Locus 14

Sequence ID sy_sa.0
Location 12,626 – 12,727
Length 101
Max. P 1.000000
window87 window88 window89 window90 window91

overview

Window 7

Location 12,626 – 12,723
Length 97
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 64.37
Mean single sequence MFE -23.40
Consensus MFE -17.05
Energy contribution -17.84
Covariance contribution 0.79
Combinations/Pair 1.32
Mean z-score -1.41
Structure conservation index 0.73
SVM decision value 2.85
SVM RNA-class probability 0.997377
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 12626 97 + 2516575/120-240
AUAUUUAAUAUGAAUCUACCUACUAUAU----GAGAACAAUCGGUUAUAGCCGUUAUUU-AGUGAGAGUGCAGUCUAAUUUUGG------------------ACUGUUAAAUAGGGUGGC
...............((((((((((.((----((.......((((....)))))))).)-)))......((((((((....)))------------------)))))......)))))). ( -22.01)
>sy_au.0 12463 119 + 2809422/120-240
AACAUAUAUAUGAAUCUACCUACUUAAUUUAAAAGAACAAUCGGUGAUAACCGUUAUUU-UAGUGAAGUGCAAUUUAGGUUUAGUGUAUCUUUAUAACUUAAAUUGUUAAAUAGGGUGGC
...............((((((((((...((((((.......((((....))))...)))-)))..))))((((((((((((.((.....))....))))))))))))......)))))). ( -25.70)
>sy_ha.0 10997 108 + 2685015/120-240
GAUUGUUAUGCGAAUCUACCUACAAUU-----GUGAACAACCGGUAAUAACCGUUAUUUUAAGGAAAGUGCAAUUUGAUACAUAUGUA-------GUGUUAAAUUGUUAAAUAGGGUGGC
...............((((((((..((-----(....))).((((....))))..............))((((((((((((.......-------))))))))))))......)))))). ( -22.50)
>consensus
AAAUUUUAUAUGAAUCUACCUACUAUAU____GAGAACAAUCGGUAAUAACCGUUAUUU_AAGGAAAGUGCAAUUUAAUUUUAGUGUA__________UUAAAUUGUUAAAUAGGGUGGC
...............((((((....................((((....))))................((((((((((((..............))))))))))))......)))))). (-17.05 = -17.84 +   0.79)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,626 – 12,726
Length 100
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.22
Mean single sequence MFE -43.17
Consensus MFE -37.17
Energy contribution -37.74
Covariance contribution 0.57
Combinations/Pair 1.26
Mean z-score -5.24
Structure conservation index 0.86
SVM decision value 3.89
SVM RNA-class probability 0.999690
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 12626 100 + 2516575/160-280
UCGGUUAUAGCCGUUAUUU-AGUGAGAGUGCAGUCUAAUUUUGG------------------ACUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUACA-GGGACGUGGUCUU
.((((....))))((((((-(........((((((((....)))------------------)))))))))))).(((....)))..(((((((((((((.....)-)))))))))))). ( -43.10)
>sy_au.0 12463 116 + 2809422/160-280
UCGGUGAUAACCGUUAUUU-UAGUGAAGUGCAAUUUAGGUUUAGUGUAUCUUUAUAACUUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUA---GGGAUGUGGUCUU
..(((....)))(((((((-((.......((((((((((((.((.....))....))))))))))))....))))))))).......((((((((((((.....---)))))))))))). ( -42.10)
>sy_ha.0 10997 113 + 2685015/160-280
CCGGUAAUAACCGUUAUUUUAAGGAAAGUGCAAUUUGAUACAUAUGUA-------GUGUUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUGAAGGGGAUGUGGUCUU
(((((....))).................((((((((((((.......-------))))))))))))......))(((....)))..((((((((((((((....)))))))))))))). ( -44.30)
>consensus
UCGGUAAUAACCGUUAUUU_AAGGAAAGUGCAAUUUAAUUUUAGUGUA__________UUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUA_A_GGGAUGUGGUCUU
.((((....))))................((((((((((((..............))))))))))))........(((....)))..((((((((((((........)))))))))))). (-37.17 = -37.74 +   0.57)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,626 – 12,726
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.22
Mean single sequence MFE -29.15
Consensus MFE -21.03
Energy contribution -21.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.14
Structure conservation index 0.72
SVM decision value 6.15
SVM RNA-class probability 0.999997
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 12626 100 + 2516575/160-280
AAGACCACGUCCC-UGUACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAGU------------------CCAAAAUUAGACUGCACUCUCACU-AAAUAACGGCUAUAACCGA
.((((((((((((-(.....))))))))))))).((.((((((....((((((.((((------------------(........))))).........)-)))))..)))...))))). ( -35.70)
>sy_au.0 12463 116 + 2809422/160-280
AAGACCACAUCCC---UACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAAGUUAUAAAGAUACACUAAACCUAAAUUGCACUUCACUA-AAAUAACGGUUAUCACCGA
.(((((((.((((---.....)))).))))))).....................(((((((.(((..............))).)))))))..........-......((((....)))). ( -26.54)
>sy_ha.0 10997 113 + 2685015/160-280
AAGACCACAUCCCCUUCACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAACAC-------UACAUAUGUAUCAAAUUGCACUUUCCUUAAAAUAACGGUUAUUACCGG
.(((((((.((((........)))).)))))))..((((((..........))))..........-------(((....))).......))................((((....)))). ( -25.20)
>consensus
AAGACCACAUCCC_U_UACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAA__________UACACAAAAAUUAAAUUGCACUUUCCUU_AAAUAACGGUUAUAACCGA
.(((((((.((((........)))).)))))))..........................................................................(((......))). (-21.03 = -21.03 +   0.00) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,626 – 12,727
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.05
Mean single sequence MFE -42.03
Consensus MFE -32.95
Energy contribution -33.74
Covariance contribution 0.79
Combinations/Pair 1.26
Mean z-score -6.10
Structure conservation index 0.78
SVM decision value 3.40
SVM RNA-class probability 0.999157
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 12626 101 + 2516575/180-300
AGUGAGAGUGCAGUCUAAUUUUGG------------------ACUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUACA-GGGACGUGGUCUUUUUGUGUUAUUAUCCAAUAA
.........((((((((....)))------------------)))))......((((((.((((((.(((((((((((((.....)-))))))))))))...)))))).))))))..... ( -47.00)
>sy_au.0 12463 114 + 2809422/180-300
UAGUGAAGUGCAAUUUAGGUUUAGUGUAUCUUUAUAACUUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUA---GGGAUGUGGUCUUUUU---UUAUUUUCUAAAAA
.........((((((((((((.((.....))....))))))))))))....(((((((....)))..((((((((((((.....---))))))))))))....---......)))).... ( -38.30)
>sy_ha.0 10997 107 + 2685015/180-300
AAGGAAAGUGCAAUUUGAUACAUAUGUA-------GUGUUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUGAAGGGGAUGUGGUCUUUUU------UUAUUGAAAAU
.........((((((((((((.......-------))))))))))))..(((((((((....)))..((((((((((((((....))))))))))))))...)------)))))...... ( -40.80)
>consensus
AAGGAAAGUGCAAUUUAAUUUUAGUGUA__________UUAAAUUGUUAAAUAGGGUGGCAACGCGUAGACCACGUCCCUUGUA_A_GGGAUGUGGUCUUUUU___UUAUUAUCCAAAAA
.........((((((((((((..............))))))))))))........(((....)))..((((((((((((........))))))))))))..................... (-32.95 = -33.74 +   0.79)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,626 – 12,727
Length 101
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.05
Mean single sequence MFE -25.68
Consensus MFE -17.95
Energy contribution -17.73
Covariance contribution -0.22
Combinations/Pair 1.16
Mean z-score -4.14
Structure conservation index 0.70
SVM decision value 7.37
SVM RNA-class probability 1.000000
Prediction RNA

Download alignment: ClustalW | MAF

>sy_sa.0 12626 101 + 2516575/180-300
UUAUUGGAUAAUAACACAAAAAGACCACGUCCC-UGUACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAGU------------------CCAAAAUUAGACUGCACUCUCACU
....(((....((((.(....((((((((((((-(.....)))))))))))))..).)))))))..........((((------------------(........))))).......... ( -33.20)
>sy_au.0 12463 114 + 2809422/180-300
UUUUUAGAAAAUAA---AAAAAGACCACAUCCC---UACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAAGUUAUAAAGAUACACUAAACCUAAAUUGCACUUCACUA
......(((.....---....(((((((.((((---.....)))).))))))).....................(((((((.(((..............))).)))))))...))).... ( -23.54)
>sy_ha.0 10997 107 + 2685015/180-300
AUUUUCAAUAA------AAAAAGACCACAUCCCCUUCACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAACAC-------UACAUAUGUAUCAAAUUGCACUUUCCUU
...........------....(((((((.((((........)))).)))))))..((((((..........))))..........-------(((....))).......))......... ( -20.30)
>consensus
UUUUUAGAUAAUAA___AAAAAGACCACAUCCC_U_UACAAGGGACGUGGUCUACGCGUUGCCACCCUAUUUAACAAUUUAA__________UACACAAAAAUUAAAUUGCACUUUCCUU
...((((..............(((((((.((((........)))).)))))))....((((..........)))).....................)))).................... (-17.95 = -17.73 +  -0.22) 
# Strand winner: forward (1.00)

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 18:51:42 2006