Locus 69

Sequence ID	pao.2543
Location	4,784,139 – 4,784,295
Length	156
Max. P	0.999970

overview

Window 0

Location	4,784,139 – 4,784,257
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.95
Mean single sequence MFE	-37.35
Consensus MFE	-32.52
Energy contribution	-32.07
Covariance contribution	-0.46
Combinations/Pair	1.20
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.16
SVM RNA-class probability	0.611862
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2543 4784139 118 - 6264404
CCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUUUCCCAAGUAAA-UCUGGCUUU-UCUUCACGAGAUUCCUAACAG
......((((........))))((.((((((.........((((..((((.........))))..))))(((((((((.......)))-))))))...-.......))))))))...... ( -38.40)
>pau.416 5794970 116 + 6537648
CCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUUUCCCAAGUAAA-UCUGGCUUU-UCUUCACGAGAUUCCUAAC--
......((((........))))((.((((((.........((((..((((.........))))..))))(((((((((.......)))-))))))...-.......))))))))....-- ( -38.40)
>pfo.3000 5722192 113 - 6438405
UCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUCACUCGGUGUG-UCUGGCUUUCUUUUCACAGGAUCUU------
...((.((((........)))).))(((((..........((((..((((.........))))..))))(((((((.(((...))).)-))))))............)))))..------ ( -37.40)
>pf5.3376 6379133 113 - 7074893
UCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUCACUCAAUGUG-UCUGGCUUUCUUUUCACAGGAUCUU------
...((.((((........)))).))(((((..........((((..((((.........))))..))))((((((..(((.....)))-))))))............)))))..------ ( -35.90)
>ppk.260 5647767 112 + 6181863
UCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAUUUCACCUCGGUGUGA--UGGCUUUCUUCUUACAGGAUCCU------
...((.((((........)))).))((..(((........((((..((((.........))))..))))((((((.(((....))).))--))))............))).)).------ ( -38.00)
>pel.240 5389335 112 + 5888780
UCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCA-UUCACCUCGGUGUGAU-UGGCUUUCUUCUCACAGGAUCCU------
...((.((((........)))).))((..(((........((((..((((.........))))..))))((((-.((((......)))).-))))............))).)).------ ( -36.00)
>consensus
UCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUACCUCAGUGUG_UCUGGCUUUCUUUUCACAGGAUCCU______
......((((........)))).(((((.......)))))((((..((((.........))))..))))((((((.((........)).))))))......................... (-32.52 = -32.07 +  -0.46)

alignment

secondary structure

dotplot

Window 1

Location	4,784,177 – 4,784,295
Length	118
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	90.28
Mean single sequence MFE	-47.03
Consensus MFE	-43.85
Energy contribution	-43.80
Covariance contribution	-0.05
Combinations/Pair	1.10
Mean z-score	-2.76
Structure conservation index	0.93
SVM decision value	3.50
SVM RNA-class probability	0.999300
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2543 4784177 118 + 6264404
GGAAAUCUGGCAGGCCAGGAGGGAAUCGAACCCCCAACCUGCGGUUUUGGAGACCGCCGCUCUGCCAAUUGAGCUACUGGCCU--GAAGCAAAAUCAGGCCGACCAUUAUGCCGGCCUGA
......((..(((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))--).)).....((((((((..........)))))))) ( -48.30)
>pau.416 5795006 118 - 6537648
GGAAAUCUGGCAGGCCAGGAGGGAAUCGAACCCCCAACCUGCGGUUUUGGAGACCGCCGCUCUGCCAAUUGAGCUACUGGCCU--GAAGCAAAAUCAGGCCGGCCAUUAUGCCGGCCUGA
......((..(((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))--).)).....((((((((((......)))))))))) ( -55.40)
>pfo.3000 5722225 118 + 6438405
GUGAAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCU--AAAACAAAAUCAGGCCGACCAUUAUGCCGGCCUGA
...........(((((((((.((..((.((..((........))..)).))..)).))((((........))))..)))))))--.........((((((((..........)))))))) ( -41.30)
>pf5.3376 6379166 119 + 7074893
GUGAAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUA-AAAACAAAAUCAGGCCGACCAUUAUGUCGGCCCGA
...........(((((((((.((..((.((..((........))..)).))..)).))((((........))))..))))))).-.........((.(((((((......))))))).)) ( -41.70)
>ppk.260 5647799 120 - 6181863
GGUGAAAUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUGUAACGCUGUAUCAGGCCGGCCAUUAUACCGGCCUGA
((((.....(((((((((((.((..((.((..((........))..)).))..)).))((((........))))..)))))))))..))))...(((((((((........))))))))) ( -52.10)
>pel.240 5389368 119 - 5888780
GGUGAA-UGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUAUAACGCUGUAUCAGGCCGGCCAUUAUACCGGCCCGA
..((((-(((((((((((((.((..((.((..((........))..)).))..)).))((((........))))..))))))).....))))).)))((((((........))))))... ( -43.40)
>consensus
GGAAAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCU__AAAGCAAAAUCAGGCCGACCAUUAUGCCGGCCUGA
...........((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))...........((((((((((......)))))))))) (-43.85 = -43.80 +  -0.05)

alignment

secondary structure

dotplot

Window 2

Location	4,784,177 – 4,784,295
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.28
Mean single sequence MFE	-51.13
Consensus MFE	-50.65
Energy contribution	-48.93
Covariance contribution	-1.72
Combinations/Pair	1.19
Mean z-score	-3.21
Structure conservation index	0.99
SVM decision value	5.04
SVM RNA-class probability	0.999970
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.2543 4784177 118 - 6264404
UCAGGCCGGCAUAAUGGUCGGCCUGAUUUUGCUUC--AGGCCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUUUCC
((((((((((......)))))))))).((((...(--(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).))))..... ( -54.60)
>pau.416 5795006 118 + 6537648
UCAGGCCGGCAUAAUGGCCGGCCUGAUUUUGCUUC--AGGCCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUUUCC
((((((((((......)))))))))).((((...(--(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).))))..... ( -57.30)
>pfo.3000 5722225 118 - 6438405
UCAGGCCGGCAUAAUGGUCGGCCUGAUUUUGUUUU--AGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUCAC
((((((((((......)))))))))).((((...(--(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).))))..... ( -48.40)
>pf5.3376 6379166 119 - 7074893
UCGGGCCGACAUAAUGGUCGGCCUGAUUUUGUUUU-UAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUCAC
((((((((((......))))))))))....(((((-.((..(.((.((((........)))).)))..))..))))).((((((..((((.........))))..))))))......... ( -47.90)
>ppk.260 5647799 120 + 6181863
UCAGGCCGGUAUAAUGGCCGGCCUGAUACAGCGUUACAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAUUUCACC
((((((((((......))))))))))..........((((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).......... ( -50.50)
>pel.240 5389368 119 + 5888780
UCGGGCCGGUAUAAUGGCCGGCCUGAUACAGCGUUAUAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCA-UUCACC
((((((((((......))))))))))..........((((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))))...-...... ( -48.10)
>consensus
UCAGGCCGGCAUAAUGGCCGGCCUGAUUUUGCUUU__AGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUUACC
((((((((((......))))))))))...........(((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))........... (-50.65 = -48.93 +  -1.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:10:38 2007