Locus 179

Sequence ID	pao.2483
Location	4,641,419 – 4,641,578
Length	159
Max. P	0.998086

overview

Window 0

Location	4,641,419 – 4,641,538
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	79.94
Mean single sequence MFE	-62.37
Consensus MFE	-43.42
Energy contribution	-41.43
Covariance contribution	-1.98
Combinations/Pair	1.26
Mean z-score	-1.91
Structure conservation index	0.70
SVM decision value	0.78
SVM RNA-class probability	0.849547
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2483 4641419 119 - 6264404
GUCCGGC-GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUGGCGGCCCGGCGCUUGUCGAGGGUCGCCGAUGGGCGCUUAA
(((((((-((.....(((.((.((..((((.((((((((((((..((((((((((((...)))))))).)))).)))).)).)))))))))).)).)).))))))))...))))...... ( -63.90)
>pau.477 5651212 119 + 6537648
GUCCGGC-GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUGGCGGCCCGGCGCUUGUCGAGGGUCGCCGAUGGGCGCUUAA
(((((((-((.....(((.((.((..((((.((((((((((((..((((((((((((...)))))))).)))).)))).)).)))))))))).)).)).))))))))...))))...... ( -63.90)
>pf5.1312 2424931 120 - 7074893
CUGCGCCUGAGACGUUGCAUGUCAGGCUGCACGGGGCCUUGGCGAGACCCUGAGACGUUGCGUCUCAGCGCCCCCACGGCGCCGCCCGGUGCUUGUCGGGAGCCGCGGAUCGGCGCUUAA
..(((((.((..(((.((.(.((.(((.((((.((((...(((......((((((((...)))))))).(((.....)))))))))).))))..))))).))).)))..))))))).... ( -59.30)
>consensus
GUCCGGC_GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUGGCGGCCCGGCGCUUGUCGAGGGUCGCCGAUGGGCGCUUAA
((((.((...((((.....)))).((.(((.(((....)))))).((((((((((((...)))))))).))))))..)).).)))..((((((..(((........)))..))))))... (-43.42 = -41.43 +  -1.98)

alignment

secondary structure

dotplot

Window 1

Location	4,641,459 – 4,641,578
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	73.82
Mean single sequence MFE	-61.70
Consensus MFE	-40.47
Energy contribution	-40.70
Covariance contribution	0.23
Combinations/Pair	1.19
Mean z-score	-2.23
Structure conservation index	0.66
SVM decision value	3.00
SVM RNA-class probability	0.998086
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2483 4641459 119 + 6264404
CACAGCCGACGACUGAGACGGAGCGUCUCAGCGUCUCGCCGGGAACCCGUGCGCGAUGACAUGGGUUGUCUC-GCCGGACGUCGCCCCGGCGGUCGCCGGCCUUCCCAUGCCGGCGCUCU
....(((((((.((((((((...))))))))))))..((((((....(((.(((((.((((.....))))))-).)).)))....)))))))))(((((((........))))))).... ( -63.40)
>pau.477 5651252 119 - 6537648
CACAGCCGACGACUGAGACGGAGCGUCUCAGCGUCUCGCCGGGAACCCGUGCGCGAUGACAUGGGUUGUCUC-GCCGGACGUCGCCCCGGCGGUCGCCGGCCUUCCCAUGCCGGCGCUCU
....(((((((.((((((((...))))))))))))..((((((....(((.(((((.((((.....))))))-).)).)))....)))))))))(((((((........))))))).... ( -63.40)
>pf5.1312 2424971 119 + 7074893
GCCGUGGGGGCGCUGAGACGCAACGUCUCAGGGUCUCGCCAAGGCCCCGUGCAGCCUGACAUGCAACGUCUCAGGCGCAGGGCUUCCCGACACCUGCAGGCGAGUGCA-ACAGCCGCUCU
((((..(((((.((((((((...)))))))).)))(((...((((((..(((.((((((.(((...))).)))))))))))))))..)))..))..).)))((((((.-...).))))). ( -58.30)
>consensus
CACAGCCGACGACUGAGACGGAGCGUCUCAGCGUCUCGCCGGGAACCCGUGCGCGAUGACAUGGGUUGUCUC_GCCGGACGUCGCCCCGGCGGUCGCCGGCCUUCCCAUGCCGGCGCUCU
..(((((((((.((((((((...))))))))))))..(((((....))).))...........))))).....(((((........(((((....)))))..........)))))..... (-40.47 = -40.70 +   0.23)

alignment

secondary structure

dotplot

Window 2

Location	4,641,459 – 4,641,578
Length	119
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	73.82
Mean single sequence MFE	-61.10
Consensus MFE	-43.47
Energy contribution	-42.27
Covariance contribution	-1.21
Combinations/Pair	1.27
Mean z-score	-1.51
Structure conservation index	0.71
SVM decision value	1.16
SVM RNA-class probability	0.924840
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2483 4641459 119 - 6264404
AGAGCGCCGGCAUGGGAAGGCCGGCGACCGCCGGGGCGACGUCCGGC-GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUG
..(((((((((........))))))...((((((((...(((.((.(-((((((.....)))).))))).)))...)))))))).((((((((((((...)))))))).)))).)))... ( -64.30)
>pau.477 5651252 119 + 6537648
AGAGCGCCGGCAUGGGAAGGCCGGCGACCGCCGGGGCGACGUCCGGC-GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUG
..(((((((((........))))))...((((((((...(((.((.(-((((((.....)))).))))).)))...)))))))).((((((((((((...)))))))).)))).)))... ( -64.30)
>pf5.1312 2424971 119 - 7074893
AGAGCGGCUGU-UGCACUCGCCUGCAGGUGUCGGGAAGCCCUGCGCCUGAGACGUUGCAUGUCAGGCUGCACGGGGCCUUGGCGAGACCCUGAGACGUUGCGUCUCAGCGCCCCCACGGC
...((((((..-((((..((.((.(((((((.(((...))).))))))))).)).)))).....)))))).(((((....((((.....((((((((...))))))))))))))).)).. ( -54.70)
>consensus
AGAGCGCCGGCAUGGGAAGGCCGGCGACCGCCGGGGCGACGUCCGGC_GAGACAACCCAUGUCAUCGCGCACGGGUUCCCGGCGAGACGCUGAGACGCUCCGUCUCAGUCGUCGGCUGUG
...((((.((((((((....(((((....)))))(....)...............))))))))...)))).(((....)))....((((((((((((...)))))))).))))....... (-43.47 = -42.27 +  -1.21)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:16:51 2007