Locus 86

Sequence ID sy_ha.0
Location 2,474,579 – 2,474,699
Length 120
Max. P 0.996635
window427 window428 window429 window430

overview

Window 7

Location 2,474,579 – 2,474,699
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 84.72
Mean single sequence MFE -33.53
Consensus MFE -32.08
Energy contribution -32.97
Covariance contribution 0.89
Combinations/Pair 1.03
Mean z-score -3.55
Structure conservation index 0.96
SVM decision value 2.70
SVM RNA-class probability 0.996439
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2474579 120 + 2685015/0-120
CUCCUUGAUAUCGUGAUGUGGUCACAGGGCUCAGUUUUGCCCUCCCACUCAUAAACAUUUCGUGACGAAAUGAGCGCUAUAAAAACGCGACCACAUUAUUUUAACACUGAACCAACUUAA
.((..((.((..(((((((((((..(((((........)))))............(((((((...))))))).(((.........))))))))))))))..)).))..)).......... ( -34.20)
>sy_au.0 2205947 119 - 2809422/0-120
CUCCUUGAUAUCGUGAUGUGGUCACAGGGCUCAGUUUUGCCCUCCCACUCUUAA-CAUUUCGUGACGAAAUGGGCGCUCUAAAAGCGCGACCACAUAAUUUUAACACUUUUCUAAUUAAA
...............((((((((..(((((........)))))...........-(((((((...))))))).(((((.....)))))))))))))........................ ( -34.90)
>sy_sa.0 2281105 120 + 2516575/0-120
CUCCUUGAUAUCGUGAUGUGGUCACAGGACUCAGUUUUGUCCUCCCACUCUUCUACAUUUCGUGACGAAAUGAACGCUCUAUGAGCGCGACCACAGUAUUAUAACAUUAACUCAUUACAU
.....((.(((.(((.(((((((..(((((........)))))............(((((((...)))))))..(((((...))))).))))))).))).))).)).............. ( -31.50)
>consensus
CUCCUUGAUAUCGUGAUGUGGUCACAGGGCUCAGUUUUGCCCUCCCACUCUUAAACAUUUCGUGACGAAAUGAGCGCUCUAAAAGCGCGACCACAUUAUUUUAACACUAAACCAAUUAAA
.....((.((..(((((((((((..(((((........)))))............(((((((...))))))).(((((.....))))))))))))))))..)).)).............. (-32.08 = -32.97 +   0.89)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,474,579 – 2,474,699
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 84.72
Mean single sequence MFE -36.00
Consensus MFE -31.45
Energy contribution -30.57
Covariance contribution -0.88
Combinations/Pair 1.12
Mean z-score -2.28
Structure conservation index 0.87
SVM decision value 1.33
SVM RNA-class probability 0.942717
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2474579 120 + 2685015/0-120
UUAAGUUGGUUCAGUGUUAAAAUAAUGUGGUCGCGUUUUUAUAGCGCUCAUUUCGUCACGAAAUGUUUAUGAGUGGGAGGGCAAAACUGAGCCCUGUGACCACAUCACGAUAUCAAGGAG
.....(((((...(((........((((((((((..........(((((((..(((......)))...)))))))..(((((........))))))))))))))))))...))))).... ( -38.70)
>sy_au.0 2205947 119 - 2809422/0-120
UUUAAUUAGAAAAGUGUUAAAAUUAUGUGGUCGCGCUUUUAGAGCGCCCAUUUCGUCACGAAAUG-UUAAGAGUGGGAGGGCAAAACUGAGCCCUGUGACCACAUCACGAUAUCAAGGAG
........((...(((........((((((((((((((...)))).(((((((...((.....))-....)))))))(((((........))))))))))))))))))....))...... ( -35.50)
>sy_sa.0 2281105 120 + 2516575/0-120
AUGUAAUGAGUUAAUGUUAUAAUACUGUGGUCGCGCUCAUAGAGCGUUCAUUUCGUCACGAAAUGUAGAAGAGUGGGAGGACAAAACUGAGUCCUGUGACCACAUCACGAUAUCAAGGAG
.((((((........))))))....(((((((((.(((((....(...(((((((...)))))))..)....)))))(((((........))))))))))))))................ ( -33.80)
>consensus
UUAAAUUGGAUAAGUGUUAAAAUAAUGUGGUCGCGCUUUUAGAGCGCUCAUUUCGUCACGAAAUGUUUAAGAGUGGGAGGGCAAAACUGAGCCCUGUGACCACAUCACGAUAUCAAGGAG
.........................((((((((((((.....))))).(((((((...)))))))..........(.(((((........))))).))))))))................ (-31.45 = -30.57 +  -0.88) 
# Strand winner: reverse (0.87)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,474,579 – 2,474,699
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 79.44
Mean single sequence MFE -26.27
Consensus MFE -24.08
Energy contribution -24.30
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.19
Structure conservation index 0.92
SVM decision value 2.73
SVM RNA-class probability 0.996635
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2474579 120 + 2685015/19-139
GGUCACAGGGCUCAGUUUUGCCCUCCCACUCAUAAACAUUUCGUGACGAAAUGAGCGCUAUAAAAACGCGACCACAUUAUUUUAACACUGAACCAACUUAAAAAGCAAUAGUAAAAUUUC
((((..(((((........)))))............(((((((...))))))).(((.........)))))))............................................... ( -23.10)
>sy_au.0 2205947 119 - 2809422/19-139
GGUCACAGGGCUCAGUUUUGCCCUCCCACUCUUAA-CAUUUCGUGACGAAAUGGGCGCUCUAAAAGCGCGACCACAUAAUUUUAACACUUUUCUAAUUAAAAAAUCAAUACUCUUUUUUA
((((..(((((........)))))...........-(((((((...))))))).(((((.....)))))))))............................................... ( -28.50)
>sy_sa.0 2281105 120 + 2516575/19-139
GGUCACAGGACUCAGUUUUGUCCUCCCACUCUUCUACAUUUCGUGACGAAAUGAACGCUCUAUGAGCGCGACCACAGUAUUAUAACAUUAACUCAUUACAUAAAGCAAUGGUGAUUUGUA
((((..(((((........)))))............(((((((...)))))))..(((((...))))).))))...........(((...((.((((.(.....).))))))....))). ( -27.20)
>consensus
GGUCACAGGGCUCAGUUUUGCCCUCCCACUCUUAAACAUUUCGUGACGAAAUGAGCGCUCUAAAAGCGCGACCACAUUAUUUUAACACUAAACCAAUUAAAAAAGCAAUAGUAAUUUUUA
((((..(((((........)))))............(((((((...))))))).(((((.....)))))))))............................................... (-24.08 = -24.30 +   0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,474,579 – 2,474,699
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.44
Mean single sequence MFE -30.40
Consensus MFE -24.75
Energy contribution -23.43
Covariance contribution -1.32
Combinations/Pair 1.30
Mean z-score -1.16
Structure conservation index 0.81
SVM decision value 0.03
SVM RNA-class probability 0.546790
Prediction RNA

Download alignment: ClustalW | MAF

>sy_ha.0 2474579 120 + 2685015/19-139
GAAAUUUUACUAUUGCUUUUUAAGUUGGUUCAGUGUUAAAAUAAUGUGGUCGCGUUUUUAUAGCGCUCAUUUCGUCACGAAAUGUUUAUGAGUGGGAGGGCAAAACUGAGCCCUGUGACC
...((((((.(((((..((.......))..))))).)))))).....((((((..........(((((((..(((......)))...)))))))..(((((........))))))))))) ( -30.20)
>sy_au.0 2205947 119 - 2809422/19-139
UAAAAAAGAGUAUUGAUUUUUUAAUUAGAAAAGUGUUAAAAUUAUGUGGUCGCGCUUUUAGAGCGCCCAUUUCGUCACGAAAUG-UUAAGAGUGGGAGGGCAAAACUGAGCCCUGUGACC
.......((.((((((((((...(((.....)))...))))))).))).))((((((...)))))).(((((((...)))))))-......((.(.(((((........))))).).)). ( -29.80)
>sy_sa.0 2281105 120 + 2516575/19-139
UACAAAUCACCAUUGCUUUAUGUAAUGAGUUAAUGUUAUAAUACUGUGGUCGCGCUCAUAGAGCGUUCAUUUCGUCACGAAAUGUAGAAGAGUGGGAGGACAAAACUGAGUCCUGUGACC
.(((....((((((((.....)))))).))...)))...........((((((.(((((....(...(((((((...)))))))..)....)))))(((((........))))))))))) ( -31.20)
>consensus
UAAAAAUCACUAUUGCUUUUUAAAUUGGAUAAGUGUUAAAAUAAUGUGGUCGCGCUUUUAGAGCGCUCAUUUCGUCACGAAAUGUUUAAGAGUGGGAGGGCAAAACUGAGCCCUGUGACC
..........(((((.(((.......))).)))))............(((((((((.....))))).(((((((...)))))))..........(.(((((........))))).))))) (-24.75 = -23.43 +  -1.32) 
# Strand winner: reverse (0.88)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 18:56:33 2006