Locus 53

Sequence ID	Eco_1
Location	2,816,494 – 2,816,679
Length	185
Max. P	0.995544

overview

Window 1

Location	2,816,494 – 2,816,609
Length	115
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.19
Mean single sequence MFE	-50.43
Consensus MFE	-44.15
Energy contribution	-44.65
Covariance contribution	0.50
Combinations/Pair	1.08
Mean z-score	-2.60
Structure conservation index	0.88
SVM decision value	1.78
SVM RNA-class probability	0.976868
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 2816494 115 + 1
AUGGUGCAUCCGGGAGGAUUCGAACCUCCGACCGCUCGGUUCGUAGCCGAGUACUCUAUCCAGCUGAGCUACGGAUGCA-----AAUGGCGGUGAGGCGGGGAUUCGAACCCCGGAUGCA
....((((((((((.(...(((((.(((((.(((((((((.....))))))).(.((..(((..((..(....)...))-----..))).)).).))))))).))))).))))))))))) ( -53.20)
>Sfl_1 1 115 + 1
AUGGUGCAUCCGGGAGGAUUCGAACCUCCGACCGCUCGGUUCGUAGCCGAGUACUCUAUCCAGCUGAGCUACGGAUGCA-----AAUGGCGGUGAGGCGGGGAUUCGAACCCCGGAUGCA
....((((((((((.(...(((((.(((((.(((((((((.....))))))).(.((..(((..((..(....)...))-----..))).)).).))))))).))))).))))))))))) ( -53.20)
>Sty_1 1 115 + 1
AUGGUGCAUCCGGGAGGAUUCGAACCUCCGACCGCUCGGUUCGUAGCCGAGUACUCUAUCCAGCUGAGCUACGGAUGCA-----AAUGGCGGUGAGGCGGGGAUUCGAACCCCGGAUGCA
....((((((((((.(...(((((.(((((.(((((((((.....))))))).(.((..(((..((..(....)...))-----..))).)).).))))))).))))).))))))))))) ( -53.20)
>Ype_1 1 120 + 1
AUGGUGCACCCAGGAAGAUUCGAACUUCCGACCGCUCGGUUCGUAGCCGAGUACUCUAUCCAGCUGAGCUAUGGGUGCAUAGUAAAUGGCGGUGAGGGAGGGAUUCGAACCCUCGAUACA
...((((((((((((((.......)))))((..(((((((.....)))))))..))...............)))))))))...........(((...(((((.......)))))..))). ( -42.10)
>consensus
AUGGUGCAUCCGGGAGGAUUCGAACCUCCGACCGCUCGGUUCGUAGCCGAGUACUCUAUCCAGCUGAGCUACGGAUGCA_____AAUGGCGGUGAGGCGGGGAUUCGAACCCCGGAUGCA
....((((((((((....((((((.(((((.(((((((((.....)))))))....((((((((...)))..)))))..................))))))).)))))).)))))))))) (-44.15 = -44.65 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	2,816,494 – 2,816,609
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.19
Mean single sequence MFE	-47.72
Consensus MFE	-44.59
Energy contribution	-44.65
Covariance contribution	0.06
Combinations/Pair	1.11
Mean z-score	-2.96
Structure conservation index	0.93
SVM decision value	2.59
SVM RNA-class probability	0.995544
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 2816494 115 - 1
UGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGUAGCUCAGCUGGAUAGAGUACUCGGCUACGAACCGAGCGGUCGGAGGUUCGAAUCCUCCCGGAUGCACCAU
(((((((((((((((((((.(((....(((((...(-----((....(((((((..(((......)))....)))))))...))))))))))).)))))))))...)))))))))).... ( -50.90)
>Sfl_1 1 115 - 1
UGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGUAGCUCAGCUGGAUAGAGUACUCGGCUACGAACCGAGCGGUCGGAGGUUCGAAUCCUCCCGGAUGCACCAU
(((((((((((((((((((.(((....(((((...(-----((....(((((((..(((......)))....)))))))...))))))))))).)))))))))...)))))))))).... ( -50.90)
>Sty_1 1 115 - 1
UGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGUAGCUCAGCUGGAUAGAGUACUCGGCUACGAACCGAGCGGUCGGAGGUUCGAAUCCUCCCGGAUGCACCAU
(((((((((((((((((((.(((....(((((...(-----((....(((((((..(((......)))....)))))))...))))))))))).)))))))))...)))))))))).... ( -50.90)
>Ype_1 1 120 - 1
UGUAUCGAGGGUUCGAAUCCCUCCCUCACCGCCAUUUACUAUGCACCCAUAGCUCAGCUGGAUAGAGUACUCGGCUACGAACCGAGCGGUCGGAAGUUCGAAUCUUCCUGGGUGCACCAU
......(((((...........)))))..............((((((((((((...))))....((.(.(((((.......))))).).))(((((.......))))))))))))).... ( -38.20)
>consensus
UGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU_____UGCAUCCGUAGCUCAGCUGGAUAGAGUACUCGGCUACGAACCGAGCGGUCGGAGGUUCGAAUCCUCCCGGAUGCACCAU
(((((((((((((((((((.(((....(((((............((((..(((...))))))).......((((.......)))))))))))).)))))))))...)))))))))).... (-44.59 = -44.65 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	2,816,564 – 2,816,679
Length	115
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.62
Mean single sequence MFE	-51.88
Consensus MFE	-47.55
Energy contribution	-46.68
Covariance contribution	-0.87
Combinations/Pair	1.09
Mean z-score	-2.54
Structure conservation index	0.92
SVM decision value	2.04
SVM RNA-class probability	0.986465
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 2816564 115 - 1
AAGAGGCGUGUGGUGAGGUGGCCGAGAGGCUGAAGGCGCUCCCCUGCUAAGGGAGUAUGCGGUCAAAAGCUGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGU
..((.(((.((((((((((((((....))))...((.((((((.......))))))(((((((.....)))))))))((((.......))))))))))))))....-----))).))... ( -53.70)
>Sfl_1 71 115 - 1
AAGAGGCGUGUGGUGAGGUGGCCGAGAGGCUGAAGGCGCUCCCCUGCUAAGGGAGUAUGCGGUCAAAAGCUGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGU
..((.(((.((((((((((((((....))))...((.((((((.......))))))(((((((.....)))))))))((((.......))))))))))))))....-----))).))... ( -53.70)
>Sty_1 71 115 - 1
AAGAGGCGUGUGGUGAGGUGGCCGAGAGGCUGAAGGCGCUCCCCUGCUAAGGGAGUAUGCGGUCAAAAGCUGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU-----UGCAUCCGU
..((.(((.((((((((((((((....))))...((.((((((.......))))))(((((((.....)))))))))((((.......))))))))))))))....-----))).))... ( -53.70)
>Ype_1 71 120 - 1
AAGAAGCGUAUGGUGAGGUGGCCGAGAGGCUGAAGGCGCUCCCCUGCUAAGGGAGUAUACGGUCAAAAGCUGUAUCGAGGGUUCGAAUCCCUCCCUCACCGCCAUUUACUAUGCACCCAU
.......((((((((((..((((....))))...(((((((((.......))))))(((((((.....))))))).(((((...........)))))...))).))))))))))...... ( -46.40)
>consensus
AAGAGGCGUGUGGUGAGGUGGCCGAGAGGCUGAAGGCGCUCCCCUGCUAAGGGAGUAUGCGGUCAAAAGCUGCAUCCGGGGUUCGAAUCCCCGCCUCACCGCCAUU_____UGCAUCCGU
.......(.(((((((((.((((....))))......((((((.......))))))(((((((.....))))))).(((((.......)))))))))))))))................. (-47.55 = -46.68 +  -0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:04:30 2006