Locus 142

Sequence ID	pao.1087
Location	1,954,710 – 1,954,782
Length	72
Max. P	0.991229

overview

Window 2

Location	1,954,710 – 1,954,782
Length	72
Sequences	6
Columns	72
Reading direction	forward
Mean pairwise identity	76.67
Mean single sequence MFE	-29.87
Consensus MFE	-19.82
Energy contribution	-20.72
Covariance contribution	0.89
Combinations/Pair	1.40
Mean z-score	-4.38
Structure conservation index	0.66
SVM decision value	2.26
SVM RNA-class probability	0.991229
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1087 1954710 72 + 6264404
GGCUCCGCAAUACUGGCGGUCGAGACAUUCGGCCGCCUCGUGGGCUUGAAAAUGCCCACAAUUGCCUUCAUC
......(((((...((((((((((...))))))))))..((((((........)))))).)))))....... ( -34.00)
>psp.1009 1962855 63 + 5928787
--------AAUGUAGGGGGUCGGCACAACCGACCGCCU-GCGGACUUGAAAAAGCCCGCAAUAGCCUUCAUC
--------.....(((.((((((.....)))))).)))-((((.(((....))).))))............. ( -27.30)
>pst.2209 2188904 63 - 6397126
--------AAUGUAGGGGGUCGGCACAACCGACCGCCU-GCGGACUUGAAAAAGCCCGCAAUAGCCUUCAUC
--------.....(((.((((((.....)))))).)))-((((.(((....))).))))............. ( -27.30)
>pf5.2419 2469150 63 - 7074893
--------AAUAGGCAUGGUCGGUUGUUCCGAUCAGUG-GCGGGCUUGAAAAAGCCCGCAAUAGCCUUCAUC
--------...((((.(((((((.....)))))))...-((((((((....))))))))....))))..... ( -33.30)
>pfo.2166 2252652 63 - 6438405
--------AAUAGGCUUGGUCGGCGCGUCUGAUCAGCG-GCGGGCUUGAAAAAGCCCGCAAUAGCCUUCAUC
--------...((((((((((((.....)))))))...-((((((((....))))))))...)))))..... ( -30.00)
>pss.1035 1985433 63 + 6093698
--------AAUGUAGGGGGUCGGCACAACCGACCGCCU-GCGGACUUGAAAAAGCCCGCAAUAGCCUUCAUC
--------.....(((.((((((.....)))))).)))-((((.(((....))).))))............. ( -27.30)
>consensus
________AAUAUAGGGGGUCGGCACAACCGACCGCCU_GCGGACUUGAAAAAGCCCGCAAUAGCCUUCAUC
..............((.((((((.....)))))).))..((((.(((....))).))))............. (-19.82 = -20.72 +   0.89)

alignment

secondary structure

dotplot

Window 3

Location	1,954,710 – 1,954,782
Length	72
Sequences	6
Columns	72
Reading direction	reverse
Mean pairwise identity	76.67
Mean single sequence MFE	-27.97
Consensus MFE	-20.18
Energy contribution	-20.13
Covariance contribution	-0.05
Combinations/Pair	1.29
Mean z-score	-3.42
Structure conservation index	0.72
SVM decision value	2.17
SVM RNA-class probability	0.989478
Prediction	RNA

Download alignment: ClustalW | MAF

>pao.1087 1954710 72 - 6264404
GAUGAAGGCAAUUGUGGGCAUUUUCAAGCCCACGAGGCGGCCGAAUGUCUCGACCGCCAGUAUUGCGGAGCC
......(((..((((((((........))))))))(((((.(((.....))).)))))...........))) ( -31.30)
>psp.1009 1962855 63 - 5928787
GAUGAAGGCUAUUGCGGGCUUUUUCAAGUCCGC-AGGCGGUCGGUUGUGCCGACCCCCUACAUU--------
((((.(((...((((((((((....))))))))-))..((((((.....)))))).))).))))-------- ( -29.60)
>pst.2209 2188904 63 + 6397126
GAUGAAGGCUAUUGCGGGCUUUUUCAAGUCCGC-AGGCGGUCGGUUGUGCCGACCCCCUACAUU--------
((((.(((...((((((((((....))))))))-))..((((((.....)))))).))).))))-------- ( -29.60)
>pf5.2419 2469150 63 + 7074893
GAUGAAGGCUAUUGCGGGCUUUUUCAAGCCCGC-CACUGAUCGGAACAACCGACCAUGCCUAUU--------
.....((((....((((((((....))))))))-...((.((((.....)))).)).))))...-------- ( -24.80)
>pfo.2166 2252652 63 + 6438405
GAUGAAGGCUAUUGCGGGCUUUUUCAAGCCCGC-CGCUGAUCAGACGCGCCGACCAAGCCUAUU--------
.....(((((...((((((((....))))))))-(((.........))).......)))))...-------- ( -22.90)
>pss.1035 1985433 63 - 6093698
GAUGAAGGCUAUUGCGGGCUUUUUCAAGUCCGC-AGGCGGUCGGUUGUGCCGACCCCCUACAUU--------
((((.(((...((((((((((....))))))))-))..((((((.....)))))).))).))))-------- ( -29.60)
>consensus
GAUGAAGGCUAUUGCGGGCUUUUUCAAGCCCGC_AGGCGGUCGGAUGUGCCGACCCCCUACAUU________
((((...(((...((((((((....))))))))..)))((((((.....)))))).....))))........ (-20.18 = -20.13 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:14:41 2007