Locus 31

Sequence ID	pao_1
Location	2,118,520 – 2,118,585
Length	65
Max. P	0.994515

overview

Window 5

Location	2,118,520 – 2,118,585
Length	65
Sequences	4
Columns	65
Reading direction	forward
Mean pairwise identity	88.43
Mean single sequence MFE	-25.65
Consensus MFE	-21.60
Energy contribution	-22.60
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.38
Structure conservation index	0.84
SVM decision value	2.46
SVM RNA-class probability	0.994235
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 2118520 65 + 1
UGUAGUGGUCUACUGAUCCCGGACACCGAUUUAGGCGAAAAUCCUCGCCGUGAGAGAGGUGUCUG
.((((....))))......((((((((..(((.(((((......)))))...)))..)))))))) ( -26.20)
>pau_1 1 65 + 1
UGUAGUGGUCUACUGAUCCCGGACACCGAUUUAGGCGAGAAUCCUCGCCGUGAGAGAGGUGUCUG
.((((....))))......((((((((..(((.((((((....))))))...)))..)))))))) ( -29.10)
>pfo_1 1 61 + 1
---AGUGGUCUAAUGAAACCGGACACCCAUUUAGGCGAAAAUGCUCGCCA-GAUAGAGGUGUCUG
---...(((........)))((((((((((((.(((((......))))))-))).).))))))). ( -22.30)
>psp_1 1 64 + 1
UGUAGUGGUCUAAUGAAACCGGACACCCAUUUAGGCGAGAAUGCUCGCCA-GAUAGAGGUGUCUG
......(((........)))((((((((((((.((((((....)))))))-))).).))))))). ( -25.00)
>consensus
UGUAGUGGUCUAAUGAAACCGGACACCCAUUUAGGCGAAAAUCCUCGCCA_GAGAGAGGUGUCUG
...................((((((((..(((.((((((....))))))...)))..)))))))) (-21.60 = -22.60 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	2,118,520 – 2,118,585
Length	65
Sequences	4
Columns	65
Reading direction	reverse
Mean pairwise identity	88.43
Mean single sequence MFE	-21.99
Consensus MFE	-18.61
Energy contribution	-18.36
Covariance contribution	-0.25
Combinations/Pair	1.07
Mean z-score	-3.35
Structure conservation index	0.85
SVM decision value	2.49
SVM RNA-class probability	0.994515
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 2118520 65 - 1
CAGACACCUCUCUCACGGCGAGGAUUUUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACA
..((((((........((((((....))))))......))))))........((((....)))). ( -18.84)
>pau_1 1 65 - 1
CAGACACCUCUCUCACGGCGAGGAUUCUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACA
..((((((........((((((....))))))......))))))........((((....)))). ( -21.54)
>pfo_1 1 61 - 1
CAGACACCUCUAUC-UGGCGAGCAUUUUCGCCUAAAUGGGUGUCCGGUUUCAUUAGACCACU---
..(((((((.....-.((((((....)))))).....))))))).((((......))))...--- ( -22.90)
>psp_1 1 64 - 1
CAGACACCUCUAUC-UGGCGAGCAUUCUCGCCUAAAUGGGUGUCCGGUUUCAUUAGACCACUACA
..(((((((.....-.((((((....)))))).....))))))).((((......))))...... ( -24.70)
>consensus
CAGACACCUCUAUC_CGGCGAGCAUUCUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACA
..((((((........((((((....))))))......)))))).((..........))...... (-18.61 = -18.36 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:47:34 2007