Locus 7141

Sequence ID	3R_DroMel_CAF1
Location	18,820,532 – 18,820,635
Length	103
Max. P	0.936897

overview

Window 5

Location	18,820,532 – 18,820,635
Length	103
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	75.49
Mean single sequence MFE	-32.23
Consensus MFE	-13.42
Energy contribution	-15.02
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.42
SVM decision value	0.74
SVM RNA-class probability	0.836757
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18820532 103 + 27905053
AAGCGCAGCAGGAGCCGGAGCAGGACUCCUUCGCAGAAUGUGCUGAUGGAAAAAAGUAAUGGCCAUAUCCAUGGAGCUCCAGUUACAGUUGCAGCUGCAUCUG------
....((((((((((((......)).)))))..((((..(((((((((((.....(....)..)))).((....))....))).)))).)))).))))).....------ ( -31.90)
>DroSec_CAF1 45790 94 + 1
GAGUGCAGCAGAGG---------CACUCCUUCGCAGGAUGUGCUGAUGGAAAAAAAUAAUGGCCAUAUCCAUGGAGCUCCACUUGCAGCUGCAGCUGCAUCUG------
(((((.(((...((---------(((((((....)))).))))).(((((.................)))))...))).)))))(((((....))))).....------ ( -32.03)
>DroSim_CAF1 48963 88 + 1
GAGCGCAGCAGGAG---------GACUCCUUCGCAGGAUGUGCUGAUGGAAAAAAGUAAUGGCCAUAUCCAUGGAGCUCCACUUGCAG------CAGCAUCUG------
..((((.(((((.(---------((((((......((((((((((.((........)).))).)))))))..)))).))).))))).)------).)).....------ ( -29.00)
>DroEre_CAF1 46025 90 + 1
AAGCGCAGCAGCAG------C-------------AGGAUGUGCUGAUGGAAAAAAGUAAUGGCCAUAUCCAUGGAGCUCCAGUUCCAGCUGCAGCUGCAGCUGCAGUUG
.((((((((.((((------(-------------.((((((((((.((........)).))).))))))).((((((....))))))))))).))))).)))....... ( -39.00)
>DroYak_CAF1 49013 91 + 1
AAGCGCCGCAGGAG------CAGGACUCCUUCGCAGGAUGUGCUGAUGGAAAAAAGUAAUGGCCAUAUCCAUGGAGCUCCAGCUCCAAC------------UGCAGUUG
.(((((.(..((((------(.(((((((......((((((((((.((........)).))).)))))))..)))).))).)))))..)------------.)).))). ( -29.20)
>consensus
AAGCGCAGCAGGAG______C__GACUCCUUCGCAGGAUGUGCUGAUGGAAAAAAGUAAUGGCCAUAUCCAUGGAGCUCCAGUUCCAGCUGCAGCUGCAUCUG______
....(((((..........................((((((((((.((........)).))).))))))).(((....)))............)))))........... (-13.42 = -15.02 +   1.60)

alignment

secondary structure

dotplot

Window 6

Location	18,820,532 – 18,820,635
Length	103
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	75.49
Mean single sequence MFE	-31.27
Consensus MFE	-11.82
Energy contribution	-14.22
Covariance contribution	2.40
Combinations/Pair	1.13
Mean z-score	-2.15
Structure conservation index	0.38
SVM decision value	1.26
SVM RNA-class probability	0.936897
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18820532 103 - 27905053
------CAGAUGCAGCUGCAACUGUAACUGGAGCUCCAUGGAUAUGGCCAUUACUUUUUUCCAUCAGCACAUUCUGCGAAGGAGUCCUGCUCCGGCUCCUGCUGCGCUU
------.((.(((((((((....)))...((((((..(((((...((......))....)))))..(((.....)))...((((.....)))))))))).)))))))). ( -31.40)
>DroSec_CAF1 45790 94 - 1
------CAGAUGCAGCUGCAGCUGCAAGUGGAGCUCCAUGGAUAUGGCCAUUAUUUUUUUCCAUCAGCACAUCCUGCGAAGGAGUG---------CCUCUGCUGCACUC
------....((((((....))))))((((.(((...(((((.................)))))..((((.((((....)))))))---------)....))).)))). ( -32.63)
>DroSim_CAF1 48963 88 - 1
------CAGAUGCUG------CUGCAAGUGGAGCUCCAUGGAUAUGGCCAUUACUUUUUUCCAUCAGCACAUCCUGCGAAGGAGUC---------CUCCUGCUGCGCUC
------..((((.((------(((...((((((....((((......)))).......)))))))))))))))..(((.((((...---------.))))....))).. ( -26.30)
>DroEre_CAF1 46025 90 - 1
CAACUGCAGCUGCAGCUGCAGCUGGAACUGGAGCUCCAUGGAUAUGGCCAUUACUUUUUUCCAUCAGCACAUCCU-------------G------CUGCUGCUGCGCUU
.......(((.(((((.(((((.(((..((..(((..(((((...((......))....))))).))).))))).-------------)------)))).)))))))). ( -33.90)
>DroYak_CAF1 49013 91 - 1
CAACUGCA------------GUUGGAGCUGGAGCUCCAUGGAUAUGGCCAUUACUUUUUUCCAUCAGCACAUCCUGCGAAGGAGUCCUG------CUCCUGCGGCGCUU
...(((((------------...(((((.(((.(((((((((...((......))....)))))..(((.....)))...))))))).)------)))))))))..... ( -32.10)
>consensus
______CAGAUGCAGCUGCAGCUGCAACUGGAGCUCCAUGGAUAUGGCCAUUACUUUUUUCCAUCAGCACAUCCUGCGAAGGAGUC__G______CUCCUGCUGCGCUU
..........((((((....((((....(((((....((((......)))).......))))).))))...((((....)))).................))))))... (-11.82 = -14.22 +   2.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:28 2006