Locus 7776

Sequence ID	3L_DroMel_CAF1
Location	20,741,563 – 20,741,722
Length	159
Max. P	0.725845

overview

Window 1

Location	20,741,563 – 20,741,683
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-42.73
Consensus MFE	-39.43
Energy contribution	-39.77
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.92
SVM decision value	-0.03
SVM RNA-class probability	0.519107
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20741563 120 - 23771897
AGCUGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUUGAGACAAAGCGACUUAUUCUACCGCCAGAGCACAUUUUGAAGCGCGG
.(((((((((.(((((.....)))......((.(((((((((((......(((...(((.(((((....))))).).))..)))....))))))))))).)))).))))))..))).... ( -43.60)
>DroSim_CAF1 20097 120 - 1
AGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAAAGCGACUUAUUCUACCGCCAGAGCACAUUUUGAAGCGCGG
.((.((((((.(((((.....)))......((.(((((((((((....((((((.((((....)))).)))((....))..).))...))))))))))).)))).))))))...)).... ( -42.40)
>DroYak_CAF1 31498 120 - 1
UGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUUAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAAAGCGACUUAUUCUACCGCCAGAGCACAUUUUGAAGCGAGG
.((.((((((.(((((.....)))......((.(((((((((((....((((((.((((....)))).)))((....))..).))...))))))))))).)))).))))))...)).... ( -42.20)
>consensus
AGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAAAGCGACUUAUUCUACCGCCAGAGCACAUUUUGAAGCGCGG
.((.((((((.(((((.....)))......((.(((((((((((......(((.(((..(((.((....)))))..)))..)))....))))))))))).)))).))))))...)).... (-39.43 = -39.77 +   0.33)

alignment

secondary structure

dotplot

Window 2

Location	20,741,603 – 20,741,722
Length	119
Sequences	3
Columns	119
Reading direction	reverse
Mean pairwise identity	96.64
Mean single sequence MFE	-42.10
Consensus MFE	-41.11
Energy contribution	-41.33
Covariance contribution	0.22
Combinations/Pair	1.03
Mean z-score	-1.66
Structure conservation index	0.98
SVM decision value	0.41
SVM RNA-class probability	0.725845
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20741603 119 - 23771897
GUUUUCGCCAGACAUAGCAUCCAAGCGAGGUCUAAGUCAAGCUGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUUGAGACAA
(((......((((...((......))...))))...((((((.((.(((((.(((.....)))..))))).((((.(((((......)))))....)))).....)).))))))))).. ( -38.30)
>DroSim_CAF1 20137 119 - 1
GUUUUCGCCAGACAUAGCAUCCAAGCGAGGUCUAAGUCCAGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAA
(((......((((...((......))...))))...(((((((((.(((((.(((.....)))..))))).((((.(((((......)))))....)))).....)))))))))))).. ( -45.30)
>DroYak_CAF1 31538 119 - 1
GUUUUCGCCAGACAUUGCAUCCAAGCGAGGUCUAAGUCCUGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUUAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAA
((((((...((((.((((......)))).)))).......(((((.(((((.(((.....)))..))))).((((.(((((......)))))....)))).....))))).)))))).. ( -42.70)
>consensus
GUUUUCGCCAGACAUAGCAUCCAAGCGAGGUCUAAGUCCAGCAGAAAUGAGCGCCGUUGAGGCCAUUCAUCGGGCGGUGGAGUUCAAUCCGCAUGUGCCCAAGUAUCUGCUGGAGACAA
(((......((((...((......))...))))...(((((((((.(((((.(((.....)))..))))).((((.(((((......)))))....)))).....)))))))))))).. (-41.11 = -41.33 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:56:42 2006