Locus 6

Sequence ID	pao_1
Location	722,190 – 722,510
Length	320
Max. P	0.982702

overview

Window 9

Location	722,190 – 722,310
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-46.02
Consensus MFE	-43.10
Energy contribution	-45.10
Covariance contribution	2.00
Combinations/Pair	1.11
Mean z-score	-1.38
Structure conservation index	0.94
SVM decision value	0.13
SVM RNA-class probability	0.597940
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722190 120 + 1
AGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUGGUAGUGGGGGAUAACGUCCGGAAACGGGCGCUAAUACCGCAUACGUCCUGAGGGAGAAAGUGGGGGAUCUUCGGACCUCACG
......(((((.........((((.(((......)))))))(((.((..((.((((((....)))))).))...)).))).)))))...........((((((..((....)))))))). ( -46.60)
>pf5_1 1 120 + 1
AGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUAGUAGUGGGGGAUAACGUCCGGAAACGGGCGCUAAUACCGCAUACGUCCUACGGGAGAAAGUGGGGGAUCUUCGGACCUCACG
..((..(((((.(((.(((..((...(..((((.((.......)).))))..)(((((....)))))))...))))))...)))))..)).......((((((..((....)))))))). ( -48.50)
>psp_1 1 120 + 1
AGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUGGUAGUGGGGGAUAACGCUCGGAAACGGACGCUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGACCUUCGGGCCUUGCG
..((..(((((.........((((.(((......)))))))(((.((..((.((..((....))..)).))...)).))).)))))..)).......((((((..((....)))))))). ( -44.50)
>pss_1 1 120 + 1
AGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUGGUAGUGGGGGAUAACGCUCGGAAACGGACGCUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGACCUUCGGGCCUUGCG
..((..(((((.........((((.(((......)))))))(((.((..((.((..((....))..)).))...)).))).)))))..)).......((((((..((....)))))))). ( -44.50)
>consensus
AGCGGCGGACGGGUGAGUAAUGCCUAGGAAUCUGCCUGGUAGUGGGGGAUAACGCCCGGAAACGGACGCUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGACCUUCGGACCUCACG
..((..(((((.(((.(((..((...(..((((.((.......)).))))..)(((((....)))))))...))))))...)))))..)).......((((((..((....)))))))). (-43.10 = -45.10 +   2.00)

alignment

secondary structure

dotplot

Window 0

Location	722,270 – 722,390
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-47.15
Consensus MFE	-43.60
Energy contribution	-46.23
Covariance contribution	2.63
Combinations/Pair	1.16
Mean z-score	-2.39
Structure conservation index	0.92
SVM decision value	1.92
SVM RNA-class probability	0.982702
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722270 120 + 1
ACGUCCUGAGGGAGAAAGUGGGGGAUCUUCGGACCUCACGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCGUAACUGGUCUGAGA
.((((.(((...((...((((((..((....)))))))).)).)))))))((.((((..((((((.(((..((((((((.......)))))))))))...))))))...)))).)).... ( -46.10)
>pf5_1 81 120 + 1
ACGUCCUACGGGAGAAAGUGGGGGAUCUUCGGACCUCACGCUAUUAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGA
...(((....)))...((((((((.((....)))))).)))).(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).. ( -45.90)
>psp_1 81 120 + 1
ACGUCCUACGGGAGAAAGCAGGGGACCUUCGGGCCUUGCGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGA
...(((....)))....((((((..((....))))))))....(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).. ( -48.30)
>pss_1 81 120 + 1
ACGUCCUACGGGAGAAAGCAGGGGACCUUCGGGCCUUGCGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGA
...(((....)))....((((((..((....))))))))....(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).. ( -48.30)
>consensus
ACGUCCUACGGGAGAAAGCAGGGGACCUUCGGACCUCACGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGA
...(((....)))....((((((..((....))))))))....(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).. (-43.60 = -46.23 +   2.63)

alignment

secondary structure

dotplot

Window 1

Location	722,310 – 722,430
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.92
Mean single sequence MFE	-40.60
Consensus MFE	-41.15
Energy contribution	-40.40
Covariance contribution	-0.75
Combinations/Pair	1.08
Mean z-score	-1.54
Structure conservation index	1.01
SVM decision value	0.06
SVM RNA-class probability	0.564203
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722310 120 + 1
CUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACU
((.(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).))(((.....)))...(((((.(((.....))))))))... ( -40.80)
>pf5_1 121 120 + 1
CUAUUAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACU
......(((((..((((..((((((.(((..((((((((.......)))))))))))...))))))...))))(((....)))...))).))...(((((.(((.....))))))))... ( -39.60)
>psp_1 121 120 + 1
CUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACU
((.(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).))(((.....)))...(((((.(((.....))))))))... ( -41.00)
>pss_1 121 120 + 1
CUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACU
((.(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).))(((.....)))...(((((.(((.....))))))))... ( -41.00)
>consensus
CUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGAGGUAAUGGCUCACCAAGGCGACGAUCCGUAACUGGUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACU
((.(((((.....((((..((((((.(((..((((((((.......)))))))))))...))))))...))))))))).))(((.....)))...(((((.(((.....))))))))... (-41.15 = -40.40 +  -0.75)

alignment

secondary structure

dotplot

Window 2

Location	722,390 – 722,510
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-45.50
Consensus MFE	-43.00
Energy contribution	-45.50
Covariance contribution	2.50
Combinations/Pair	1.00
Mean z-score	-2.25
Structure conservation index	0.95
SVM decision value	0.34
SVM RNA-class probability	0.696080
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722390 120 + 1
GGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGUCU
....((((..((((((((((.(((.....)))))))).((((....))))((.(((.(((......(((((...(((((....))))).))))))))))).))...)))))....)))). ( -45.50)
>pf5_1 201 120 + 1
GGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGUCU
....((((..((((((((((.(((.....)))))))).((((....))))((.(((.(((......(((((...(((((....))))).))))))))))).))...)))))....)))). ( -45.50)
>psp_1 201 120 + 1
GGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGUCU
....((((..((((((((((.(((.....)))))))).((((....))))((.(((.(((......(((((...(((((....))))).))))))))))).))...)))))....)))). ( -45.50)
>pss_1 201 120 + 1
GGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGUCU
....((((..((((((((((.(((.....)))))))).((((....))))((.(((.(((......(((((...(((((....))))).))))))))))).))...)))))....)))). ( -45.50)
>consensus
GGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGUCU
....((((..((((((((((.(((.....)))))))).((((....))))((.(((.(((......(((((...(((((....))))).))))))))))).))...)))))....)))). (-43.00 = -45.50 +   2.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:45:42 2007