Locus 136

Sequence ID sp_pn.0
Location 1,318,576 – 1,318,686
Length 110
Max. P 0.979466
window842 window843

overview

Window 2

Location 1,318,576 – 1,318,681
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 56.66
Mean single sequence MFE -25.87
Consensus MFE -15.45
Energy contribution -11.70
Covariance contribution -3.75
Combinations/Pair 1.80
Mean z-score -1.18
Structure conservation index 0.60
SVM decision value 1.33
SVM RNA-class probability 0.942675
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1318576 105 + 2038615/40-160
AGGAAAGAAAGUCUUAUGGC-GUUCUUCAAGCGAGCUUGGGAUAGUGGGAGCCAAGUAGGGCAAAAUAAAGGGCUGGCGCUUUCU--------GUAGUAUUUUCAAAAAC------AAUG
.((((((((.(((....)))-.)))..((((....))))(((.((((..((((...((........))...))))..)))).)))--------......)))))......------.... ( -23.00)
>sp_mu.0 1616400 119 - 2030921/40-160
AAGAAAGAGAGUUUUGUGGC-GUUUCUGCAGCGAACCUGAGAGAGUGUAAGUCAGGUGAAACAAAAUAAAGGACUGGCACUUUCUCUUGGCUAAUAGCCAAGCUAACAAUCAGAUAAAUG
..((.((((((((....)))-.)))))..(((......((((((((((.((((..((........))....)))).))))))))))(((((.....)))))))).....))......... ( -32.80)
>sp_ag.0 1886578 110 - 2160267/40-160
AAGAAGAGGUGUUCAUCAGCUGUUUUUUUAGCGAGCUCAAGGUAGUGAAAGUUGGGUAGAAUAGGAUGAA-UAUUGGCACUUUUUAGUGAGUAAAAGUACAAUCAAA---------AAUG
.....((((((((((((.((((......))))..((((((..(.....)..)))))).......))))))-))))..((((....)))).............))...---------.... ( -21.80)
>consensus
AAGAAAGAGAGUUUUAUGGC_GUUUUUCAAGCGAGCUUGAGAUAGUGAAAGUCAGGUAGAACAAAAUAAAGGACUGGCACUUUCU__UG__UAAUAGUAAAAUCAAAAA_______AAUG
.((((((..((((((.((...(((((........((((((...........)))))))))))....)).))))))....))))))................................... (-15.45 = -11.70 +  -3.75) 
# Strand winner: reverse (0.98)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 1,318,576 – 1,318,686
Length 110
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 60.89
Mean single sequence MFE -30.80
Consensus MFE -15.45
Energy contribution -11.70
Covariance contribution -3.75
Combinations/Pair 1.80
Mean z-score -1.88
Structure conservation index 0.50
SVM decision value 1.84
SVM RNA-class probability 0.979466
Prediction RNA

Download alignment: ClustalW | MAF

>sp_pn.0 1318576 110 + 2038615/61-181
UUUUUGAUAUAAUAG-UCAGCAGGAAAGAAAGUCUUAUGGC-GUUCUUCAAGCGAGCUUGGGAUAGUGGGAGCCAAGUAGGGCAAAAUAAAGGGCUGGCGCUUUCU--------GUAGUA
....((((......)-)))((..(((.(((.(((....)))-.))))))..))..(((..(((.((((..((((...((........))...))))..)))).)))--------..))). ( -26.50)
>sp_mu.0 1616400 118 - 2030921/61-181
UUUUUGCUAUAAUCU-UUGUUAAGAAAGAGAGUUUUGUGGC-GUUUCUGCAGCGAACCUGAGAGAGUGUAAGUCAGGUGAAACAAAAUAAAGGACUGGCACUUUCUCUUGGCUAAUAGCC
.....(((((..(((-((........)))))..(((((.((-(....))).)))))((.((((((((((.((((..((........))....)))).))))))))))..))...))))). ( -33.10)
>sp_ag.0 1886578 119 - 2160267/61-181
UUUUUGUUAUACUGUCUCAGUAAGAAGAGGUGUUCAUCAGCUGUUUUUUUAGCGAGCUCAAGGUAGUGAAAGUUGGGUAGAAUAGGAUGAA-UAUUGGCACUUUUUAGUGAGUAAAAGUA
.........((((..((((.(((((((.((((((((((.((((......))))..((((((..(.....)..)))))).......))))))-))))....))))))).))))....)))) ( -32.80)
>consensus
UUUUUGAUAUAAUAU_UCAGUAAGAAAGAGAGUUUUAUGGC_GUUUUUCAAGCGAGCUUGAGAUAGUGAAAGUCAGGUAGAACAAAAUAAAGGACUGGCACUUUCU__UG__UAAUAGUA
......................((((((..((((((.((...(((((........((((((...........)))))))))))....)).))))))....)))))).............. (-15.45 = -11.70 +  -3.75) 
# Strand winner: reverse (1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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