Locus 6287

Sequence ID	3R_DroMel_CAF1
Location	16,405,534 – 16,405,672
Length	138
Max. P	0.942337

overview

Window 4

Location	16,405,534 – 16,405,637
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	92.52
Mean single sequence MFE	-29.76
Consensus MFE	-25.10
Energy contribution	-25.74
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.75
Structure conservation index	0.84
SVM decision value	1.33
SVM RNA-class probability	0.942337
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16405534 103 - 27905053
GCAUUAGACAACGAAGGCCGCUGACCCUGAACUAUCGAUAGCUCACUAUCGAUGCGACCAUCGAUGGUUUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
................((.((((...((.(((((.....((((.((((((((((....)))))))))).....)))).....))))).))....)))).)).. ( -30.60)
>DroSec_CAF1 1149 103 - 1
GCACUAGACUACGAAGGCCGCUGACCCUGAACUAUCGAUAGCACACUAUCGAUGCGACCAUCGAUGGUUUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
................((.((((...((.(((((.....(((..((((((((((....))))))))))......))).....))))).))....)))).)).. ( -28.90)
>DroSim_CAF1 1155 103 - 1
GCACUAGACUACGAAGGCCGCUGACCCUGAACUAUCGAUAGCACACUAUCGAUGCGACCAUCGAUGGUUUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
................((.((((...((.(((((.....(((..((((((((((....))))))))))......))).....))))).))....)))).)).. ( -28.90)
>DroEre_CAF1 1132 103 - 1
GGGCCAGAUCAUGACGGCCGCUGACCCUGAACUAUCGAUACAAUACUAUCGAUGCGACCAUCGAUGGUAUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
.((((..........))))((((...((.(((((..((....((((((((((((....))))))))))))......))....))))).))....))))..... ( -33.60)
>DroYak_CAF1 1120 103 - 1
GGUCUAGACAAUGAAGGACGCUGACCCUGAACUAUCGAUACAAUACUAUCGGUGCGACCAUCGAUGGUUUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
.((((..........))))((((...(((..((.((....(((.((((((((((....))))))))))))).(((((......))))).)).))))))))).. ( -26.80)
>consensus
GCACUAGACAACGAAGGCCGCUGACCCUGAACUAUCGAUAGCACACUAUCGAUGCGACCAUCGAUGGUUUGACAGCUCUAAUUAGUUGAGAAAGCAGCAGCAA
................((.((((.....(((((((((((((....)))))((((....))))))))))))..(((((......)))))......)))).)).. (-25.10 = -25.74 +   0.64)

alignment

secondary structure

dotplot

Window 5

Location	16,405,559 – 16,405,672
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-36.26
Consensus MFE	-25.86
Energy contribution	-25.46
Covariance contribution	-0.40
Combinations/Pair	1.13
Mean z-score	-1.69
Structure conservation index	0.71
SVM decision value	-0.04
SVM RNA-class probability	0.511116
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16405559 113 + 27905053
GAGCUGUCAAACCAUCGAUGGUCGCAUCGAUAGUGAGCUAUCGAUAGUUCAGGGUCAGCGGCCUUCGUUGUCUAAUGCCAUCGCUAAUCCGAUAUUAUUGCAGGGCUUUUAGC
..((((....((.(((((((....))))))).))(((((..(((((((...((((.(((((....((((....))))...))))).))))...)))))))...))))).)))) ( -33.10)
>DroSec_CAF1 1174 113 + 1
GAGCUGUCAAACCAUCGAUGGUCGCAUCGAUAGUGUGCUAUCGAUAGUUCAGGGUCAGCGGCCUUCGUAGUCUAGUGCCAUCGCUAGUCCGAUAUUAUUGCAGCGCUUUUAGC
..((((.(((.....(((.((((((((((((((....)))))))).(........).)))))).)))..(.((((((....)))))).)........)))))))......... ( -36.60)
>DroSim_CAF1 1180 113 + 1
GAGCUGUCAAACCAUCGAUGGUCGCAUCGAUAGUGUGCUAUCGAUAGUUCAGGGUCAGCGGCCUUCGUAGUCUAGUGCCAUCGCUAGUCCGAUAUUAUUGCAGCGCUUUUAGC
..((((.(((.....(((.((((((((((((((....)))))))).(........).)))))).)))..(.((((((....)))))).)........)))))))......... ( -36.60)
>DroEre_CAF1 1157 113 + 1
GAGCUGUCAUACCAUCGAUGGUCGCAUCGAUAGUAUUGUAUCGAUAGUUCAGGGUCAGCGGCCGUCAUGAUCUGGCCCCAUCGCUAUUCCGAUACCAUUGCACAGCUCUCAGC
((((((((((((.(((((((....))))))).)))..(((((((((((...(((((((...(......)..)))))))....)))))..))))))...)).)))))))..... ( -41.50)
>DroYak_CAF1 1145 113 + 1
GAGCUGUCAAACCAUCGAUGGUCGCACCGAUAGUAUUGUAUCGAUAGUUCAGGGUCAGCGUCCUUCAUUGUCUAGACCCAUCGCUAUUCCGAUACUACUGCACAGCUUUUAAC
(((((((...((((....)))).(((....((((((((....((((((...(((((((((........)).)).)))))...)))))).)))))))).))))))))))..... ( -33.50)
>consensus
GAGCUGUCAAACCAUCGAUGGUCGCAUCGAUAGUGUGCUAUCGAUAGUUCAGGGUCAGCGGCCUUCGUAGUCUAGUGCCAUCGCUAGUCCGAUAUUAUUGCAGAGCUUUUAGC
((((......((.(((((((....))))))).))..(((..(((((((...(((..((((.....................))))..)))...))))))).)))))))..... (-25.86 = -25.46 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:44 2006