Locus 7

Sequence ID	pao_1
Location	722,630 – 722,870
Length	240
Max. P	0.952468

overview

Window 3

Location	722,630 – 722,750
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.42
Mean single sequence MFE	-40.75
Consensus MFE	-41.66
Energy contribution	-40.85
Covariance contribution	-0.81
Combinations/Pair	1.11
Mean z-score	-1.70
Structure conservation index	1.02
SVM decision value	0.97
SVM RNA-class probability	0.891299
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722630 120 + 1
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCGCGUAGGUGGUUCAGCAAGUUGGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUACUGAGCUAGAGUACG
.((((..................(((.((((.....)))).))).((((((((....(((((((((...((((.((......)).))))..))))))))).....))))))))..)))). ( -43.70)
>pf5_1 441 120 + 1
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCGCGUAGGUGGUUUGUUAAGUUGGAUGUGAAAGCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUG
.((((..................(((.((((.....)))).))).((((((((((..((((((((......((((((.....))))))....))))))))...))))))))))..)))). ( -41.90)
>psp_1 441 120 + 1
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCGCGUAGGUGGUUUGUUAAGUUGGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUG
.((((..................(((.((((.....)))).))).((((((((((..(((((((((...((((.((......)).))))..)))))))))...))))))))))..)))). ( -42.10)
>pss_1 441 120 + 1
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCGCGUAGGUGGUUUGUUAAGUUGAAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUG
.((((..................(((.((((.....)))).))).((((((((((..(((.(((((...((((.((......)).))))..))))).)))...))))))))))..)))). ( -35.30)
>consensus
GGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCGCGUAGGUGGUUUGUUAAGUUGGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUG
.((((..................(((.((((.....)))).))).((((((((((..((((((((......((((((.....))))))....))))))))...))))))))))..)))). (-41.66 = -40.85 +  -0.81)

alignment

secondary structure

dotplot

Window 4

Location	722,710 – 722,830
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.92
Mean single sequence MFE	-40.12
Consensus MFE	-38.92
Energy contribution	-38.17
Covariance contribution	-0.75
Combinations/Pair	1.08
Mean z-score	-2.51
Structure conservation index	0.97
SVM decision value	1.42
SVM RNA-class probability	0.952468
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722710 120 + 1
AACCUGGGAACUGCAUCCAAAACUACUGAGCUAGAGUACGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCU
..(((.(((......)))....((((((.((....)).))))))))).(((((...((((((((((.(((......)))....))))))))))...)))))((((((....)).)))).. ( -42.30)
>pf5_1 521 120 + 1
AACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCU
.(((..(((......)))....((((....)))).....)))..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..))) ( -39.40)
>psp_1 521 120 + 1
AACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCU
.(((..(((......)))....((((....)))).....)))..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..))) ( -39.40)
>pss_1 521 120 + 1
AACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCU
.(((..(((......)))....((((....)))).....)))..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..))) ( -39.40)
>consensus
AACCUGGGAACUGCAUCCAAAACUGGCAAGCUAGAGUAUGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCU
..(((.(((......)))....(((.((.((....)).)).)))))).(((((...((((((((((.(((......)))....))))))))))...)))))((((((....)).)))).. (-38.92 = -38.17 +  -0.75)

alignment

secondary structure

dotplot

Window 5

Location	722,750 – 722,870
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-40.90
Consensus MFE	-40.90
Energy contribution	-40.90
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.75
Structure conservation index	1.00
SVM decision value	1.00
SVM RNA-class probability	0.897367
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 722750 120 + 1
GUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCA
((..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..)))..)).(...((.((((....))((....)))).))...). ( -40.90)
>pf5_1 561 120 + 1
GUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCA
((..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..)))..)).(...((.((((....))((....)))).))...). ( -40.90)
>psp_1 561 120 + 1
GUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCA
((..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..)))..)).(...((.((((....))((....)))).))...). ( -40.90)
>pss_1 561 120 + 1
GUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCA
((..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..)))..)).(...((.((((....))((....)))).))...). ( -40.90)
>consensus
GUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAGUGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAGGUGCGAAAGCGUGGGGAGCA
((..(((.(((((...((((((((((.(((......)))....))))))))))...)))))((.((....)).))..)))..)).(...((.((((....))((....)))).))...). (-40.90 = -40.90 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:45:46 2007