Locus 133

Sequence ID sp_mu.0
Location 935,475 – 935,574
Length 99
Max. P 0.990460
window832 window833 window834 window835

overview

Window 2

Location 935,475 – 935,574
Length 99
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 76.36
Mean single sequence MFE -30.97
Consensus MFE -24.81
Energy contribution -23.43
Covariance contribution -1.38
Combinations/Pair 1.32
Mean z-score -1.92
Structure conservation index 0.80
SVM decision value 2.21
SVM RNA-class probability 0.990460
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 935475 99 + 2030921
AAACUAUGCGAUGAGUCGAU-UGUGGUUUAU--ACCACAUACG--C-UAAGGAGAUCAUAA-UGCAGGAGCAGAUCUUGGCAAGUUGUGUGAACCUGCUUGCCACA
.............((.((..-((((((....--))))))..))--)-)...((((((....-(((....)))))))))(((((((.(.(....)).)))))))... ( -29.20)
>sp_ag.0 1096970 101 - 2160267
CUGUUAUGCGAUGAGUCGAUAUGUGGUUU-U--ACCACUAUUG--CGCAGGGAGAUUAUAAACGCAGGAGCGGAUCUUGAUAAGUUGUGUGAACCUUCUUGUCACA
..............(.(((((.((((...-.--.)))))))))--)((((((((.((((((((.(((((.....)))))....))).)))))..)))))))).... ( -24.40)
>sp_pn.0 905032 105 + 2038615
AGAAUAUGCGAUGAGUCGAUAGGUAGUCUUCGGACUACUAUUGAGCAUAAGGAGGUCAUAA-CGCAGGAGCGGACCUUGAUGAGUUGUGUGAACCUGCUCAUCACA
....(((((......(((((((.(((((....)))))))))))))))))..((((((....-(((....)))))))))(((((((.(.(....)).)))))))... ( -39.30)
>consensus
AAAAUAUGCGAUGAGUCGAUAUGUGGUUU_U__ACCACUAUUG__C_UAAGGAGAUCAUAA_CGCAGGAGCGGAUCUUGAUAAGUUGUGUGAACCUGCUUGUCACA
........(((....)))....(((((......))))).............((((((.....(((....)))))))))((((((..(.(....))..))))))... (-24.81 = -23.43 +  -1.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 935,475 – 935,574
Length 99
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 76.36
Mean single sequence MFE -24.47
Consensus MFE -20.27
Energy contribution -18.50
Covariance contribution -1.77
Combinations/Pair 1.29
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 2.09
SVM RNA-class probability 0.987692
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 935475 99 + 2030921
UGUGGCAAGCAGGUUCACACAACUUGCCAAGAUCUGCUCCUGCA-UUAUGAUCUCCUUA-G--CGUAUGUGGU--AUAAACCACA-AUCGACUCAUCGCAUAGUUU
((((((..(((((((.....)))))))..((((((((....)))-....))))).....-)--)...((((((--....))))))-..........))))...... ( -25.20)
>sp_ag.0 1096970 101 - 2160267
UGUGACAAGAAGGUUCACACAACUUAUCAAGAUCCGCUCCUGCGUUUAUAAUCUCCCUGCG--CAAUAGUGGU--A-AAACCACAUAUCGACUCAUCGCAUAACAG
(((((..((.(((((.....)))))........(((((..(((((.............)))--))..))))).--.-..............))..)))))...... ( -18.42)
>sp_pn.0 905032 105 + 2038615
UGUGAUGAGCAGGUUCACACAACUCAUCAAGGUCCGCUCCUGCG-UUAUGACCUCCUUAUGCUCAAUAGUAGUCCGAAGACUACCUAUCGACUCAUCGCAUAUUCU
(((((((((..(((...............((((((((....)))-....)))))..............((((((....))))))..)))..)))))))))...... ( -29.80)
>consensus
UGUGACAAGCAGGUUCACACAACUUAUCAAGAUCCGCUCCUGCG_UUAUGAUCUCCUUA_G__CAAUAGUGGU__A_AAACCACAUAUCGACUCAUCGCAUAAUAU
..(((((((..(.......)..)))))))((((((((....))).....)))))..............(((((......)))))...................... (-20.27 = -18.50 +  -1.77) 
# Strand winner: forward (1.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 935,475 – 935,574
Length 99
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 76.36
Mean single sequence MFE -30.97
Consensus MFE -24.81
Energy contribution -23.43
Covariance contribution -1.38
Combinations/Pair 1.32
Mean z-score -1.92
Structure conservation index 0.80
SVM decision value 2.21
SVM RNA-class probability 0.990460
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 935475 99 + 2030921/0-106
AAACUAUGCGAUGAGUCGAU-UGUGGUUUAU--ACCACAUACG--C-UAAGGAGAUCAUAA-UGCAGGAGCAGAUCUUGGCAAGUUGUGUGAACCUGCUUGCCACA
.............((.((..-((((((....--))))))..))--)-)...((((((....-(((....)))))))))(((((((.(.(....)).)))))))... ( -29.20)
>sp_ag.0 1096970 101 - 2160267/0-106
CUGUUAUGCGAUGAGUCGAUAUGUGGUUU-U--ACCACUAUUG--CGCAGGGAGAUUAUAAACGCAGGAGCGGAUCUUGAUAAGUUGUGUGAACCUUCUUGUCACA
..............(.(((((.((((...-.--.)))))))))--)((((((((.((((((((.(((((.....)))))....))).)))))..)))))))).... ( -24.40)
>sp_pn.0 905032 105 + 2038615/0-106
AGAAUAUGCGAUGAGUCGAUAGGUAGUCUUCGGACUACUAUUGAGCAUAAGGAGGUCAUAA-CGCAGGAGCGGACCUUGAUGAGUUGUGUGAACCUGCUCAUCACA
....(((((......(((((((.(((((....)))))))))))))))))..((((((....-(((....)))))))))(((((((.(.(....)).)))))))... ( -39.30)
>consensus
AAAAUAUGCGAUGAGUCGAUAUGUGGUUU_U__ACCACUAUUG__C_UAAGGAGAUCAUAA_CGCAGGAGCGGAUCUUGAUAAGUUGUGUGAACCUGCUUGUCACA
........(((....)))....(((((......))))).............((((((.....(((....)))))))))((((((..(.(....))..))))))... (-24.81 = -23.43 +  -1.38)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 935,475 – 935,574
Length 99
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 76.36
Mean single sequence MFE -24.47
Consensus MFE -20.27
Energy contribution -18.50
Covariance contribution -1.77
Combinations/Pair 1.29
Mean z-score -1.80
Structure conservation index 0.83
SVM decision value 2.09
SVM RNA-class probability 0.987692
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 935475 99 + 2030921/0-106
UGUGGCAAGCAGGUUCACACAACUUGCCAAGAUCUGCUCCUGCA-UUAUGAUCUCCUUA-G--CGUAUGUGGU--AUAAACCACA-AUCGACUCAUCGCAUAGUUU
((((((..(((((((.....)))))))..((((((((....)))-....))))).....-)--)...((((((--....))))))-..........))))...... ( -25.20)
>sp_ag.0 1096970 101 - 2160267/0-106
UGUGACAAGAAGGUUCACACAACUUAUCAAGAUCCGCUCCUGCGUUUAUAAUCUCCCUGCG--CAAUAGUGGU--A-AAACCACAUAUCGACUCAUCGCAUAACAG
(((((..((.(((((.....)))))........(((((..(((((.............)))--))..))))).--.-..............))..)))))...... ( -18.42)
>sp_pn.0 905032 105 + 2038615/0-106
UGUGAUGAGCAGGUUCACACAACUCAUCAAGGUCCGCUCCUGCG-UUAUGACCUCCUUAUGCUCAAUAGUAGUCCGAAGACUACCUAUCGACUCAUCGCAUAUUCU
(((((((((..(((...............((((((((....)))-....)))))..............((((((....))))))..)))..)))))))))...... ( -29.80)
>consensus
UGUGACAAGCAGGUUCACACAACUUAUCAAGAUCCGCUCCUGCG_UUAUGAUCUCCUUA_G__CAAUAGUGGU__A_AAACCACAUAUCGACUCAUCGCAUAAUAU
..(((((((..(.......)..)))))))((((((((....))).....)))))..............(((((......)))))...................... (-20.27 = -18.50 +  -1.77) 
# 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 19:02:13 2006