Locus 1583

Sequence ID 2R_DroMel_CAF1
Location 5,942,565 – 5,942,756
Length 191
Max. P 0.963965
window2653 window2654

overview

Window 3

Location 5,942,565 – 5,942,682
Length 117
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 96.58
Mean single sequence MFE -42.88
Consensus MFE -40.72
Energy contribution -40.60
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.95
SVM decision value 1.49
SVM RNA-class probability 0.958646
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5942565 117 - 20766785
GUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAGCUUCCGUUUCAGAUGCAUUCAAUGGGGGACUAGGGUGAUCGGGAUGGGGUUGGUCGUGAGAGGACGCGGGGACGGGC
........(.((((....)))).).(((..(((((((((.(.(((((..(.(((.(((((..(((....))))))))))))..)))))...).)))))))))..)))(....).... ( -41.60)
>DroSec_CAF1 84649 117 - 1
GUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAGCCUCCGUUUCAGAUGCAUUCAAUGGGGGACUCGGGUGAUCGGGAUGGGGUUGGUCGUGAGAGGACGCGGGGACGGGG
.....(.((.((((....)))).)).)...(((((((((.(((((((..(.(((.(((((...((....)).)))))))))..))))))..).)))))))))..(.((....)).). ( -42.60)
>DroSim_CAF1 82509 117 - 1
GUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAGCCUCCGUUUCAGAUGCAUUCAAUGGGGGACUCGGGUGAUCGGGAUGGGGUUGGUCGUGAGAGGACGCGGGGACGGGG
.....(.((.((((....)))).)).)...(((((((((.(((((((..(.(((.(((((...((....)).)))))))))..))))))..).)))))))))..(.((....)).). ( -42.60)
>DroYak_CAF1 87400 117 - 1
GUAGGAGUGGGUGAGUGAUCAUGUGGUGAGUUCUCGCGAGCCUCCGUUUCAGAUGCAUUCAAUGGGGGACUCGAGUGAUCGGGAUGGGGUUGGUCGUGAGAUGGCGCGGGGGCGGGG
.....(.((.((((....)))).)).)..(((((((((((((.((((..(.(((.(((((...((....)).)))))))))..)))))))).(((....)))..))))))))).... ( -44.70)
>consensus
GUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAGCCUCCGUUUCAGAUGCAUUCAAUGGGGGACUCGGGUGAUCGGGAUGGGGUUGGUCGUGAGAGGACGCGGGGACGGGG
.....(.((.((((....)))).)).)...(((((((((.(((((((..(.(((.(((((...((....)).)))))))))..))))))..).)))))))))..(.((....)).). (-40.72 = -40.60 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,942,642 – 5,942,756
Length 114
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 91.28
Mean single sequence MFE -48.73
Consensus MFE -48.54
Energy contribution -48.10
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 1.00
SVM decision value 1.56
SVM RNA-class probability 0.963965
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5942642 114 - 20766785
GCUGC---UGCUGCUCCCGCUCGUCCCGCUGCGGUGCCGUCGAUGAAGUCGUGGGUGGCGGUGCAGUCUGGUGGAAAGUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAG
.(..(---(.(((((.(((((.(....((((((.((((..(.(((....))).)..)))).))))))).)))))..))))).))..)(((((...((((...))))...)))))... ( -48.20)
>DroSec_CAF1 84726 112 - 1
-----UGUUGCUGCUCCCGCUCGUCCCGCUGCGGUGCCGUCGAUGAAGUCGUGGGUGGCGGUGCGGUCUGGUGGAAAGUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAG
-----.....(..((((..((..((((((((((.((((..(.(((....))).)..)))).))))))..)).))..))..))))..)(((((...((((...))))...)))))... ( -47.40)
>DroYak_CAF1 87477 108 - 1
G---------CUGCUCCCGCUCUUCCCGCUGCAGUGCCGUCGAUGAGGUCGUGGGUGGCGGUGCAGUCUGGUGGAAAGUAGGAGUGGGUGAGUGAUCAUGUGGUGAGUUCUCGCGAG
.---------(..((((..((.(((((((((((.((((..(.(((....))).)..)))).))))))..)).))).))..))))..)(((((...((((...))))...)))))... ( -50.60)
>consensus
G_______UGCUGCUCCCGCUCGUCCCGCUGCGGUGCCGUCGAUGAAGUCGUGGGUGGCGGUGCAGUCUGGUGGAAAGUAGGAGUGGGUGAGUGAUCAUGUGGUGAAUUCUCGCGAG
..........(..((((..((..((((((((((.((((..(.(((....))).)..)))).))))))..)).))..))..))))..)(((((...((((...))))...)))))... (-48.54 = -48.10 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:06 2006