Locus 57

Sequence ID	pao_1
Location	4,784,181 – 4,784,296
Length	115
Max. P	0.979513

overview

Window 1

Location	4,784,181 – 4,784,296
Length	115
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	88.90
Mean single sequence MFE	-42.37
Consensus MFE	-32.58
Energy contribution	-32.05
Covariance contribution	-0.53
Combinations/Pair	1.12
Mean z-score	-2.69
Structure conservation index	0.77
SVM decision value	0.15
SVM RNA-class probability	0.609353
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4784181 115 + 1
AAUCUGGCAGGCCAGGAGGGAAUCGAACCCCCAACCUGCGGUUUUGGAGACCGCCGCUCUGCCAAUUGAGCUACUGGCCUGAAG--CAAAAUCAGGCCGACCAUUAUGCCGGCCUGA
...((..(((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))).))--.....((((((((..........)))))))) ( -48.30)
>pau_1 1 115 + 1
AAUCUGGCAGGCCAGGAGGGAAUCGAACCCCCAACCUGCGGUUUUGGAGACCGCCGCUCUGCCAAUUGAGCUACUGGCCUGAAG--CAAAAUCAGGCCGGCCAUUAUGCCGGCCUGA
...((..(((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))).))--.....((((((((((......)))))))))) ( -55.40)
>pf5_1 1 113 + 1
AAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUAAAAA-CAAAAUCAGGCCGACCAUUAUGUCGGCC---
........(((((((((.((..((.((..((........))..)).))..)).))((((........))))..))))))).....-........(((((((......)))))))--- ( -40.10)
>ppk_1 1 113 + 1
----UGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUGUAACGCUGUAUCAGGCCGGCCAUUAUACCGGCCUGA
----..(((((((((((.((..((.((..((........))..)).))..)).))((((........))))..))))))))).........(((((((((........))))))))) ( -49.80)
>psp_1 1 108 + 1
AAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUAAAAG-CAAAAUCAGGCCGACCAUUAUGC--------
....(((((((((((((.((..((.((..((........))..)).))..)).))((((........))))..)))))))....(-(........)).).)))......-------- ( -30.30)
>pss_1 1 108 + 1
AAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUAAAAG-CAAAAUCAGGCCGACCAUUAUGC--------
....(((((((((((((.((..((.((..((........))..)).))..)).))((((........))))..)))))))....(-(........)).).)))......-------- ( -30.30)
>consensus
AAUCUGGCAGGUCAGGAGGGAAUCGAACCCCCAACCUACGGUUUUGGAGACCGUCGCUCUGCCAAUUGAGCUACUGACCUAAAA__CAAAAUCAGGCCGACCAUUAUGCCGGCC___
.....(((((((((((.(((........)))).....((((((.....)))))).((((........))))..)))))))..............((....)).....)))....... (-32.58 = -32.05 +  -0.53)

alignment

secondary structure

dotplot

Window 2

Location	4,784,181 – 4,784,296
Length	115
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	88.90
Mean single sequence MFE	-46.78
Consensus MFE	-40.02
Energy contribution	-40.05
Covariance contribution	0.03
Combinations/Pair	1.21
Mean z-score	-2.87
Structure conservation index	0.86
SVM decision value	1.84
SVM RNA-class probability	0.979513
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 4784181 115 - 1
UCAGGCCGGCAUAAUGGUCGGCCUGAUUUUG--CUUCAGGCCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUU
((((((((((......)))))))))).((((--...((((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).)))).. ( -54.60)
>pau_1 1 115 - 1
UCAGGCCGGCAUAAUGGCCGGCCUGAUUUUG--CUUCAGGCCAGUAGCUCAAUUGGCAGAGCGGCGGUCUCCAAAACCGCAGGUUGGGGGUUCGAUUCCCUCCUGGCCUGCCAGAUU
((((((((((......)))))))))).((((--...((((((((..((((........)))).(((((.......))))).....(((((.......))))))))))))).)))).. ( -57.30)
>pf5_1 1 113 - 1
---GGCCGACAUAAUGGUCGGCCUGAUUUUG-UUUUUAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUU
---(((((((......))))))).......(-((((.((..(.((.((((........)))).)))..))..))))).((((((..((((.........))))..))))))...... ( -43.10)
>ppk_1 1 113 - 1
UCAGGCCGGUAUAAUGGCCGGCCUGAUACAGCGUUACAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCA----
((((((((((......))))))))))..........((((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))))...---- ( -50.50)
>psp_1 1 108 - 1
--------GCAUAAUGGUCGGCCUGAUUUUG-CUUUUAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUU
--------........((((((((((.....-...)))))))....((((........)))))))(((.......)))((((((..((((.........))))..))))))...... ( -37.60)
>pss_1 1 108 - 1
--------GCAUAAUGGUCGGCCUGAUUUUG-CUUUUAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUU
--------........((((((((((.....-...)))))))....((((........)))))))(((.......)))((((((..((((.........))))..))))))...... ( -37.60)
>consensus
___GGCCGGCAUAAUGGUCGGCCUGAUUUUG__UUUCAGGUCAGUAGCUCAAUUGGCAGAGCGACGGUCUCCAAAACCGUAGGUUGGGGGUUCGAUUCCCUCCUGACCUGCCAGAUU
...(((((((......))))))).............((((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))))....... (-40.02 = -40.05 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:48:47 2007