Locus 74

Sequence ID sp_ag.0
Location 2,131,690 – 2,131,770
Length 80
Max. P 0.999970
window369 window370 window371 window372

overview

Window 9

Location 2,131,690 – 2,131,770
Length 80
Sequences 6
Columns 80
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -29.80
Consensus MFE -27.19
Energy contribution -26.25
Covariance contribution -0.94
Combinations/Pair 1.10
Mean z-score -2.62
Structure conservation index 0.91
SVM decision value 3.19
SVM RNA-class probability 0.998690
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 2131690 80 - 2160267
AUUAAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sp_pn.0 1690871 80 + 2038615
AUUAAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sp_mu.0 2007429 80 - 2030921
AUAUAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sy_au.0 1980340 80 + 2809422
AAUGGUGGGCCUAAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUAUAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -30.60)
>sy_sa.0 1555202 80 - 2516575
AAUGGUGGGCCUAAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUAUAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -30.60)
>sy_ha.0 1580155 80 - 2685015
AAUGGUGGGCCUGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -32.40)
>consensus
AAUGAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACACGCCCA
.....(((((.((.((((.......))))......((((((.....)))))).((((.........))))..)).))))) (-27.19 = -26.25 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,131,690 – 2,131,770
Length 80
Sequences 6
Columns 80
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -34.75
Consensus MFE -34.53
Energy contribution -33.42
Covariance contribution -1.11
Combinations/Pair 1.11
Mean z-score -2.67
Structure conservation index 0.99
SVM decision value 5.04
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 2131690 80 - 2160267
UGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUUAAU
((((((((..(((((((((((......)).)))))))...))(((.(.((((....)))).).))).))))))))..... ( -33.60)
>sp_pn.0 1690871 80 + 2038615
UGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUUAAU
((((((((..(((((((((((......)).)))))))...))(((.(.((((....)))).).))).))))))))..... ( -33.60)
>sp_mu.0 2007429 80 - 2030921
UGGGCGCGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUAUAU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.10)
>sy_au.0 1980340 80 + 2809422
UGGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.00)
>sy_sa.0 1555202 80 - 2516575
UGGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.00)
>sy_ha.0 1580155 80 - 2685015
UGGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -36.20)
>consensus
UGGGCCCGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCAAU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... (-34.53 = -33.42 +  -1.11) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,131,690 – 2,131,770
Length 80
Sequences 6
Columns 80
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -29.80
Consensus MFE -27.19
Energy contribution -26.25
Covariance contribution -0.94
Combinations/Pair 1.10
Mean z-score -2.62
Structure conservation index 0.91
SVM decision value 3.19
SVM RNA-class probability 0.998690
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 2131690 80 - 2160267/0-80
AUUAAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sp_pn.0 1690871 80 + 2038615/0-80
AUUAAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCACCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sp_mu.0 2007429 80 - 2030921/0-80
AUAUAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACGCGCCCA
.....(((((..(((((((.(((......)))..)).))))).....(((((.((((.........)))))))))))))) ( -28.40)
>sy_au.0 1980340 80 + 2809422/0-80
AAUGGUGGGCCUAAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUAUAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -30.60)
>sy_sa.0 1555202 80 - 2516575/0-80
AAUGGUGGGCCUAAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUAUAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -30.60)
>sy_ha.0 1580155 80 - 2685015/0-80
AAUGGUGGGCCUGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACAGGCCCA
.....((((((((.((((.......))))......((((((.....)))))).((((.........))))..)))))))) ( -32.40)
>consensus
AAUGAUGGGCACGAGUGGACUCGAACCACCGACCUCACGCUUAUCAGGCGUGCGCUCUAACCAGCUGAGCUACACGCCCA
.....(((((.((.((((.......))))......((((((.....)))))).((((.........))))..)).))))) (-27.19 = -26.25 +  -0.94)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,131,690 – 2,131,770
Length 80
Sequences 6
Columns 80
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -34.75
Consensus MFE -34.53
Energy contribution -33.42
Covariance contribution -1.11
Combinations/Pair 1.11
Mean z-score -2.67
Structure conservation index 0.99
SVM decision value 5.04
SVM RNA-class probability 0.999970
Prediction RNA

Download alignment: ClustalW | MAF

>sp_ag.0 2131690 80 - 2160267/0-80
UGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUUAAU
((((((((..(((((((((((......)).)))))))...))(((.(.((((....)))).).))).))))))))..... ( -33.60)
>sp_pn.0 1690871 80 + 2038615/0-80
UGGGCGCGUAGCUCAGGUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUUAAU
((((((((..(((((((((((......)).)))))))...))(((.(.((((....)))).).))).))))))))..... ( -33.60)
>sp_mu.0 2007429 80 - 2030921/0-80
UGGGCGCGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCGUGCCCAUAUAU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.10)
>sy_au.0 1980340 80 + 2809422/0-80
UGGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.00)
>sy_sa.0 1555202 80 - 2516575/0-80
UGGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -35.00)
>sy_ha.0 1580155 80 - 2685015/0-80
UGGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCAUU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... ( -36.20)
>consensus
UGGGCCCGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCAAU
((((((((...(((((((.(((((.((....))))))).))).))))...(((((.......)))))))))))))..... (-34.53 = -33.42 +  -1.11) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:55:45 2006