Locus 3

Sequence ID pao.3275
Location 6,183,694 – 6,183,783
Length 89
Max. P 0.978755
window8 window9

overview

Window 8

Location 6,183,694 – 6,183,783
Length 89
Sequences 4
Columns 89
Reading direction forward
Mean pairwise identity 43.32
Mean single sequence MFE -21.10
Consensus MFE -4.19
Energy contribution -6.25
Covariance contribution 2.06
Combinations/Pair 1.23
Mean z-score -1.54
Structure conservation index 0.20
SVM decision value 0.05
SVM RNA-class probability 0.560546
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.3275 6183694 89 + 6264404
GCGCGCCGCGAAAAACUUUUCCACGGCACCCUCCCCGGGCCCUCCGGACCUGGUCGCAAGGCCCGCCAUACGGGCCUCGCAACCGUUCA
(.((((((.((((....))))..)))).......((((.....))))....(((.((.(((((((.....))))))).)).))))).). ( -35.60)
>pau.3414 6456605 87 + 6537648
GCGCGCCGCGAAAAACUUUUCCACGGCACCCUCCCCGGGCACUCCGGACCUGCUCGCAAGGCCCGCCAUACGGGCCUCGCAACCGUU--
(.((((((.((((....))))..)))).......((((.....))))....)).)((.(((((((.....))))))).)).......-- ( -33.60)
>pfo.30 60939 52 + 6438405
AUUCUUUUCAAAAAACUUUGG-A----AUAAGCUCAAGAACAAUCCGACCUAAGCCC--------------------------------
.....(((((((....)))))-)----).............................-------------------------------- (  -2.80)
>pf5.51 6993214 53 - 7074893
GCCGGUUGCAAAAACUAUUGGCA----AUAAUCGAUGAAAUUUUCGGUGCUAAUAGC--------------------------------
((.....)).....(((((((((----....((((........))))))))))))).-------------------------------- ( -12.40)
>consensus
GCGCGCCGCAAAAAACUUUGCCA____ACAAUCCCCGGAACCUCCGGACCUAAUCGC________________________________
..................................((((.....))))........((.(((((((.....))))))).))......... ( -4.19 =  -6.25 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 6,183,694 – 6,183,783
Length 89
Sequences 4
Columns 89
Reading direction reverse
Mean pairwise identity 43.32
Mean single sequence MFE -30.12
Consensus MFE -9.91
Energy contribution -15.97
Covariance contribution 6.06
Combinations/Pair 1.19
Mean z-score -2.37
Structure conservation index 0.33
SVM decision value 1.82
SVM RNA-class probability 0.978755
Prediction RNA
WARNING Mean pairwise identity too low.

Download alignment: ClustalW | MAF

>pao.3275 6183694 89 - 6264404
UGAACGGUUGCGAGGCCCGUAUGGCGGGCCUUGCGACCAGGUCCGGAGGGCCCGGGGAGGGUGCCGUGGAAAAGUUUUUCGCGGCGCGC
.....((((((((((((((.....))))))))))))))...(((((.....)))))..(.(((((((((((.....))))))))))).) ( -54.80)
>pau.3414 6456605 87 - 6537648
--AACGGUUGCGAGGCCCGUAUGGCGGGCCUUGCGAGCAGGUCCGGAGUGCCCGGGGAGGGUGCCGUGGAAAAGUUUUUCGCGGCGCGC
--...(.((((((((((((.....)))))))))))).)...(((((.....)))))..(.(((((((((((.....))))))))))).) ( -50.30)
>pfo.30 60939 52 - 6438405
--------------------------------GGGCUUAGGUCGGAUUGUUCUUGAGCUUAU----U-CCAAAGUUUUUUGAAAAGAAU
--------------------------------(((((((((..........)))))))))..----.-........((((....)))). (  -8.70)
>pf5.51 6993214 53 + 7074893
--------------------------------GCUAUUAGCACCGAAAAUUUCAUCGAUUAU----UGCCAAUAGUUUUUGCAACCGGC
--------------------------------((((((.(((.(((........))).....----))).))))))............. (  -6.70)
>consensus
________________________________GCGAUCAGGUCCGAAGGGCCCGGGGAGGAU____UGCAAAAGUUUUUCGCAACGCGC
.........((((((((((.....)))))))))).......(((((.....)))))....(((((((((((.....))))))))))).. ( -9.91 = -15.97 +   6.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Thu Jan 18 21:03:22 2007