Locus 128

Sequence ID sp_mu.0
Location 642,196 – 642,315
Length 119
Max. P 0.999999
window815 window816 window817 window818

overview

Window 5

Location 642,196 – 642,315
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.13
Mean single sequence MFE -31.43
Consensus MFE -17.51
Energy contribution -14.97
Covariance contribution -2.54
Combinations/Pair 1.32
Mean z-score -2.71
Structure conservation index 0.56
SVM decision value 4.73
SVM RNA-class probability 0.999944
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 642196 119 - 2030921/0-120
UAUCUUUCUAAAUUGAACACGGGGCUAAUUUCCUAUGAAAAAAGAUAAUCUUUCCUAGACGCAAGAGUCUUUGU-CAGAUUUCCUAUUUUUCUACGGAAAUUUUCAGCAAGCUGAAUCGC
.....(((......)))..(((....(((((((...((((((((..(((((..(..((((......))))..).-.)))))..)).))))))...)))))))(((((....)))))))). ( -25.40)
>sp_ag.0 43257 119 + 2160267/0-120
UAGUUUGCCUAACUGAACACGGGAUUAAAUUUCUAGGAAAAAAGAUAAAACGACUUAGACGCAAGCGUCGUUGU-UCGUUUUCCUAUUUUUCUACGAAAUUUUUCGGCAAGCCGAAUCAU
..(((((((...(((....)))((..(((((((((((((((.((..((((((((...((((....))))...).-))))))).)).)))))))).))))))).)))))))))........ ( -36.30)
>sp_pn.0 515516 120 + 2038615/0-120
UAUCUUGAUGACUUGAAUUUUGGUCUCAUUUCUUAGGAAAAAAGAUAAGCUUCCUAGCACUCGUCGAGUGCGACGUCACCUUCCUAUUUUUCUACAGAAAUGUUCGGCAAGCCGAACCGU
......((.((((........))))))((((((((((((((.((....(((....)))...(((((....)))))........)).)))))))).))))))((((((....))))))... ( -32.60)
>consensus
UAUCUUGCUAAAUUGAACACGGGACUAAUUUCCUAGGAAAAAAGAUAAACUUACUUAGACGCAAGAGUCGUUGU_UCGAUUUCCUAUUUUUCUACGGAAAUUUUCGGCAAGCCGAAUCGU
.....................((...(((((((((((((((.((...............(....)..(((......)))....)).)))))))).)))))))(((((....))))))).. (-17.51 = -14.97 +  -2.54)

alignment

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secondary structure

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dotplot

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Window 6

Location 642,196 – 642,315
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.13
Mean single sequence MFE -30.97
Consensus MFE -20.39
Energy contribution -17.96
Covariance contribution -2.43
Combinations/Pair 1.36
Mean z-score -2.21
Structure conservation index 0.66
SVM decision value 4.85
SVM RNA-class probability 0.999956
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 642196 119 - 2030921/0-120
GCGAUUCAGCUUGCUGAAAAUUUCCGUAGAAAAAUAGGAAAUCUG-ACAAAGACUCUUGCGUCUAGGAAAGAUUAUCUUUUUUCAUAGGAAAUUAGCCCCGUGUUCAAUUUAGAAAGAUA
(((.(((((....)))))(((((((...((((((.(((.(((((.-.(..((((......))))..)..))))).)))))))))...))))))).....))).................. ( -28.00)
>sp_ag.0 43257 119 + 2160267/0-120
AUGAUUCGGCUUGCCGAAAAAUUUCGUAGAAAAAUAGGAAAACGA-ACAACGACGCUUGCGUCUAAGUCGUUUUAUCUUUUUUCCUAGAAAUUUAAUCCCGUGUUCAGUUAGGCAAACUA
.((((((((....)))))(((((((...((((((.((((((((((-.....((((....))))....))))))).)))))))))...)))))))..........)))............. ( -29.10)
>sp_pn.0 515516 120 + 2038615/0-120
ACGGUUCGGCUUGCCGAACAUUUCUGUAGAAAAAUAGGAAGGUGACGUCGCACUCGACGAGUGCUAGGAAGCUUAUCUUUUUUCCUAAGAAAUGAGACCAAAAUUCAAGUCAUCAAGAUA
...((((((....)))))).(((((((......)))))))((((((...((((((...))))))..((...(((((.((((.....)))).))))).)).........))))))...... ( -35.80)
>consensus
ACGAUUCGGCUUGCCGAAAAUUUCCGUAGAAAAAUAGGAAAACGA_ACAACGACCCUUGCGUCUAAGAAAGAUUAUCUUUUUUCCUAGGAAAUUAGACCCGUGUUCAAUUAAGCAAGAUA
....(((((....)))))(((((((...((((((.(((.((((........(((......))).......)))).)))))))))...))))))).......................... (-20.39 = -17.96 +  -2.43) 
# Strand winner: reverse (0.75)

alignment

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secondary structure

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dotplot

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Window 7

Location 642,196 – 642,315
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.13
Mean single sequence MFE -33.40
Consensus MFE -20.72
Energy contribution -18.07
Covariance contribution -2.65
Combinations/Pair 1.33
Mean z-score -3.24
Structure conservation index 0.62
SVM decision value 6.94
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 642196 119 - 2030921/2-122
UCUUUCUAAAUUGAACACGGGGCUAAUUUCCUAUGAAAAAAGAUAAUCUUUCCUAGACGCAAGAGUCUUUGU-CAGAUUUCCUAUUUUUCUACGGAAAUUUUCAGCAAGCUGAAUCGCCC
...(((......)))....((((.(((((((...((((((((..(((((..(..((((......))))..).-.)))))..)).))))))...)))))))(((((....)))))..)))) ( -31.50)
>sp_ag.0 43257 119 + 2160267/2-122
GUUUGCCUAACUGAACACGGGAUUAAAUUUCUAGGAAAAAAGAUAAAACGACUUAGACGCAAGCGUCGUUGU-UCGUUUUCCUAUUUUUCUACGAAAUUUUUCGGCAAGCCGAAUCAUCC
(((((((...(((....)))((..(((((((((((((((.((..((((((((...((((....))))...).-))))))).)).)))))))).))))))).))))))))).......... ( -36.10)
>sp_pn.0 515516 120 + 2038615/2-122
UCUUGAUGACUUGAAUUUUGGUCUCAUUUCUUAGGAAAAAAGAUAAGCUUCCUAGCACUCGUCGAGUGCGACGUCACCUUCCUAUUUUUCUACAGAAAUGUUCGGCAAGCCGAACCGUCC
....((.((((........))))))((((((((((((((.((....(((....)))...(((((....)))))........)).)))))))).))))))((((((....))))))..... ( -32.60)
>consensus
UCUUGCUAAAUUGAACACGGGACUAAUUUCCUAGGAAAAAAGAUAAACUUACUUAGACGCAAGAGUCGUUGU_UCGAUUUCCUAUUUUUCUACGGAAAUUUUCGGCAAGCCGAAUCGUCC
...................((((.(((((((((((((((.((...............(....)..(((......)))....)).)))))))).)))))))(((((....)))))..)))) (-20.72 = -18.07 +  -2.65)

alignment

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secondary structure

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dotplot

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Window 8

Location 642,196 – 642,315
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.13
Mean single sequence MFE -34.07
Consensus MFE -25.36
Energy contribution -22.59
Covariance contribution -2.76
Combinations/Pair 1.38
Mean z-score -2.64
Structure conservation index 0.74
SVM decision value 6.69
SVM RNA-class probability 0.999999
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 642196 119 - 2030921/2-122
GGGCGAUUCAGCUUGCUGAAAAUUUCCGUAGAAAAAUAGGAAAUCUG-ACAAAGACUCUUGCGUCUAGGAAAGAUUAUCUUUUUUCAUAGGAAAUUAGCCCCGUGUUCAAUUUAGAAAGA
((((..(((((....)))))(((((((...((((((.(((.(((((.-.(..((((......))))..)..))))).)))))))))...))))))).))))................... ( -34.20)
>sp_ag.0 43257 119 + 2160267/2-122
GGAUGAUUCGGCUUGCCGAAAAAUUUCGUAGAAAAAUAGGAAAACGA-ACAACGACGCUUGCGUCUAAGUCGUUUUAUCUUUUUUCCUAGAAAUUUAAUCCCGUGUUCAGUUAGGCAAAC
((((..(((((....)))))(((((((...((((((.((((((((((-.....((((....))))....))))))).)))))))))...))))))).))))..((((......))))... ( -32.20)
>sp_pn.0 515516 120 + 2038615/2-122
GGACGGUUCGGCUUGCCGAACAUUUCUGUAGAAAAAUAGGAAGGUGACGUCGCACUCGACGAGUGCUAGGAAGCUUAUCUUUUUUCCUAAGAAAUGAGACCAAAAUUCAAGUCAUCAAGA
.....((((((....)))))).(((((((......)))))))((((((...((((((...))))))..((...(((((.((((.....)))).))))).)).........)))))).... ( -35.80)
>consensus
GGACGAUUCGGCUUGCCGAAAAUUUCCGUAGAAAAAUAGGAAAACGA_ACAACGACCCUUGCGUCUAAGAAAGAUUAUCUUUUUUCCUAGGAAAUUAGACCCGUGUUCAAUUAAGCAAGA
((((..(((((....)))))(((((((...((((((.(((.((((........(((......))).......)))).)))))))))...))))))).))))................... (-25.36 = -22.59 +  -2.76) 
# Strand winner: reverse (0.92)

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 19:02:00 2006