Locus 123

Sequence ID sp_mu.0
Location 145,538 – 1,146,731
Length 1001193
Max. P 0.999778
window795 window796 window797 window798 window799 window800

overview

Window 5

Location 1,146,657 – 1,146,731
Length 74
Sequences 3
Columns 74
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -15.70
Consensus MFE -15.07
Energy contribution -13.30
Covariance contribution -1.77
Combinations/Pair 1.31
Mean z-score -1.40
Structure conservation index 0.96
SVM decision value 2.17
SVM RNA-class probability 0.989615
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1146657 74 + 2030921
GAAAUCUGACGAAGAUGCUUCAGCAUCUAGGAAGAUUUAUCUUUUUUCCUAGGAAUUUAGUCCCGUGUUCAAUU
(((....(((...(((((....)))))((((((((........))))))))........))).....))).... ( -18.70)
>sp_ag.0 2100870 74 - 2160267
GAAAUCUGACGAAGAUGCUUUAGCAUCUAGGAAGAUUUAUCUUUUUCACUAGAAAAUUAGUCCCGUGUUCAGUU
.((((((..(..((((((....)))))).)..))))))....(((((....))))).................. ( -15.60)
>sp_pn.0 202492 73 + 2038615
GAAACUUGACGAAGAAACUAAAGUUUCUAGGAAAGUUUAUCUUUUUCACACAGAGUUUAG-CCCGGGUUCAAUU
.((((((..(..((((((....)))))).)..))))))...............((((.((-(....))).)))) ( -12.80)
>consensus
GAAAUCUGACGAAGAUGCUUAAGCAUCUAGGAAGAUUUAUCUUUUUCACUAGGAAUUUAGUCCCGUGUUCAAUU
.((((((..(..((((((....)))))).)..)))))).................................... (-15.07 = -13.30 +  -1.77)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,146,657 – 1,146,731
Length 74
Sequences 3
Columns 74
Reading direction reverse
Mean pairwise identity 80.63
Mean single sequence MFE -13.57
Consensus MFE -11.88
Energy contribution -10.00
Covariance contribution -1.88
Combinations/Pair 1.35
Mean z-score -1.16
Structure conservation index 0.88
SVM decision value 0.47
SVM RNA-class probability 0.749167
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1146657 74 + 2030921
AAUUGAACACGGGACUAAAUUCCUAGGAAAAAAGAUAAAUCUUCCUAGAUGCUGAAGCAUCUUCGUCAGAUUUC
..((((....((((......))))(((((............)))))((((((....))))))...))))..... ( -14.20)
>sp_ag.0 2100870 74 - 2160267
AACUGAACACGGGACUAAUUUUCUAGUGAAAAAGAUAAAUCUUCCUAGAUGCUAAAGCAUCUUCGUCAGAUUUC
..((((....((((....(((((....)))))(((....)))))))((((((....))))))...))))..... ( -16.20)
>sp_pn.0 202492 73 + 2038615
AAUUGAACCCGGG-CUAAACUCUGUGUGAAAAAGAUAAACUUUCCUAGAAACUUUAGUUUCUUCGUCAAGUUUC
..((..((.((((-......)))).))..)).....((((((..(.((((((....))))))..)..)))))). ( -10.30)
>consensus
AAUUGAACACGGGACUAAAUUCCUAGUGAAAAAGAUAAAUCUUCCUAGAUGCUAAAGCAUCUUCGUCAGAUUUC
..........((((.....)))).............((((((..(.((((((....))))))..)..)))))). (-11.88 = -10.00 +  -1.88) 
# Strand winner: forward (0.99)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,146,657 – 1,146,731
Length 74
Sequences 3
Columns 74
Reading direction forward
Mean pairwise identity 80.63
Mean single sequence MFE -15.70
Consensus MFE -15.07
Energy contribution -13.30
Covariance contribution -1.77
Combinations/Pair 1.31
Mean z-score -1.40
Structure conservation index 0.96
SVM decision value 2.17
SVM RNA-class probability 0.989615
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1146657 74 + 2030921/0-74
GAAAUCUGACGAAGAUGCUUCAGCAUCUAGGAAGAUUUAUCUUUUUUCCUAGGAAUUUAGUCCCGUGUUCAAUU
(((....(((...(((((....)))))((((((((........))))))))........))).....))).... ( -18.70)
>sp_ag.0 2100870 74 - 2160267/0-74
GAAAUCUGACGAAGAUGCUUUAGCAUCUAGGAAGAUUUAUCUUUUUCACUAGAAAAUUAGUCCCGUGUUCAGUU
.((((((..(..((((((....)))))).)..))))))....(((((....))))).................. ( -15.60)
>sp_pn.0 202492 73 + 2038615/0-74
GAAACUUGACGAAGAAACUAAAGUUUCUAGGAAAGUUUAUCUUUUUCACACAGAGUUUAG-CCCGGGUUCAAUU
.((((((..(..((((((....)))))).)..))))))...............((((.((-(....))).)))) ( -12.80)
>consensus
GAAAUCUGACGAAGAUGCUUAAGCAUCUAGGAAGAUUUAUCUUUUUCACUAGGAAUUUAGUCCCGUGUUCAAUU
.((((((..(..((((((....)))))).)..)))))).................................... (-15.07 = -13.30 +  -1.77)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,146,657 – 1,146,731
Length 74
Sequences 3
Columns 74
Reading direction reverse
Mean pairwise identity 80.63
Mean single sequence MFE -13.57
Consensus MFE -11.88
Energy contribution -10.00
Covariance contribution -1.88
Combinations/Pair 1.35
Mean z-score -1.16
Structure conservation index 0.88
SVM decision value 0.47
SVM RNA-class probability 0.749167
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 1146657 74 + 2030921/0-74
AAUUGAACACGGGACUAAAUUCCUAGGAAAAAAGAUAAAUCUUCCUAGAUGCUGAAGCAUCUUCGUCAGAUUUC
..((((....((((......))))(((((............)))))((((((....))))))...))))..... ( -14.20)
>sp_ag.0 2100870 74 - 2160267/0-74
AACUGAACACGGGACUAAUUUUCUAGUGAAAAAGAUAAAUCUUCCUAGAUGCUAAAGCAUCUUCGUCAGAUUUC
..((((....((((....(((((....)))))(((....)))))))((((((....))))))...))))..... ( -16.20)
>sp_pn.0 202492 73 + 2038615/0-74
AAUUGAACCCGGG-CUAAACUCUGUGUGAAAAAGAUAAACUUUCCUAGAAACUUUAGUUUCUUCGUCAAGUUUC
..((..((.((((-......)))).))..)).....((((((..(.((((((....))))))..)..)))))). ( -10.30)
>consensus
AAUUGAACACGGGACUAAAUUCCUAGUGAAAAAGAUAAAUCUUCCUAGAUGCUAAAGCAUCUUCGUCAGAUUUC
..........((((.....)))).............((((((..(.((((((....))))))..)..)))))). (-11.88 = -10.00 +  -1.88) 
# Strand winner: forward (0.99)

alignment

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secondary structure

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dotplot

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Window 9

Location 145,538 – 145,612
Length 74
Sequences 3
Columns 75
Reading direction forward
Mean pairwise identity 79.46
Mean single sequence MFE -23.43
Consensus MFE -23.93
Energy contribution -20.83
Covariance contribution -3.10
Combinations/Pair 1.53
Mean z-score -3.11
Structure conservation index 1.02
SVM decision value 4.06
SVM RNA-class probability 0.999778
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 145538 74 - 2030921
UUAGUAUAGGCGAGUUUUUAUAGGGAACA-CCUUUUCCCCUAUAAAGGCGCUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((....-.......))))))))))))....))....)))............. ( -19.10)
>sp_ag.0 85398 74 + 2160267
AUCGUAUAGGCGAGUCUUUGCGGGGAGUA-CCUUUUCCCUCGUAAAGGCGUUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((((..-....))))).)))))))))....))....)))............. ( -25.10)
>sp_pn.0 205074 75 + 2038615
AUCGUAUAGGCGAGUUGAUGGGGGAGACAACCUUUUCUCCCUUAUCGGCGCUAGCAUUUUACAAAAGAGGAGAAA
...(((...((..((((((((((((((........))))))))))))))....))....)))............. ( -26.10)
>consensus
AUCGUAUAGGCGAGUUUUUGCGGGGAACA_CCUUUUCCCCCAUAAAGGCGCUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((............))))))))))))....))....)))............. (-23.93 = -20.83 +  -3.10)

alignment

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secondary structure

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dotplot

Postscript

Window 0

Location 145,538 – 145,612
Length 74
Sequences 3
Columns 75
Reading direction forward
Mean pairwise identity 79.46
Mean single sequence MFE -23.43
Consensus MFE -23.93
Energy contribution -20.83
Covariance contribution -3.10
Combinations/Pair 1.53
Mean z-score -3.11
Structure conservation index 1.02
SVM decision value 4.06
SVM RNA-class probability 0.999778
Prediction RNA

Download alignment: ClustalW | MAF

>sp_mu.0 145538 74 - 2030921/0-75
UUAGUAUAGGCGAGUUUUUAUAGGGAACA-CCUUUUCCCCUAUAAAGGCGCUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((....-.......))))))))))))....))....)))............. ( -19.10)
>sp_ag.0 85398 74 + 2160267/0-75
AUCGUAUAGGCGAGUCUUUGCGGGGAGUA-CCUUUUCCCUCGUAAAGGCGUUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((((..-....))))).)))))))))....))....)))............. ( -25.10)
>sp_pn.0 205074 75 + 2038615/0-75
AUCGUAUAGGCGAGUUGAUGGGGGAGACAACCUUUUCUCCCUUAUCGGCGCUAGCAUUUUACAAAAGAGGAGAAA
...(((...((..((((((((((((((........))))))))))))))....))....)))............. ( -26.10)
>consensus
AUCGUAUAGGCGAGUUUUUGCGGGGAACA_CCUUUUCCCCCAUAAAGGCGCUAGCAUUUUACAAAUAAGGAGAAA
...(((...((..((((((((((((............))))))))))))....))....)))............. (-23.93 = -20.83 +  -3.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 19:01:45 2006