Locus 93

Sequence ID sy_ha.0
Location 1,799,767 – 1,799,842
Length 75
Max. P 0.999935
window479 window480 window481 window482

overview

Window 9

Location 1,799,767 – 1,799,842
Length 75
Sequences 5
Columns 75
Reading direction forward
Mean pairwise identity 92.53
Mean single sequence MFE -26.54
Consensus MFE -23.78
Energy contribution -22.66
Covariance contribution -1.12
Combinations/Pair 1.15
Mean z-score -2.24
Structure conservation index 0.90
SVM decision value 3.25
SVM RNA-class probability 0.998850
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799767 75 - 2685015
CUGGGCUAGCUGGAUUCGAACCAGCGCGUGACGGAGUCAAAGUCCGUUGCCUUACCGCUUGGCUAUAGCCCAUUA
.((((((((((((.......)))))..(..(((((.......)))))..)...............)))))))... ( -29.30)
>sy_sa.0 1767481 75 - 2516575
CUGGGCUAGCUGGAUUCGAACCAGCGCGUGAUGGAGUCAAAGUCCAUUGCCUUACCGCUUGGCUAUAGCCCAUUA
.((((((((((((.......)))))..(..(((((.......)))))..)...............)))))))... ( -27.90)
>sy_au.0 2228061 75 + 2809422
CUGGGCUAGCUGGAUUCGAACCAACGAGUGACGGAGUCAAAGUCCGUUGCCUUACCGCUUGGCUAUAGCCCAAUA
.(((((((((..(..(((......)))(..(((((.......)))))..)........)..)))..))))))... ( -26.10)
>sp_ag.0 1366871 75 + 2160267
CUGGGGUAGCUGGAUUCGAACCAACGCAUGAGGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUACCCCAAAA
.((((((((((((.......)))..))..((((((.......))))))(((.........)))..)))))))... ( -24.70)
>sp_mu.0 1142215 75 + 2030921
CUGGGGUAGCUGGAUUCGAACCAACGCAUGAGGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUACCCCAAAA
.((((((((((((.......)))..))..((((((.......))))))(((.........)))..)))))))... ( -24.70)
>consensus
CUGGGCUAGCUGGAUUCGAACCAACGCGUGACGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUAGCCCAAUA
.((((((((.(((.......))).)....((((((.......))))))(((.........)))..)))))))... (-23.78 = -22.66 +  -1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,799,767 – 1,799,842
Length 75
Sequences 5
Columns 75
Reading direction reverse
Mean pairwise identity 92.53
Mean single sequence MFE -27.10
Consensus MFE -27.40
Energy contribution -26.04
Covariance contribution -1.36
Combinations/Pair 1.20
Mean z-score -2.25
Structure conservation index 1.01
SVM decision value 4.66
SVM RNA-class probability 0.999935
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799767 75 - 2685015
UAAUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCGUCACGCGCUGGUUCGAAUCCAGCUAGCCCAG
...(((((((.......(((((..(....)..))..((((...)))))))(((((.......)))))))))))). ( -28.50)
>sy_sa.0 1767481 75 - 2516575
UAAUGGGCUAUAGCCAAGCGGUAAGGCAAUGGACUUUGACUCCAUCACGCGCUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((....)))...((.(((((.......)))))...))(((((.......)))))))))))). ( -26.40)
>sy_au.0 2228061 75 + 2809422
UAUUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCGUCACUCGUUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))). ( -25.00)
>sp_ag.0 1366871 75 + 2160267
UUUUGGGGUAUAGCCAAGCGGUAAGGCAAGGGACUUUGACUCCCUCAUGCGUUGGUUCGAAUCCAGCUACCCCAG
...(((((((..(((....)))...((((((((.......)))))..)))(((((.......)))))))))))). ( -27.80)
>sp_mu.0 1142215 75 + 2030921
UUUUGGGGUAUAGCCAAGCGGUAAGGCAAGGGACUUUGACUCCCUCAUGCGUUGGUUCGAAUCCAGCUACCCCAG
...(((((((..(((....)))...((((((((.......)))))..)))(((((.......)))))))))))). ( -27.80)
>consensus
UAUUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCCUCACGCGUUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))). (-27.40 = -26.04 +  -1.36) 
# Strand winner: reverse (0.55)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,799,767 – 1,799,842
Length 75
Sequences 5
Columns 75
Reading direction forward
Mean pairwise identity 92.53
Mean single sequence MFE -26.54
Consensus MFE -23.78
Energy contribution -22.66
Covariance contribution -1.12
Combinations/Pair 1.15
Mean z-score -2.24
Structure conservation index 0.90
SVM decision value 3.25
SVM RNA-class probability 0.998850
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799767 75 - 2685015/0-75
CUGGGCUAGCUGGAUUCGAACCAGCGCGUGACGGAGUCAAAGUCCGUUGCCUUACCGCUUGGCUAUAGCCCAUUA
.((((((((((((.......)))))..(..(((((.......)))))..)...............)))))))... ( -29.30)
>sy_sa.0 1767481 75 - 2516575/0-75
CUGGGCUAGCUGGAUUCGAACCAGCGCGUGAUGGAGUCAAAGUCCAUUGCCUUACCGCUUGGCUAUAGCCCAUUA
.((((((((((((.......)))))..(..(((((.......)))))..)...............)))))))... ( -27.90)
>sy_au.0 2228061 75 + 2809422/0-75
CUGGGCUAGCUGGAUUCGAACCAACGAGUGACGGAGUCAAAGUCCGUUGCCUUACCGCUUGGCUAUAGCCCAAUA
.(((((((((..(..(((......)))(..(((((.......)))))..)........)..)))..))))))... ( -26.10)
>sp_ag.0 1366871 75 + 2160267/0-75
CUGGGGUAGCUGGAUUCGAACCAACGCAUGAGGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUACCCCAAAA
.((((((((((((.......)))..))..((((((.......))))))(((.........)))..)))))))... ( -24.70)
>sp_mu.0 1142215 75 + 2030921/0-75
CUGGGGUAGCUGGAUUCGAACCAACGCAUGAGGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUACCCCAAAA
.((((((((((((.......)))..))..((((((.......))))))(((.........)))..)))))))... ( -24.70)
>consensus
CUGGGCUAGCUGGAUUCGAACCAACGCGUGACGGAGUCAAAGUCCCUUGCCUUACCGCUUGGCUAUAGCCCAAUA
.((((((((.(((.......))).)....((((((.......))))))(((.........)))..)))))))... (-23.78 = -22.66 +  -1.12)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 1,799,767 – 1,799,842
Length 75
Sequences 5
Columns 75
Reading direction reverse
Mean pairwise identity 92.53
Mean single sequence MFE -27.10
Consensus MFE -27.40
Energy contribution -26.04
Covariance contribution -1.36
Combinations/Pair 1.20
Mean z-score -2.25
Structure conservation index 1.01
SVM decision value 4.66
SVM RNA-class probability 0.999935
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 1799767 75 - 2685015/0-75
UAAUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCGUCACGCGCUGGUUCGAAUCCAGCUAGCCCAG
...(((((((.......(((((..(....)..))..((((...)))))))(((((.......)))))))))))). ( -28.50)
>sy_sa.0 1767481 75 - 2516575/0-75
UAAUGGGCUAUAGCCAAGCGGUAAGGCAAUGGACUUUGACUCCAUCACGCGCUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((....)))...((.(((((.......)))))...))(((((.......)))))))))))). ( -26.40)
>sy_au.0 2228061 75 + 2809422/0-75
UAUUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCGUCACUCGUUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))). ( -25.00)
>sp_ag.0 1366871 75 + 2160267/0-75
UUUUGGGGUAUAGCCAAGCGGUAAGGCAAGGGACUUUGACUCCCUCAUGCGUUGGUUCGAAUCCAGCUACCCCAG
...(((((((..(((....)))...((((((((.......)))))..)))(((((.......)))))))))))). ( -27.80)
>sp_mu.0 1142215 75 + 2030921/0-75
UUUUGGGGUAUAGCCAAGCGGUAAGGCAAGGGACUUUGACUCCCUCAUGCGUUGGUUCGAAUCCAGCUACCCCAG
...(((((((..(((....)))...((((((((.......)))))..)))(((((.......)))))))))))). ( -27.80)
>consensus
UAUUGGGCUAUAGCCAAGCGGUAAGGCAACGGACUUUGACUCCCUCACGCGUUGGUUCGAAUCCAGCUAGCCCAG
...(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))). (-27.40 = -26.04 +  -1.36) 
# Strand winner: reverse (0.55)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:57:15 2006