Locus 129

Sequence ID sp_mu.0
Location 660,473 – 888,822
Length 228349
Max. P 0.962234
window819 window820 window821 window822

overview

Window 9

Location 888,707 – 888,822
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 54.57
Mean single sequence MFE -28.43
Consensus MFE -9.39
Energy contribution -9.30
Covariance contribution -0.09
Combinations/Pair 1.50
Mean z-score -2.20
Structure conservation index 0.33
SVM decision value 0.26
SVM RNA-class probability 0.657911
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 888707 115 - 2030921/0-120
CAGAGGUAUUAGACCAA----GUCUAAGACCGUCAGAGAUAUGCGUCUAGUUGUUUGUCCUUGCGGGAUACCUUGUGAAA-UAUAUUGUUAUCAAGAGAUAAAGAGGGUUUAUUUCUUGU
..((((((((((((...----))))....((((.((.((((.(((......))).)))))).))))))))))))......-...........(((((((((((.....))))))))))). ( -32.00)
>sp_ag.0 1006131 108 - 2160267/0-120
CAAAGGUAUCAAACUUUU---GUUUGACACCGUCAAAGAGAUA-------UUUGUUGUCCUUGCGGGUUACCUUGAGAAAAUAUAUUGUUAUCAAAAGCUAGCUCGG--CUAGCUUUUGU
..((((((((((((....---))))))..((((..(((.((((-------.....)))))))))))..))))))..................(((((((((((...)--)))))))))). ( -34.40)
>sp_pn.0 759602 110 + 2038615/0-120
UUAGGGUAUUUUAUUUUUAUAAUUGAAAGACGUGAAUGAUAUG--------AACAUGUCCUUGCUGGUGCUUAGGAAAAAAAUUAUAAGUAUGUCAAGUUUAAGAAAAACU--UGAUUGU
....((((......(((((....)))))((((((.........--------..))))))..)))).(((((((.((......)).)))))))(((((((((.....)))))--))))... ( -18.90)
>consensus
CAAAGGUAUUAAACUUUU___GUUUAAAACCGUCAAAGAUAUG_______UUACUUGUCCUUGCGGGUUACCUUGAGAAAAUAUAUUGUUAUCAAAAGAUAAAGAGG__CUA_UUAUUGU
(((.(((.((((((.......)))))).)))...........................((.....))..................)))....((((((((((.......)))))))))). ( -9.39 =  -9.30 +  -0.09)

alignment

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secondary structure

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dotplot

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Window 0

Location 888,707 – 888,822
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 54.57
Mean single sequence MFE -24.81
Consensus MFE -4.91
Energy contribution -5.47
Covariance contribution 0.56
Combinations/Pair 1.27
Mean z-score -3.85
Structure conservation index 0.20
SVM decision value 0.57
SVM RNA-class probability 0.785673
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 888707 115 - 2030921/0-120
ACAAGAAAUAAACCCUCUUUAUCUCUUGAUAACAAUAUA-UUUCACAAGGUAUCCCGCAAGGACAAACAACUAGACGCAUAUCUCUGACGGUCUUAGAC----UUGGUCUAAUACCUCUG
.(((((.(((((.....))))).)))))...........-.......((((((.((....)).........(((((.((..(((..(.....)..))).----.)))))))))))))... ( -24.40)
>sp_ag.0 1006131 108 - 2160267/0-120
ACAAAAGCUAG--CCGAGCUAGCUUUUGAUAACAAUAUAUUUUCUCAAGGUAACCCGCAAGGACAACAAA-------UAUCUCUUUGACGGUGUCAAAC---AAAAGUUUGAUACCUUUG
.((((((((((--(...)))))))))))................((((((....((....))........-------.....)))))).((((((((((---....)))))))))).... ( -34.63)
>sp_pn.0 759602 110 + 2038615/0-120
ACAAUCA--AGUUUUUCUUAAACUUGACAUACUUAUAAUUUUUUUCCUAAGCACCAGCAAGGACAUGUU--------CAUAUCAUUCACGUCUUUCAAUUAUAAAAAUAAAAUACCCUAA
....(((--(((((.....)))))))).....((((((((..........((....))((((((.((..--------.........)).)))))).))))))))................ ( -15.40)
>consensus
ACAAAAA_UAG__CCUCUUUAACUUUUGAUAACAAUAUAUUUUCUCAAGGUAACCCGCAAGGACAAAAAA_______CAUAUCUUUGACGGUCUUAAAC___AAAAGUAUAAUACCUUUG
......................................................((....))...........................(((.((((((.......)))))).))).... ( -4.91 =  -5.47 +   0.56) 
# Strand winner: forward (0.64)

alignment

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secondary structure

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dotplot

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Window 1

Location 660,473 – 660,551
Length 78
Sequences 3
Columns 78
Reading direction forward
Mean pairwise identity 78.63
Mean single sequence MFE -19.10
Consensus MFE -17.33
Energy contribution -16.73
Covariance contribution -0.60
Combinations/Pair 1.33
Mean z-score -1.30
Structure conservation index 0.91
SVM decision value 1.54
SVM RNA-class probability 0.962234
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 660473 78 + 2030921
UUCUAUUUUAAGUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAAAGUUGUCUGGCCCAACAUGUUAAAG
......((((((((......(.((((((....)))))))(((..(((((.....)))))..)))....))).))))). ( -18.20)
>sp_ag.0 766044 77 - 2160267
UACUAGUUGCAAUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAG-GUUGUCUGGCCCAACAUGUCAAGA
.....((((...........(.((((((....)))))))(((..(((((....-)))))..))).))))......... ( -19.70)
>sp_pn.0 855158 78 + 2038615
UCAUAUAAAAGUUGAGAAAAGCAGAAGUGAGAGCUUCUCGCCUUGUGACAUUAAGUUGCCUGGCCCUACGGAUGAAAA
((((......(((......)))((((((....)))))).(((..(..((.....))..)..))).......))))... ( -19.40)
>consensus
UACUAUUUAAAAUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAAAGUUGUCUGGCCCAACAUGUCAAAA
...........(((......(.((((((....)))))))(((..(((((.....)))))..)))....)))....... (-17.33 = -16.73 +  -0.60)

alignment

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secondary structure

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dotplot

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Window 2

Location 660,473 – 660,551
Length 78
Sequences 3
Columns 78
Reading direction forward
Mean pairwise identity 78.63
Mean single sequence MFE -19.10
Consensus MFE -17.33
Energy contribution -16.73
Covariance contribution -0.60
Combinations/Pair 1.33
Mean z-score -1.30
Structure conservation index 0.91
SVM decision value 1.54
SVM RNA-class probability 0.962234
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 660473 78 + 2030921/0-78
UUCUAUUUUAAGUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAAAGUUGUCUGGCCCAACAUGUUAAAG
......((((((((......(.((((((....)))))))(((..(((((.....)))))..)))....))).))))). ( -18.20)
>sp_ag.0 766044 77 - 2160267/0-78
UACUAGUUGCAAUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAG-GUUGUCUGGCCCAACAUGUCAAGA
.....((((...........(.((((((....)))))))(((..(((((....-)))))..))).))))......... ( -19.70)
>sp_pn.0 855158 78 + 2038615/0-78
UCAUAUAAAAGUUGAGAAAAGCAGAAGUGAGAGCUUCUCGCCUUGUGACAUUAAGUUGCCUGGCCCUACGGAUGAAAA
((((......(((......)))((((((....)))))).(((..(..((.....))..)..))).......))))... ( -19.40)
>consensus
UACUAUUUAAAAUGAGAAAAGCAGAAGUGAGAACUUCUCGCCUUGCGACUUAAAGUUGUCUGGCCCAACAUGUCAAAA
...........(((......(.((((((....)))))))(((..(((((.....)))))..)))....)))....... (-17.33 = -16.73 +  -0.60)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:02:03 2006