Locus 141

Sequence ID sp_mu.0
Location 1,864,304 – 1,864,424
Length 120
Max. P 0.999932
window861 window862 window863 window864 window865

overview

Window 1

Location 1,864,304 – 1,864,424
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 74.58
Mean single sequence MFE -27.60
Consensus MFE -15.72
Energy contribution -13.85
Covariance contribution -1.87
Combinations/Pair 1.41
Mean z-score -3.04
Structure conservation index 0.57
SVM decision value 3.44
SVM RNA-class probability 0.999209
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1864304 120 + 2030921/0-120
UCCAAACAAAGCUCACAGCAGUUAAAUCAAGCUUUAAUGAAGUCCGAUUUAGCUGCUCUUUUUAUGCUUAAUUUUAGAAAAAAAGAUAAAUGUAAUCUAUAUUUAAAAAUUCUGAAAAUU
........((((....((((((((((((..(((((...)))))..))))))))))))........))))..((((((((.......((((((((...))))))))....))))))))... ( -26.60)
>sp_ag.0 1981093 118 - 2160267/0-120
UCCGACCUAGAUAUACAGCAGUUAAAUCAA--CUUGAUAAAGUGAGAUUUAGCUGCUCUUUUUGUGCCUAAUUUUAAGAAAAAAGGUUAUUGUAAUAUAUAUUUAAACUUUCUGAAAAUU
...(((((.........(((((((((((.(--(((....))))..)))))))))))((((...((.....))...))))....)))))................................ ( -24.20)
>sp_pn.0 1751729 117 + 2038615/0-120
UCCAGACAAGGCUCACAGCAGUUAAAUCU---UCUGAAAAAGUCAGAUUUAGCUGCUCUUUUUGUGCUUUUUUUCAAGAUUAUGAGCAUUUGUAACAGAGGCUUAAAGAUUCUGAAAAUU
.......(((((.((.(((((((((((((---.((.....))..))))))))))))).....)).)))))((((((..(((.(((((.((((...)))).)))))..)))..)))))).. ( -32.00)
>consensus
UCCAAACAAGGCUCACAGCAGUUAAAUCAA__UUUGAUAAAGUCAGAUUUAGCUGCUCUUUUUGUGCUUAAUUUUAAGAAAAAAGGUAAUUGUAAUAUAUAUUUAAAAAUUCUGAAAAUU
.......(((((....((((((((((((.................))))))))))))........))))).(((((.(((...((((.............))))....))).)))))... (-15.72 = -13.85 +  -1.87) 
# Strand winner: reverse (0.99)

alignment

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secondary structure

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Window 2

Location 1,864,304 – 1,864,422
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.70
Mean single sequence MFE -25.70
Consensus MFE -22.64
Energy contribution -22.76
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -2.90
Structure conservation index 0.88
SVM decision value 4.47
SVM RNA-class probability 0.999903
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1864304 118 + 2030921/40-160
UUUCUAAAAUUAAGCAUAAAAAGAGCAGCUAAAUCGGACUUCAUUAAAGCUUGAUUUAACUGCUGUGAGCUUUGUUUGGACAAUAUUUCAACCAAAGCAAACGACAAAUAAUAA--UAAA
.......................(((((.(((((((..(((.....)))..))))))).)))))((..((((((.(((((......))))).))))))..))............--.... ( -26.20)
>sp_ag.0 1981093 118 - 2160267/40-160
UUCUUAAAAUUAGGCACAAAAAGAGCAGCUAAAUCUCACUUUAUCAAG--UUGAUUUAACUGCUGUAUAUCUAGGUCGGACAAUAUUUCAACCUAGACAGACGACAAAUAGUUACGUACA
.......................(((((.((((((..((((....)))--).)))))).)))))((((.(((((((.(((......))).)))))))..(((........)))..)))). ( -26.30)
>sp_pn.0 1751729 117 + 2038615/40-160
AUCUUGAAAAAAAGCACAAAAAGAGCAGCUAAAUCUGACUUUUUCAGA---AGAUUUAACUGCUGUGAGCCUUGUCUGGACAAUAUUUCAGACAAAACCUACGACAAAUGAUUACCCAUA
...(((.................(((((.(((((((..((.....)).---))))))).)))))(((.(..(((((((((......)))))))))..).)))..)))............. ( -24.60)
>consensus
UUCUUAAAAUUAAGCACAAAAAGAGCAGCUAAAUCUGACUUUAUCAAA__UUGAUUUAACUGCUGUGAGCCUUGUUUGGACAAUAUUUCAACCAAAACAAACGACAAAUAAUUAC_UAAA
.......................(((((.((((((.................)))))).)))))((..((((((((((((......))))))))))))..)).................. (-22.64 = -22.76 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,864,304 – 1,864,422
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.70
Mean single sequence MFE -33.67
Consensus MFE -29.73
Energy contribution -26.86
Covariance contribution -2.87
Combinations/Pair 1.47
Mean z-score -3.86
Structure conservation index 0.88
SVM decision value 4.64
SVM RNA-class probability 0.999932
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1864304 118 + 2030921/40-160
UUUA--UUAUUAUUUGUCGUUUGCUUUGGUUGAAAUAUUGUCCAAACAAAGCUCACAGCAGUUAAAUCAAGCUUUAAUGAAGUCCGAUUUAGCUGCUCUUUUUAUGCUUAAUUUUAGAAA
((((--..((((...((.((..((((((.(((..........))).))))))..))((((((((((((..(((((...)))))..))))))))))))........)).))))..)))).. ( -29.00)
>sp_ag.0 1981093 118 - 2160267/40-160
UGUACGUAACUAUUUGUCGUCUGUCUAGGUUGAAAUAUUGUCCGACCUAGAUAUACAGCAGUUAAAUCAA--CUUGAUAAAGUGAGAUUUAGCUGCUCUUUUUGUGCCUAAUUUUAAGAA
.(((((............((.(((((((((((..........))))))))))).))((((((((((((.(--(((....))))..)))))))))))).....)))))............. ( -38.10)
>sp_pn.0 1751729 117 + 2038615/40-160
UAUGGGUAAUCAUUUGUCGUAGGUUUUGUCUGAAAUAUUGUCCAGACAAGGCUCACAGCAGUUAAAUCU---UCUGAAAAAGUCAGAUUUAGCUGCUCUUUUUGUGCUUUUUUUCAAGAU
...(((((..........((..((((((((((..........))))))))))..))(((((((((((((---.((.....))..))))))))))))).......)))))........... ( -33.90)
>consensus
UAUA_GUAAUUAUUUGUCGUAUGUUUUGGUUGAAAUAUUGUCCAAACAAGGCUCACAGCAGUUAAAUCAA__UUUGAUAAAGUCAGAUUUAGCUGCUCUUUUUGUGCUUAAUUUUAAGAA
..................((.(((((((((((..........))))))))))).))((((((((((((.................))))))))))))..(((((..........))))). (-29.73 = -26.86 +  -2.87) 
# Strand winner: reverse (1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,864,304 – 1,864,422
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 72.35
Mean single sequence MFE -20.73
Consensus MFE -14.94
Energy contribution -15.06
Covariance contribution 0.12
Combinations/Pair 1.22
Mean z-score -1.81
Structure conservation index 0.72
SVM decision value 2.61
SVM RNA-class probability 0.995783
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1864304 118 + 2030921/68-188
CUAAAUCGGACUUCAUUAAAGCUUGAUUUAACUGCUGUGAGCUUUGUUUGGACAAUAUUUCAACCAAAGCAAACGACAAAUAAUAA--UAAAUUAUACAUUAUAUUGACUGAUUUGUCAA
.(((((((..(((.....)))..)))))))......((..((((((.(((((......))))).))))))..))(((((((..(((--((.(........).)))))....))))))).. ( -23.80)
>sp_ag.0 1981093 118 - 2160267/68-188
CUAAAUCUCACUUUAUCAAG--UUGAUUUAACUGCUGUAUAUCUAGGUCGGACAAUAUUUCAACCUAGACAGACGACAAAUAGUUACGUACAUUAUAACUUAUUUUCACCAAUAAAUCAA
....................--((((((((......((...(((((((.(((......))).)))))))...))((.(((((((((.(.....).)))).))))))).....)))))))) ( -19.00)
>sp_pn.0 1751729 117 + 2038615/68-188
CUAAAUCUGACUUUUUCAGA---AGAUUUAACUGCUGUGAGCCUUGUCUGGACAAUAUUUCAGACAAAACCUACGACAAAUGAUUACCCAUAUUAUACCCUAUUUAGCUAGAUUUUUCAA
.....(((((.....)))))---(((((((.(((.((((.(..(((((((((......)))))))))..).))))....(((((.......)))))........))).)))))))..... ( -19.40)
>consensus
CUAAAUCUGACUUUAUCAAA__UUGAUUUAACUGCUGUGAGCCUUGUUUGGACAAUAUUUCAACCAAAACAAACGACAAAUAAUUAC_UAAAUUAUACCUUAUUUUGACAGAUUUAUCAA
.((((((.................))))))..((.(((..((((((((((((......))))))))))))..))).)).......................................... (-14.94 = -15.06 +   0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,864,304 – 1,864,422
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 72.35
Mean single sequence MFE -25.73
Consensus MFE -19.62
Energy contribution -17.63
Covariance contribution -1.99
Combinations/Pair 1.43
Mean z-score -1.63
Structure conservation index 0.76
SVM decision value 2.30
SVM RNA-class probability 0.992012
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1864304 118 + 2030921/68-188
UUGACAAAUCAGUCAAUAUAAUGUAUAAUUUA--UUAUUAUUUGUCGUUUGCUUUGGUUGAAAUAUUGUCCAAACAAAGCUCACAGCAGUUAAAUCAAGCUUUAAUGAAGUCCGAUUUAG
(((((......))))).((((((.......))--))))...((((.((..((((((.(((..........))).))))))..)).)))).((((((..(((((...)))))..)))))). ( -21.70)
>sp_ag.0 1981093 118 - 2160267/68-188
UUGAUUUAUUGGUGAAAAUAAGUUAUAAUGUACGUAACUAUUUGUCGUCUGUCUAGGUUGAAAUAUUGUCCGACCUAGAUAUACAGCAGUUAAAUCAA--CUUGAUAAAGUGAGAUUUAG
.(((((((((......)))))))))................((((.((.(((((((((((..........))))))))))).)).)))).((((((.(--(((....))))..)))))). ( -29.50)
>sp_pn.0 1751729 117 + 2038615/68-188
UUGAAAAAUCUAGCUAAAUAGGGUAUAAUAUGGGUAAUCAUUUGUCGUAGGUUUUGUCUGAAAUAUUGUCCAGACAAGGCUCACAGCAGUUAAAUCU---UCUGAAAAAGUCAGAUUUAG
.....((((((..((....(((((.((((((((....)))).(((.((..((((((((((..........))))))))))..)).))))))).))))---).......))..)))))).. ( -26.00)
>consensus
UUGAAAAAUCAGUCAAAAUAAGGUAUAAUAUA_GUAAUUAUUUGUCGUAUGUUUUGGUUGAAAUAUUGUCCAAACAAGGCUCACAGCAGUUAAAUCAA__UUUGAUAAAGUCAGAUUUAG
.........................................((((.((.(((((((((((..........))))))))))).)).)))).((((((.................)))))). (-19.62 = -17.63 +  -1.99) 
# Strand winner: reverse (0.99)

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 18:49:11 2006