Locus 83

Sequence ID Eco_1
Location 3,941,754 – 3,941,954
Length 200
Max. P 0.999515
window269 window270 window271 window272 window273 window274

overview

Window 9

Location 3,941,754 – 3,941,874
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -41.60
Consensus MFE -43.01
Energy contribution -40.82
Covariance contribution -2.19
Combinations/Pair 1.24
Mean z-score -1.92
Structure conservation index 1.03
SVM decision value 1.85
SVM RNA-class probability 0.980034
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941754 120 + 1
AUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACAC
.(((((((.....))).)))).....(((..(((......))).....(((((((..(((.......)))......)))))))...)))...((((....))))((((((....)))))) ( -40.80)
>Sfl_1 41 120 + 1
AUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACAC
..((((((.....))).)))(((((((((..(((......))).....(((((((..(((.......)))......)))))))...)))...((((....))))......)))))).... ( -41.10)
>Sty_1 41 120 + 1
AUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGCCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACAC
..((((((.....))).)))(((((((((..(((......))).....(((((((..(((.......)))......)))))))...)))...((((....))))......)))))).... ( -43.80)
>Ype_1 41 120 + 1
AUGCCUAGGCAGUCAGAGGCGAUGAAGGGCGUGCUAAUCUGCGAAAAGCGUCGGUAAGCUGAUAUGAAGCGUUAUAACCGACGAUACCCGAAUGGGGAAACCCAGUGCAAUACGUUGCAC
.(((....))).......((((((..(((..(((......))......(((((((..(((.......)))......))))))))..)))(..((((....))))...)....)))))).. ( -40.70)
>consensus
AUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACAC
.(((((((.....))).)))).....(((..(((......))).....(((((((..(((.......)))......)))))))...)))...((((....))))((((((....)))))) (-43.01 = -40.82 +  -2.19) 

alignment

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secondary structure

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Window 0

Location 3,941,754 – 3,941,874
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -34.45
Consensus MFE -34.25
Energy contribution -33.00
Covariance contribution -1.25
Combinations/Pair 1.19
Mean z-score -1.24
Structure conservation index 0.99
SVM decision value 0.06
SVM RNA-class probability 0.565298
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941754 120 - 1
GUGUGUCGAAACACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGCAGAUUAGCACGUCCUUCAUCGCCUCUGACUGCCAGGGCAU
((((((....))))))..(((((((......)))))))((..(((....((((............))))..((.....)).)))..))............(((.(((.....)))))).. ( -32.20)
>Sfl_1 41 120 - 1
GUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGCAGAUUAGCACGUCCUUCAUCGCCUCUGACUGCCAGGGCAU
((((((....))))))..(((((((......)))))))((..(((....((((............))))..((.....)).)))..))............(((.(((.....)))))).. ( -32.30)
>Sty_1 41 120 - 1
GUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGGCGCUUAUCGCAGAUUAGCACGUCCUUCAUCGCCUCUGACUGCCAGGGCAU
((((((....))))))..(((((((......)))))))((((((......(((.......)))..))))))(((.(((...))).)))............(((.(((.....)))))).. ( -38.10)
>Ype_1 41 120 - 1
GUGCAACGUAUUGCACUGGGUUUCCCCAUUCGGGUAUCGUCGGUUAUAACGCUUCAUAUCAGCUUACCGACGCUUUUCGCAGAUUAGCACGCCCUUCAUCGCCUCUGACUGCCUAGGCAU
((((((....))))))((((....))))...((((...((((((......(((.......)))..))))))(((..((...))..)))..))))......((((..(....)..)))).. ( -35.20)
>consensus
GUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGCAGAUUAGCACGUCCUUCAUCGCCUCUGACUGCCAGGGCAU
((((((....))))))..(((((((......)))))))((((((......(((.......)))..))))))((((...((((.((((..((........))...))))))))..)))).. (-34.25 = -33.00 +  -1.25) 

alignment

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secondary structure

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Window 1

Location 3,941,794 – 3,941,914
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.25
Mean single sequence MFE -42.70
Consensus MFE -45.74
Energy contribution -42.55
Covariance contribution -3.19
Combinations/Pair 1.29
Mean z-score -3.28
Structure conservation index 1.07
SVM decision value 3.67
SVM RNA-class probability 0.999515
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941794 120 + 1
GCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGG
((.....))((((((..(((.......)))......)))))).....(((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))). ( -40.60)
>Sfl_1 81 120 + 1
GCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGG
((.....))((((((..(((.......)))......)))))).....(((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))). ( -40.90)
>Sty_1 81 120 + 1
GCGAUAAGCGCCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGG
((.....))((((((..(((.......)))......)))))).....(((...(((....)))(((((((....))))))).(((((((((.........))))))))).......))). ( -43.60)
>Ype_1 81 120 + 1
GCGAAAAGCGUCGGUAAGCUGAUAUGAAGCGUUAUAACCGACGAUACCCGAAUGGGGAAACCCAGUGCAAUACGUUGCACUAUCGUUAGAUGAAUACAUAGUCUAACGAGGCGAACCGGG
((.....))((((((..(((.......)))......))))))....((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......)))) ( -45.70)
>consensus
GCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGG
((.....))((((((..(((.......)))......))))))....((((...(((....)))(((((((....))))))).(((((((((.........))))))))).......)))) (-45.74 = -42.55 +  -3.19) 

alignment

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secondary structure

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dotplot

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Window 2

Location 3,941,794 – 3,941,914
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.25
Mean single sequence MFE -35.20
Consensus MFE -35.06
Energy contribution -33.12
Covariance contribution -1.94
Combinations/Pair 1.24
Mean z-score -2.28
Structure conservation index 1.00
SVM decision value 2.46
SVM RNA-class probability 0.994252
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941794 120 - 1
CCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGUCGAAACACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGC
.(((((.....((((((((...........))))))))((((((((....))))))))(((((((......))))))))))))......((((............))))........... ( -33.10)
>Sfl_1 81 120 - 1
CCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGC
.(((((.....((((((((...........))))))))((((((((....))))))))(((((((......))))))))))))......((((............))))........... ( -33.20)
>Sty_1 81 120 - 1
CCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGGCGCUUAUCGC
..((((..((.((((((((...........))))))))((((((((....))))))))(((((((......)))))))((((((......(((.......)))..))))))))..)))). ( -38.20)
>Ype_1 81 120 - 1
CCCGGUUCGCCUCGUUAGACUAUGUAUUCAUCUAACGAUAGUGCAACGUAUUGCACUGGGUUUCCCCAUUCGGGUAUCGUCGGUUAUAACGCUUCAUAUCAGCUUACCGACGCUUUUCGC
(((((......((((((((...((....)))))))))).(((((((....)))))))(((....)))..)))))...(((((((......(((.......)))..)))))))........ ( -36.30)
>consensus
CCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGCCGGUUAUAACGGUUCAUAUCACCUUACCGACGCUUAUCGC
..((((..((.((((((((...........))))))))((((((((....))))))))(((((((......)))))))((((((......(((.......)))..))))))))..)))). (-35.06 = -33.12 +  -1.94) 

alignment

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secondary structure

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dotplot

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Window 3

Location 3,941,834 – 3,941,954
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -42.50
Consensus MFE -44.08
Energy contribution -42.32
Covariance contribution -1.75
Combinations/Pair 1.17
Mean z-score -4.74
Structure conservation index 1.04
SVM decision value 2.52
SVM RNA-class probability 0.994882
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941834 120 + 1
GCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAA
..((((((((...(((....)))(((((((....))))))).(((((((((.........)))))))))..))..((.((((.(((..........))).))))..))....)))))).. ( -42.70)
>Sfl_1 121 120 + 1
GCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAA
..((((((((...(((....)))(((((((....))))))).(((((((((.........)))))))))..))..((.((((.(((..........))).))))..))....)))))).. ( -43.00)
>Sty_1 121 120 + 1
GCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAA
..((((((((...(((....)))(((((((....))))))).(((((((((.........)))))))))..))..((.((((.(((..........))).))))..))....)))))).. ( -43.00)
>Ype_1 121 120 + 1
ACGAUACCCGAAUGGGGAAACCCAGUGCAAUACGUUGCACUAUCGUUAGAUGAAUACAUAGUCUAACGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAA
..(((.(((....(((....)))(((((((....))))))).(((((((((.........))))))))))).)..((.((((.(((..........))).))))..)).......))).. ( -41.30)
>consensus
GCGAUUUCCGAAUGGGGAAACCCAGUGUGAUUCGUCACACUAUCAUUAACUGAAUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAA
..((((((((...(((....)))(((((((....))))))).(((((((((.........)))))))))..))..((.((((.(((..........))).))))..))....)))))).. (-44.08 = -42.32 +  -1.75) 

alignment

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secondary structure

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dotplot

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Window 4

Location 3,941,834 – 3,941,954
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -34.25
Consensus MFE -36.69
Energy contribution -34.50
Covariance contribution -2.19
Combinations/Pair 1.19
Mean z-score -2.17
Structure conservation index 1.07
SVM decision value 2.44
SVM RNA-class probability 0.994015
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3941834 120 - 1
UUGAUUUCUUUUCCUCGGGGUACUUAGAUGUUUCAGUUCCCCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGUCGAAACACACUGGGUUUCCCCAUUCGGAAAUCGC
..(((((((.......((((.(((..((....))))).)))).((...(((((((((((...........))))))))((((((((....)))))))))))..))......))))))).. ( -34.70)
>Sfl_1 121 120 - 1
UUGAUUUCUUUUCCUCGGGGUACUUAGAUGUUUCAGUUCCCCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGC
..(((((((.......((((.(((..((....))))).)))).((...(((((((((((...........))))))))((((((((....)))))))))))..))......))))))).. ( -34.80)
>Sty_1 121 120 - 1
UUGAUUUCUUUUCCUCGGGGUACUUAGAUGUUUCAGUUCCCCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGC
..(((((((.......((((.(((..((....))))).)))).((...(((((((((((...........))))))))((((((((....)))))))))))..))......))))))).. ( -34.80)
>Ype_1 121 120 - 1
UUGAUUUCUUUUCCUCGGGGUACUUAGAUGUUUCAGUUCCCCCGGUUCGCCUCGUUAGACUAUGUAUUCAUCUAACGAUAGUGCAACGUAUUGCACUGGGUUUCCCCAUUCGGGUAUCGU
..............((((((.(((..((....)))))..))))))...(((((((((((...((....))))))))))((((((((....)))))))))))...(((....)))...... ( -32.70)
>consensus
UUGAUUUCUUUUCCUCGGGGUACUUAGAUGUUUCAGUUCCCCCGGUUCGCCUCAUUAACCUAUGGAUUCAGUUAAUGAUAGUGUGACGAAUCACACUGGGUUUCCCCAUUCGGAAAUCGC
..(((((((.......((((.(((..((....))))).)))).((...(((((((((((...........))))))))((((((((....)))))))))))..))......))))))).. (-36.69 = -34.50 +  -2.19) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:05:58 2006