Locus 23

Sequence ID	pao_1
Location	1,062,370 – 1,062,440
Length	70
Max. P	0.997219

overview

Window 0

Location	1,062,370 – 1,062,440
Length	70
Sequences	4
Columns	70
Reading direction	forward
Mean pairwise identity	86.87
Mean single sequence MFE	-23.28
Consensus MFE	-17.95
Energy contribution	-18.95
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.17
Structure conservation index	0.77
SVM decision value	2.07
SVM RNA-class probability	0.987069
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 1062370 70 + 1
CAGACACCUCUUUCACGGCGAGGAUUCUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACACUGCC
..((((((..(((...((((((....)))))).)))..))))))..((....((((....))))....)) ( -22.20)
>pau_1 1 70 + 1
CAGACACCUCUUUCACGGCGAGGAUUCUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACACUGCC
..((((((..(((...((((((....)))))).)))..))))))..((....((((....))))....)) ( -22.20)
>ppk_1 1 64 + 1
CAGACACCUCUUUGG-GGCGAGCAUUCUCGCCUAAAUGAGUGUCCGGUUUCAUUAGACCACUACA-----
..(((((.((....(-((((((....)))))))....))))))).((((......))))......----- ( -24.00)
>psp_1 1 69 + 1
CAGACACCUCUAUCU-GGCGAGCAUUCUCGCCUAAAUGGGUGUCCGGUUUCAUUAGACCACUACAAUGCC
..(((((((......-((((((....)))))).....))))))).((((......))))........... ( -24.70)
>consensus
CAGACACCUCUUUCA_GGCGAGCAUUCUCGCCUAAAUCGGUGUCCGGGAUCAGUAGACCACUACACUGCC
..(((((((.(((...((((((....)))))).))).))))))).((..........))........... (-17.95 = -18.95 +   1.00)

alignment

secondary structure

dotplot

Window 1

Location	1,062,370 – 1,062,440
Length	70
Sequences	4
Columns	70
Reading direction	reverse
Mean pairwise identity	86.87
Mean single sequence MFE	-27.25
Consensus MFE	-24.29
Energy contribution	-24.85
Covariance contribution	0.56
Combinations/Pair	1.09
Mean z-score	-3.12
Structure conservation index	0.89
SVM decision value	2.82
SVM RNA-class probability	0.997219
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 1062370 70 - 1
GGCAGUGUAGUGGUCUACUGAUCCCGGACACCGAUUUAGGCGAGAAUCCUCGCCGUGAAAGAGGUGUCUG
((....((((....))))....))((((((((..(((.((((((....))))))...)))..)))))))) ( -30.30)
>pau_1 1 70 - 1
GGCAGUGUAGUGGUCUACUGAUCCCGGACACCGAUUUAGGCGAGAAUCCUCGCCGUGAAAGAGGUGUCUG
((....((((....))))....))((((((((..(((.((((((....))))))...)))..)))))))) ( -30.30)
>ppk_1 1 64 - 1
-----UGUAGUGGUCUAAUGAAACCGGACACUCAUUUAGGCGAGAAUGCUCGCC-CCAAAGAGGUGUCUG
-----......(((........)))(((((((..(((.((((((....))))))-..)))..))))))). ( -22.90)
>psp_1 1 69 - 1
GGCAUUGUAGUGGUCUAAUGAAACCGGACACCCAUUUAGGCGAGAAUGCUCGCC-AGAUAGAGGUGUCUG
..(((((........)))))....(((((((((((((.((((((....))))))-)))).).)))))))) ( -25.50)
>consensus
GGCAGUGUAGUGGUCUAAUGAAACCGGACACCCAUUUAGGCGAGAAUCCUCGCC_UGAAAGAGGUGUCUG
..(((((........)))))....((((((((..(((.((((((....))))))...)))..)))))))) (-24.29 = -24.85 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:47:15 2007