Locus 9

Sequence ID	pao_1
Location	723,190 – 723,429
Length	239
Max. P	0.957513

overview

Window 7

Location	723,190 – 723,309
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.92
Mean single sequence MFE	-44.83
Consensus MFE	-44.75
Energy contribution	-44.75
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	1.00
SVM decision value	0.12
SVM RNA-class probability	0.594009
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 723190 119 + 1
AACGAGCGCAACCCUUGUCCUUAGUUACCAGCACCUCG-GGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCA
...........(((...(((((.((((((..((((...-))))((((.(((....))).))))))))))......)))))....)))((((((.....)))))).(((((.....))))) ( -46.40)
>pf5_1 1001 120 + 1
AACGAGCGCAACCCUUGUCCUUAGUUACCAGCACGUUAUGGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCU
...........(((...(((((.((((((..(((......)))((((.(((....))).))))))))))......)))))....)))((((((.....))))))..((((.....)))). ( -44.30)
>psp_1 1001 120 + 1
AACGAGCGCAACCCUUGUCCUUAGUUACCAGCACGUUAUGGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCU
...........(((...(((((.((((((..(((......)))((((.(((....))).))))))))))......)))))....)))((((((.....))))))..((((.....)))). ( -44.30)
>pss_1 1001 120 + 1
AACGAGCGCAACCCUUGUCCUUAGUUACCAGCACGUUAUGGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCU
...........(((...(((((.((((((..(((......)))((((.(((....))).))))))))))......)))))....)))((((((.....))))))..((((.....)))). ( -44.30)
>consensus
AACGAGCGCAACCCUUGUCCUUAGUUACCAGCACGUUAUGGUGGGCACUCUAAGGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCU
...........(((...(((((.((((((..(((......)))((((.(((....))).))))))))))......)))))....)))((((((.....))))))..((((.....)))). (-44.75 = -44.75 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	723,269 – 723,389
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.92
Mean single sequence MFE	-46.22
Consensus MFE	-45.42
Energy contribution	-45.18
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-2.25
Structure conservation index	0.98
SVM decision value	1.21
SVM RNA-class probability	0.930848
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 723269 120 + 1
AGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCAGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCAUAAAACCGAUCGUA
..((((.((((((.....)))))).(((((((.......)))))))........)))).(((((((((.....(((..((...(((....)))...))....))).....))))))))). ( -47.10)
>pf5_1 1081 120 + 1
AGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCUGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCAUAAAACCGAUCGUA
..((((.((((((.....)))))).((((((.........))))))........)))).(((((((((.....(((..((...(((....)))...))....))).....))))))))). ( -46.40)
>psp_1 1081 120 + 1
AGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCUGGGCUACACACGUGCUACAAUGGUCGGUACAGAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCUCACAAAACCGAUCGUA
..((((.((((((.....)))))).((((((.........))))))........)))).(((((((((...((((...((...(((....)))...))...)))).....))))))))). ( -45.70)
>pss_1 1081 120 + 1
AGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCUGGGCUACACACGUGCUACAAUGGUCGGUACAGAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCUCACAAAACCGAUCGUA
..((((.((((((.....)))))).((((((.........))))))........)))).(((((((((...((((...((...(((....)))...))...)))).....))))))))). ( -45.70)
>consensus
AGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCUGGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCACAAAACCGAUCGUA
..((((.((((((.....)))))).((((((.........))))))........)))).(((((((((.....(((((((...(((....)))...)).)))))......))))))))). (-45.42 = -45.18 +  -0.25)

alignment

secondary structure

dotplot

Window 9

Location	723,309 – 723,429
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	98.33
Mean single sequence MFE	-48.25
Consensus MFE	-47.70
Energy contribution	-47.45
Covariance contribution	-0.25
Combinations/Pair	1.03
Mean z-score	-2.62
Structure conservation index	0.99
SVM decision value	1.48
SVM RNA-class probability	0.957513
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 723309 120 + 1
GGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCAUAAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGA
.((((.(((.((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..))....((((((........))))))))).))))... ( -48.60)
>pf5_1 1121 120 + 1
GGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCAUAAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGA
.((((.(((.((..((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))..))....((((((........))))))))).))))... ( -48.60)
>psp_1 1121 120 + 1
GGGCUACACACGUGCUACAAUGGUCGGUACAGAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCUCACAAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGA
.((((.(((.((..((((...(((((((...((((...((...(((....)))...))...)))).....)))))))))))..))....((((((........))))))))).))))... ( -47.90)
>pss_1 1121 120 + 1
GGGCUACACACGUGCUACAAUGGUCGGUACAGAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCUCACAAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGA
.((((.(((.((..((((...(((((((...((((...((...(((....)))...))...)))).....)))))))))))..))....((((((........))))))))).))))... ( -47.90)
>consensus
GGGCUACACACGUGCUACAAUGGUCGGUACAAAGGGUUGCCAAGCCGCGAGGUGGAGCUAAUCCCACAAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGA
.((((.(((.((..((((...(((((((.....(((((((...(((....)))...)).)))))......)))))))))))..))....((((((........))))))))).))))... (-47.70 = -47.45 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:45:51 2007