Locus 22

Sequence ID	pao_1
Location	1,060,354 – 1,060,434
Length	80
Max. P	0.999995

overview

Window 8

Location	1,060,354 – 1,060,434
Length	80
Sequences	6
Columns	80
Reading direction	forward
Mean pairwise identity	97.16
Mean single sequence MFE	-31.53
Consensus MFE	-30.90
Energy contribution	-31.57
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-4.06
Structure conservation index	0.98
SVM decision value	5.63
SVM RNA-class probability	0.999991
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 1060354 80 + 1
UUGGGUCGUUAGCUCAGUCGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAUU
.((((((((..............((.(((((((.......))))))).))(((((.......)))))))))))))..... ( -30.80)
>pau_1 1 80 + 1
UUGGGUCGUUAGCUCAGUCGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAUU
.((((((((..............((.(((((((.......))))))).))(((((.......)))))))))))))..... ( -30.80)
>pel_1 1 77 + 1
--GGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU-
--(((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......)))))))))))).....- ( -33.70)
>ppk_1 1 79 + 1
UUGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAU-
.((((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......)))))))))))))....- ( -34.30)
>psp_1 1 80 + 1
UUGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCCACACGACCCACCAUU
.((((((((..(..(((((((((((((.....)))))..))))))))..)((.((.......)).))))))))))..... ( -29.80)
>pss_1 1 80 + 1
UUGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCCACACGACCCACCAUU
.((((((((..(..(((((((((((((.....)))))..))))))))..)((.((.......)).))))))))))..... ( -29.80)
>consensus
UUGGGUCGUUAGCUCAGUUGGUAGAGCAGUUGGCUUUUAACCAAUUGGUCGUAGGUUCGAAUCCUACACGACCCACCAUU
..(((((((..(..(((((((((((((.....)))))..))))))))..)(((((.......))))))))))))...... (-30.90 = -31.57 +   0.67)

alignment

secondary structure

dotplot

Window 9

Location	1,060,354 – 1,060,434
Length	80
Sequences	6
Columns	80
Reading direction	reverse
Mean pairwise identity	97.16
Mean single sequence MFE	-28.77
Consensus MFE	-28.74
Energy contribution	-28.68
Covariance contribution	-0.05
Combinations/Pair	1.05
Mean z-score	-3.73
Structure conservation index	1.00
SVM decision value	5.95
SVM RNA-class probability	0.999995
Prediction	RNA

Download alignment: ClustalW | MAF

>pao_1 1060354 80 - 1
AAUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAA
.....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). ( -29.30)
>pau_1 1 80 - 1
AAUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCGACUGAGCUAACGACCCAA
.....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). ( -29.30)
>pel_1 1 77 - 1
-AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCC--
-.....((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))-- ( -26.70)
>ppk_1 1 79 - 1
-AUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCAA
-....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). ( -29.30)
>psp_1 1 80 - 1
AAUGGUGGGUCGUGUGGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCAA
.....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). ( -29.00)
>pss_1 1 80 - 1
AAUGGUGGGUCGUGUGGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCAA
.....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). ( -29.00)
>consensus
AAUGGUGGGUCGUGUAGGAUUCGAACCUACGACCAAUUGGUUAAAAGCCAACUGCUCUACCAACUGAGCUAACGACCCAA
.....(((((((((((((.......)))))......(((((.....)))))..((((........))))..)))))))). (-28.74 = -28.68 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 11:47:12 2007