Locus 2728

Sequence ID	2R_DroMel_CAF1
Location	9,557,311 – 9,557,401
Length	90
Max. P	0.990311

overview

Window 1

Location	9,557,311 – 9,557,401
Length	90
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	81.46
Mean single sequence MFE	-33.62
Consensus MFE	-26.38
Energy contribution	-26.42
Covariance contribution	0.04
Combinations/Pair	1.28
Mean z-score	-2.62
Structure conservation index	0.78
SVM decision value	2.21
SVM RNA-class probability	0.990311
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9557311 90 + 20766785
AGCGAGUGUCCUGGCGCUGCGGGCUUCUCUC----GUCGGCGUCCACCGACCUCAGCCAGUCGCUUUUCCC---------------GCCACCCCACUUGCCUCGAAUUU
.(((((((...(((((..(((((((......----(((((......)))))...))))...)))......)---------------))))...)))))))......... ( -31.20)
>DroSec_CAF1 33900 90 + 1
AGCGAGUGUCCUGGCGCUGUGGGCUUCUCUC----GUCGGCGUCCACCGACCUCAGCCCGUCGCUUUUCCC---------------GCCACCCCACUCGCUACGAAUUU
((((((((...((((((..((((((......----(((((......)))))...))))))..)).......---------------))))...))))))))........ ( -36.01)
>DroSim_CAF1 33540 90 + 1
AGCGAGUGUCCUGGCGCUGCGGGCUUCUCUC----GUCGGCGUCCACCGACCUCAGCCCGUCGCUUUUCCC---------------GCCACCCCACUCGCCACGAAUUU
.(((((((...((((((.(((((((......----(((((......)))))...))))))).)).......---------------))))...)))))))......... ( -37.81)
>DroEre_CAF1 36069 104 + 1
AGCGAGUGUCCUGUCGCCGCGGGCCUCUCUC----GUCGUUGUCCACCGACCUCUGCCUGUCGCUCUUCCCACUCGCCGCCCGCUCGCCA-CCCACUCGCUUCGAAUUU
((((((((....((.((.((((((.......----((((........))))....((..((.(......).))..)).))))))..)).)-).))))))))........ ( -31.40)
>DroYak_CAF1 35279 96 + 1
AGCGAGUGUCCUGGCGCUGCGG-UCUCUCUCAGUUGUUGGUGUCCACCGACCUCUGUCUGCCGCUUUUCUCACAC-----------GUCA-CCCACUUGCCUCGAAUUU
.(((((((...(((((..((((-(......(((..((((((....))))))..)))...)))))..........)-----------))))-..)))))))......... ( -31.70)
>consensus
AGCGAGUGUCCUGGCGCUGCGGGCUUCUCUC____GUCGGCGUCCACCGACCUCAGCCCGUCGCUUUUCCC_______________GCCACCCCACUCGCCUCGAAUUU
.(((((((...((((((.(((((((..........(((((......)))))...))))))).))......................))))...)))))))......... (-26.38 = -26.42 +   0.04)

alignment

secondary structure

dotplot

Window 2

Location	9,557,311 – 9,557,401
Length	90
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	81.46
Mean single sequence MFE	-37.10
Consensus MFE	-22.50
Energy contribution	-22.74
Covariance contribution	0.24
Combinations/Pair	1.15
Mean z-score	-2.04
Structure conservation index	0.61
SVM decision value	0.51
SVM RNA-class probability	0.764259
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9557311 90 - 20766785
AAAUUCGAGGCAAGUGGGGUGGC---------------GGGAAAAGCGACUGGCUGAGGUCGGUGGACGCCGAC----GAGAGAAGCCCGCAGCGCCAGGACACUCGCU
........(((.((((.((((((---------------(((...(((.....)))...((((((....))))))----........)))))..))))....)))).))) ( -35.10)
>DroSec_CAF1 33900 90 - 1
AAAUUCGUAGCGAGUGGGGUGGC---------------GGGAAAAGCGACGGGCUGAGGUCGGUGGACGCCGAC----GAGAGAAGCCCACAGCGCCAGGACACUCGCU
........((((((((.((((((---------------.......))...(((((...((((((....))))))----......)))))....))))....)))))))) ( -39.80)
>DroSim_CAF1 33540 90 - 1
AAAUUCGUGGCGAGUGGGGUGGC---------------GGGAAAAGCGACGGGCUGAGGUCGGUGGACGCCGAC----GAGAGAAGCCCGCAGCGCCAGGACACUCGCU
........((((((((...((((---------------.......((..((((((...((((((....))))))----......))))))..))))))...)))))))) ( -42.21)
>DroEre_CAF1 36069 104 - 1
AAAUUCGAAGCGAGUGGG-UGGCGAGCGGGCGGCGAGUGGGAAGAGCGACAGGCAGAGGUCGGUGGACAACGAC----GAGAGAGGCCCGCGGCGACAGGACACUCGCU
........((((((((.(-(.((..((((((.((..((.(......).))..))....((((........))))----.......)))))).)).))....)))))))) ( -42.90)
>DroYak_CAF1 35279 96 - 1
AAAUUCGAGGCAAGUGGG-UGAC-----------GUGUGAGAAAAGCGGCAGACAGAGGUCGGUGGACACCAACAACUGAGAGAGA-CCGCAGCGCCAGGACACUCGCU
............((((((-((.(-----------.((.(.(....(((((...(((..((.(((....))).))..))).....).-))))..).))).).)))))))) ( -25.50)
>consensus
AAAUUCGAGGCGAGUGGGGUGGC_______________GGGAAAAGCGACAGGCUGAGGUCGGUGGACGCCGAC____GAGAGAAGCCCGCAGCGCCAGGACACUCGCU
........((((((((...((((.......................((((........))))((((.....................))))...))))...)))))))) (-22.50 = -22.74 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:58 2006