Locus 121

Sequence ID	Eco_1
Location	4,390,606 – 4,390,686
Length	80
Max. P	0.999969

overview

Window 4

Location	4,390,606 – 4,390,686
Length	80
Sequences	6
Columns	80
Reading direction	forward
Mean pairwise identity	96.16
Mean single sequence MFE	-32.62
Consensus MFE	-32.61
Energy contribution	-32.50
Covariance contribution	-0.11
Combinations/Pair	1.08
Mean z-score	-2.38
Structure conservation index	1.00
SVM decision value	5.02
SVM RNA-class probability	0.999969
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4390606 80 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAUU
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))........ ( -33.60)
>Hin_1 1 80 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGCCUCGUUUCCCGCUCCAAAUU
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))........ ( -33.10)
>Lpn_1 1 80 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCAUAACCUUGCCAAGGUUAGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAUU
(((((((..((((........)))).((((((.....))))))(((.(.((....)).).)))..)))))))........ ( -28.20)
>Sfl_1 1 78 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAA--
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))......-- ( -33.60)
>Sty_1 1 78 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAA--
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))......-- ( -33.60)
>Ype_1 1 80 + 1
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAGUU
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))........ ( -33.60)
>consensus
GCGGGAAUAGCUCAGUUGGUAGAGCACGACCUUGCCAAGGUCGGGGUCGCGAGUUCGAGUCUCGUUUCCCGCUCCAAAUU
(((((((..((((........))))..((((((((....).)))))))(((((.......))))))))))))........ (-32.61 = -32.50 +  -0.11)

alignment

secondary structure

dotplot

Window 5

Location	4,390,606 – 4,390,686
Length	80
Sequences	6
Columns	80
Reading direction	reverse
Mean pairwise identity	96.16
Mean single sequence MFE	-27.83
Consensus MFE	-28.22
Energy contribution	-27.67
Covariance contribution	-0.55
Combinations/Pair	1.10
Mean z-score	-1.87
Structure conservation index	1.01
SVM decision value	4.22
SVM RNA-class probability	0.999840
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4390606 80 - 1
AAUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
........(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))) ( -28.20)
>Hin_1 1 80 - 1
AAUUUGGAGCGGGAAACGAGGCUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
........(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))) ( -29.50)
>Lpn_1 1 80 - 1
AAUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCUAACCUUGGCAAGGUUAUGCUCUACCAACUGAGCUAUUCCCGC
........(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))) ( -24.70)
>Sfl_1 1 78 - 1
--UUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
--......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))) ( -28.20)
>Sty_1 1 78 - 1
--UUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
--......(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))) ( -28.20)
>Ype_1 1 80 - 1
AACUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
........(((((((..(((.......)))(((((((((....)))...))))))((((........))))..))))))) ( -28.20)
>consensus
AAUUUGGAGCGGGAAACGAGACUCGAACUCGCGACCCCGACCUUGGCAAGGUCGUGCUCUACCAACUGAGCUAUUCCCGC
........(((((((.((((.......))))......((((((.....)))))).((((........))))..))))))) (-28.22 = -27.67 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:08:20 2006