Locus 33

Sequence ID	Eco_1
Location	4,164,776 – 4,165,120
Length	344
Max. P	0.817212

overview

Window 3

Location	4,164,776 – 4,164,896
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	99.44
Mean single sequence MFE	-41.57
Consensus MFE	-41.40
Energy contribution	-41.40
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	1.00
SVM decision value	0.60
SVM RNA-class probability	0.796873
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4164776 120 + 1
AGGUGGGUGACGAAGCGGUUGCCAUGACCUGCGUUUGCAAACACCGGUACCGACAGGACAGGGUGGAGAACGAGUGAGGGGCGACUCGCAGAGUCAGUUGGACCGCAAUGUUAAGAAUAA
..((...(((((..((((((....((((((((((((.....((((.((.((....))))..))))..))))......(((....))))))).))))....))))))..)))))...)).. ( -41.40)
>Sfl_1 241 120 + 1
AGGUGGGUGACGAAGCGGUUGCCAUGACCUGCGUUUGCAAACACCGGUACCGACAGGACAGGGUGGAGAACGAGUGAGGGGCGACUCGCAGAGUCAGUUGGACCGCAAUGUUAAGAAUAA
..((...(((((..((((((....((((((((((((.....((((.((.((....))))..))))..))))......(((....))))))).))))....))))))..)))))...)).. ( -41.40)
>Sty_1 241 120 + 1
AGGUGGGUGACGAAGCGGUUGCCAUGACCUGCGUUUGCAAACACCGGUACCGACAGGACAGGGUGGAGAACGGGUGAGGGGCGACUCGCAGAGUCAGUUGGACCGCAAUGUUAAGAAUAA
..((...(((((..((((((....(((((((((.((((...((((.((.((.((........)).).).)).))))....))))..))))).))))....))))))..)))))...)).. ( -41.90)
>consensus
AGGUGGGUGACGAAGCGGUUGCCAUGACCUGCGUUUGCAAACACCGGUACCGACAGGACAGGGUGGAGAACGAGUGAGGGGCGACUCGCAGAGUCAGUUGGACCGCAAUGUUAAGAAUAA
..((...(((((..((((((....((((((((((((.....((((.((.((....))))..))))..))))......(((....))))))).))))....))))))..)))))...)).. (-41.40 = -41.40 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	4,164,776 – 4,164,896
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	99.44
Mean single sequence MFE	-32.27
Consensus MFE	-31.20
Energy contribution	-31.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.97
SVM decision value	0.21
SVM RNA-class probability	0.634393
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4164776 120 - 1
UUAUUCUUAACAUUGCGGUCCAACUGACUCUGCGAGUCGCCCCUCACUCGUUCUCCACCCUGUCCUGUCGGUACCGGUGUUUGCAAACGCAGGUCAUGGCAACCGCUUCGUCACCCACCU
..............((((((((..((((.((((((((........))))((....((((..((((....)).)).))))...))....)))))))))))..))))).............. ( -32.30)
>Sfl_1 241 120 - 1
UUAUUCUUAACAUUGCGGUCCAACUGACUCUGCGAGUCGCCCCUCACUCGUUCUCCACCCUGUCCUGUCGGUACCGGUGUUUGCAAACGCAGGUCAUGGCAACCGCUUCGUCACCCACCU
..............((((((((..((((.((((((((........))))((....((((..((((....)).)).))))...))....)))))))))))..))))).............. ( -32.30)
>Sty_1 241 120 - 1
UUAUUCUUAACAUUGCGGUCCAACUGACUCUGCGAGUCGCCCCUCACCCGUUCUCCACCCUGUCCUGUCGGUACCGGUGUUUGCAAACGCAGGUCAUGGCAACCGCUUCGUCACCCACCU
..............((((((((..((((.(((((..(.((....((((.((...((((........)).)).)).))))...)))..))))))))))))..))))).............. ( -32.20)
>consensus
UUAUUCUUAACAUUGCGGUCCAACUGACUCUGCGAGUCGCCCCUCACUCGUUCUCCACCCUGUCCUGUCGGUACCGGUGUUUGCAAACGCAGGUCAUGGCAACCGCUUCGUCACCCACCU
..............((((((((..((((.(((((((......)))....((....((((..((((....)).)).))))...))....)))))))))))..))))).............. (-31.20 = -31.20 +  -0.00)

alignment

secondary structure

dotplot

Window 5

Location	4,164,896 – 4,165,016
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	97.22
Mean single sequence MFE	-43.77
Consensus MFE	-42.83
Energy contribution	-43.17
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.98
SVM decision value	0.67
SVM RNA-class probability	0.817212
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4164896 120 - 1
ACGCACUCGGGAGGACGAUCCCUUUUUCGUGGGAGCCUCUUACGAGUGCGGGGUUCCGCGGUCAAUCCAGCACGCUCUGUAUACCCCCGUACAAUUUAUCAGAGGCCCAGACAUCCCUGA
.(((((((((((((....((((........)))).)))))..))))))))((((..((((((.......)).)))..(((((......)))))........)..))))............ ( -44.00)
>Sfl_1 361 120 - 1
ACGCACUCGGGAGGACGAUCCCUUUUUCGUGGGAGCCUCUUACGAGUGCGGGGUUCCGCGGUCAAUCCAGCACGCUCUGUAUACCCCCGUACAAUUUAUCAGAGGCCCAGACAUCCCUGA
.(((((((((((((....((((........)))).)))))..))))))))((((..((((((.......)).)))..(((((......)))))........)..))))............ ( -44.00)
>Sty_1 361 120 - 1
ACGCACUCGGGAGGACGAUCCCUUUUUCGUGGGAGCCUCUUACGAGUGCGGGGUUCCGCGGACAAUCCAGCACGCUUUGUAAACUCCCGUACAAUUUAUCAGAGGCCCUGACAUCCCUGA
.(((((((((((((....((((........)))).)))))..))))))))((((..((((..(......)..))).(((((........))))).......)..))))............ ( -43.30)
>consensus
ACGCACUCGGGAGGACGAUCCCUUUUUCGUGGGAGCCUCUUACGAGUGCGGGGUUCCGCGGUCAAUCCAGCACGCUCUGUAUACCCCCGUACAAUUUAUCAGAGGCCCAGACAUCCCUGA
.(((((((((((((....((((........)))).)))))..))))))))((((..((((..(......)..)))..(((((......)))))........)..))))............ (-42.83 = -43.17 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	4,164,960 – 4,165,080
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-46.03
Consensus MFE	-40.45
Energy contribution	-41.23
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.88
SVM decision value	-0.03
SVM RNA-class probability	0.520104
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4164960 120 + 1
CGGAGGCUAUAUCGCGGUGGAUACCCGACAAAGAACAGACAUUUCGGCAUAUAUGCCAGAGCUACCAAUGGCAGGGCCGCGGUAUCACCGCGGCAUGGCGAACGGUACUGUAGCGAAGCC
....((((...((((((.(....)))........((((((..((((.(((...(((((..........)))))..(((((((.....)))))))))).))))..)).)))).)))))))) ( -47.10)
>Hin_1 278 120 + 1
GGGAGGGUAUAUCGCGGUGGAUACCCGACAAAGAACAGACAUUUCGGCAUAUAUGCCAGAGCUACCAAUGGCAGGGCCGCGGUAUCACCGCGCCAUGGCGGAUGGCACUGUGGCGAAGCC
.(..((((((.((.....))))))))..)................(((.....(((((..........)))))..((((((((..((((((......)))).))..))))))))...))) ( -43.90)
>Ype_1 281 120 + 1
CGGAGGCUAUAUCGCGGUGGAUACCCGACAAAGAACAGACAUUUCGGCAUAUAUGCCAGAGCUACCAAUGGCAGGGCCGCGGUAUCACCGCGGCAUGGCGAACGGUACUGUAGCGAAGCC
....((((...((((((.(....)))........((((((..((((.(((...(((((..........)))))..(((((((.....)))))))))).))))..)).)))).)))))))) ( -47.10)
>consensus
CGGAGGCUAUAUCGCGGUGGAUACCCGACAAAGAACAGACAUUUCGGCAUAUAUGCCAGAGCUACCAAUGGCAGGGCCGCGGUAUCACCGCGGCAUGGCGAACGGUACUGUAGCGAAGCC
....((((...((((((.(....)))........((((((..((((.(((...(((((..........)))))..(((((((.....)))))))))).))))..)).)))).)))))))) (-40.45 = -41.23 +   0.78)

alignment

secondary structure

dotplot

Window 7

Location	4,165,000 – 4,165,120
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-45.20
Consensus MFE	-41.01
Energy contribution	-41.23
Covariance contribution	0.23
Combinations/Pair	1.05
Mean z-score	-1.84
Structure conservation index	0.91
SVM decision value	0.25
SVM RNA-class probability	0.653560
Prediction	RNA

Download alignment: ClustalW | MAF

>Eco_1 4165000 120 + 1
AGGGACUGAAGCAAAUGCUAUCCUGUCUAGGCCCCGGAGACCAUCAGGUUGGACGAAACGUGUACCUACGUUUGGGGAUAGAGGGGAAACAGCUGUGGGCUGGGAUACCCGAUCCAGUCA
...(((((.(((..(((((.((((.((((..(((((..((((....))))...).(((((((....))))))))))).)))).))))...))).))..)))(((...)))....))))). ( -44.90)
>Hin_1 318 120 + 1
AGGGACUGAAGCAAAUGCUAUCCUGUCUAGGCCCCGGAGACCAUCAGGUUGGGCGAAACGUGAACGUACGUCUGGGGAUAGAGGGGAAUGAGCUGUGGGCUGGGAUACCCGAUCCACUCA
................(((.((((.((((..((((...((((....))))(((((..(((....))).))))))))).)))).))))...))).((((..((((...))))..))))... ( -46.70)
>Ype_1 321 120 + 1
AGGGACUGAAGCAAAUGCUAUCCUGUCUAGGCCCCGGAGACCAUCAGGUUGGACGAAACGCGUACCUACGUUUGGGGAUAGAGGGGAAACAGCUGUGGGCUGGGAUACCCGAUCCGGUCA
...(((((.(((..(((((.((((.((((..(((((((((((....))))(((((.....))).))....))))))).)))).))))...))).))..)))(((...)))....))))). ( -44.00)
>consensus
AGGGACUGAAGCAAAUGCUAUCCUGUCUAGGCCCCGGAGACCAUCAGGUUGGACGAAACGUGUACCUACGUUUGGGGAUAGAGGGGAAACAGCUGUGGGCUGGGAUACCCGAUCCAGUCA
...(((((.(((..(((((.((((.((((..(((((((((((....))))........((((....))))))))))).)))).))))...))).))..)))(((...)))....))))). (-41.01 = -41.23 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Dec 7 14:12:20 2006