CACAACUUGCCACAUGUGGCAAAUUAAGUUAAAAUUAAGCAAUUAAUUUAAUUAGUGCACUG
..(--(..((-----....---.)-)..---)).......(-----(((...((((((....))))))....(((((((.((((....))))))))))).)))).... ( -21.40)
>DroYak_CAF1 139556 100 + 1
ACG--UGUGC-GGGAUUUGUGUGGACUGAGAGGACAACGAG-----GAGAAGUUGCCACAUGUGGCAAAUUAACUUUAAAUUAAGCAAUUAAUUUAAUUAGAGCACGG
.((--(((.(-..(((((((((((.((....)).((((...-----.....)))))))).....)))))))....(((((((((....)))))))))...).))))). ( -26.00)
>DroMoj_CAF1 220633 97 + 1
ACGUGUGAGC-----AAUG---GGGCAA---ACAAAACGAGGCGAACACAACUUGCCACAUGUGGCAAAUUAAGUUAAAAUUAAGCAAUUAAUUUAAUUAGUGCACUG
..((((..((-----..((---......---......))..))..))))...((((((....))))))(((((....(((((((....)))))))..)))))...... ( -20.50)
>DroAna_CAF1 136082 90 + 1
ACG--UGAGUAGUGCAUUGUCUGGGCGG--AGGACAAC--------------UUGCCACAUGUGGCAAAUUAACUUAAAAUUAAGCAAUUAAUUUAAUUAGAGCACGG
((.--...)).((((.((((((......--.)))))).--------------((((((....)))))).........(((((((....))))))).......)))).. ( -25.00)
>DroPer_CAF1 138974 91 + 1
-CG--UGUGA-GGGCAUUGUCUGCACUC--------ACAAG-----GACAUCAUGCCACAUGUGGCAAAUUAACUUAAAAUUAAGCAAUUAAUUUAAUUAUAGCCGGG
-..--(((((-(.(((.....))).)))--------))).(-----(.(....(((((....)))))..........(((((((....))))))).......)))... ( -24.20)
>consensus
ACG__UGAGC_G_GCAUUGUCUGGACAG___GGACAACGAG_____GACAACUUGCCACAUGUGGCAAAUUAACUUAAAAUUAAGCAAUUAAUUUAAUUAGAGCACGG
....................................................((((((....)))))).........(((((((....)))))))............. ( -9.62 = -11.28 +   1.67)

alignment

secondary structure

dotplot

Window 3

Location	15,160,470 – 15,160,570
Length	100
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	74.90
Mean single sequence MFE	-20.40
Consensus MFE	-8.60
Energy contribution	-8.93
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.42
SVM decision value	0.08
SVM RNA-class probability	0.575991
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15160470 100 - 20766785
CCGUGCUCUAAUUAAAUUAAUUGCUUAAUUUAAAGUUAAUUUGCCACAUGUGGCAACCUCUC-----CUCGUUGUCCUCUCUGGCCAGACAAAGCAC-GCACA--CGU
.((((((....(((((((((....))))))))).(((.....((((...(.((((((.....-----...)))).)).)..))))..)))..)))))-)....--... ( -22.90)
>DroVir_CAF1 213556 89 - 1
CAGUGCACUAAUUAAAUUAAUUGCUUAAUUUUAACUUAAUUUGCCACAUGUGGCAAGUUGUG-----CUCGUUUUGU---UGG-CC---CAUU-----GCUCA--CGU
..(.((((.....(((((((....)))))))......(((((((((....))))))))))))-----).).....((---.((-(.---....-----))).)--).. ( -20.90)
>DroYak_CAF1 139556 100 - 1
CCGUGCUCUAAUUAAAUUAAUUGCUUAAUUUAAAGUUAAUUUGCCACAUGUGGCAACUUCUC-----CUCGUUGUCCUCUCAGUCCACACAAAUCCC-GCACA--CGU
..((((.....(((((((((....))))))))).......((((((....))))))......-----...((((..(.....)..)).)).......-)))).--... ( -18.10)
>DroMoj_CAF1 220633 97 - 1
CAGUGCACUAAUUAAAUUAAUUGCUUAAUUUUAACUUAAUUUGCCACAUGUGGCAAGUUGUGUUCGCCUCGUUUUGU---UUGCCC---CAUU-----GCUCACACGU
.((.((.......(((((((....))))))).(((.((((((((((....)))))))))).))).)))).....(((---..((..---....-----))..)))... ( -18.30)
>DroAna_CAF1 136082 90 - 1
CCGUGCUCUAAUUAAAUUAAUUGCUUAAUUUUAAGUUAAUUUGCCACAUGUGGCAA--------------GUUGUCCU--CCGCCCAGACAAUGCACUACUCA--CGU
..((((..((((((((((((....)))))))..)))))..((((((....))))))--------------((((((..--.......))))))))))......--... ( -19.20)
>DroPer_CAF1 138974 91 - 1
CCCGGCUAUAAUUAAAUUAAUUGCUUAAUUUUAAGUUAAUUUGCCACAUGUGGCAUGAUGUC-----CUUGU--------GAGUGCAGACAAUGCCC-UCACA--CG-
...((.(((....(((((((((...........)))))))))((((....))))...))).)-----).(((--------(((.(((.....))).)-)))))--..- ( -23.00)
>consensus
CCGUGCUCUAAUUAAAUUAAUUGCUUAAUUUUAAGUUAAUUUGCCACAUGUGGCAAGUUGUC_____CUCGUUGUCC___CAGCCCAGACAAUGC_C_GCACA__CGU
.............(((((((((...........)))))))))((((....))))...................................................... ( -8.60 =  -8.93 +   0.33)

alignment

secondary structure

dotplot

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