Locus 214

Sequence ID 3R_DroMel_CAF1
Location 880,445 – 880,596
Length 151
Max. P 0.886398
window381 window382

overview

Window 1

Location 880,445 – 880,565
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.93
Mean single sequence MFE -47.90
Consensus MFE -39.41
Energy contribution -40.23
Covariance contribution 0.81
Combinations/Pair 1.08
Mean z-score -1.95
Structure conservation index 0.82
SVM decision value 0.94
SVM RNA-class probability 0.886398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 880445 120 + 27905053
GGUCGGGGCAGCACGAACACGUGACUCGGAUUCCUCCGACGAGGCGGUUUUUAUUUUCACUCGUUGGAGGCUUUGGAACACUACUCUGAGGUGACCUCCGCCUCCAGGUUCCUCCGGCCA
((((((((.(((........(((..((.((..(((((((((((..((.........)).)))))))))))..)).)).)))....((((((((.....))))).)))))).)))))))). ( -52.00)
>DroSec_CAF1 48466 119 + 1
GGUCGGGGCAGCAUGAACACGUGACUCGGAUUCCUCCGACCAGGCGGUUUUUAUUUUCGCUCGUUGGAGGCU-UGGAACGCUACUCGGAGGUGACCUCCGCCUCCAGGUUCCUCCGGCCA
((((((((.(((........(((..((.((..((((((((..(((((.........))))).)))))))).)-).)).)))..((.(((((((.....)))))))))))).)))))))). ( -51.70)
>DroSim_CAF1 47677 119 + 1
GGUCGGGGCAGCACGAACACGUGACUCGGAUUCCUCCGACCAGGCGGUUUUUAUUUUCACUCGUUGGAGGCU-UGGAACGCUACUCGGAGGUGACCUCCGCCUCCAGGUUCCUCCGGCCA
((((((((.(((........(((..(((((....)))))((((((((.........)).(((....))))))-)))..)))..((.(((((((.....)))))))))))).)))))))). ( -48.90)
>DroEre_CAF1 47457 106 + 1
GGUCGGGGCAGCAU-------------GGAUUUCUCCUGCUAGGCGC-UUUUAUUUUCACUCGUUGGAGGCUUUGAGACGUUGCUGGGAGCUGACCUCCGCCUCCAGGUUCCUCCGGCCA
((((((((.((((.-------------(((....)))))))......-...............((((((((....((......)).((((.....))))))))))))....)))))))). ( -39.00)
>consensus
GGUCGGGGCAGCACGAACACGUGACUCGGAUUCCUCCGACCAGGCGGUUUUUAUUUUCACUCGUUGGAGGCU_UGGAACGCUACUCGGAGGUGACCUCCGCCUCCAGGUUCCUCCGGCCA
((((((((.(((........((((...(((..((.((.....)).))..)))....))))...((((((((..(((....)))...((((.....))))))))))))))).)))))))). (-39.41 = -40.23 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 880,485 – 880,596
Length 111
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.87
Mean single sequence MFE -42.17
Consensus MFE -36.65
Energy contribution -37.65
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.87
SVM decision value 0.17
SVM RNA-class probability 0.619237
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 880485 111 - 27905053
---------UGGGCUUCCAAGGCCAGAGUGUGGCAACAAUUGGCCGGAGGAACCUGGAGGCGGAGGUCACCUCAGAGUAGUGUUCCAAAGCCUCCAACGAGUGAAAAUAAAAACCGCCUC
---------.((((((((..((((((....((....)).))))))...))))..(((((((...((.(((.........)))..))...)))))))...................)))). ( -38.60)
>DroSec_CAF1 48506 119 - 1
CCCAUUGUGUGGGCUUCCAAGGCCAGAGUGUGGCAACAAUUGGCCGGAGGAACCUGGAGGCGGAGGUCACCUCCGAGUAGCGUUCCA-AGCCUCCAACGAGCGAAAAUAAAAACCGCCUG
(((((...)))))(((((..((((((....((....)).)))))))))))....((((((((((((...)))))(((.....)))..-.)))))))....(((...........)))... ( -44.00)
>DroSim_CAF1 47717 119 - 1
CCCAUUGUGGGGGCUUCCAAGGCCAGAGUGUGGCAACAAUUGGCCGGAGGAACCUGGAGGCGGAGGUCACCUCCGAGUAGCGUUCCA-AGCCUCCAACGAGUGAAAAUAAAAACCGCCUG
..((((.(((((((((((..((((((....((....)).)))))))))((((((((....((((((...))))))..))).))))).-))))))))...))))................. ( -48.00)
>DroEre_CAF1 47484 119 - 1
CCCGUUGUGUGGGCUUCCAAGGCCAGAGUGAGGCAGCAAUUGGCCGGAGGAACCUGGAGGCGGAGGUCAGCUCCCAGCAACGUCUCAAAGCCUCCAACGAGUGAAAAUAAAA-GCGCCUA
......(((((((.((((..((((((..((......)).))))))...)))))))((((((.((((...((.....))....))))...)))))).................-))))... ( -38.10)
>consensus
CCCAUUGUGUGGGCUUCCAAGGCCAGAGUGUGGCAACAAUUGGCCGGAGGAACCUGGAGGCGGAGGUCACCUCCGAGUAGCGUUCCA_AGCCUCCAACGAGUGAAAAUAAAAACCGCCUG
..........((((((((..((((((..(((....))).))))))...))))..(((((((((((.....))))(((.....)))....)))))))...................)))). (-36.65 = -37.65 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:45 2006