Locus 1288

Sequence ID	X_DroMel_CAF1
Location	3,831,199 – 3,831,318
Length	119
Max. P	0.942466

overview

Window 1

Location	3,831,199 – 3,831,290
Length	91
Sequences	4
Columns	119
Reading direction	reverse
Mean pairwise identity	65.94
Mean single sequence MFE	-36.83
Consensus MFE	-15.83
Energy contribution	-15.77
Covariance contribution	-0.06
Combinations/Pair	1.27
Mean z-score	-2.38
Structure conservation index	0.43
SVM decision value	1.33
SVM RNA-class probability	0.942466
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3831199 91 - 22224390
ACCUGUGCUU-AGCCUUCGAUGUGGCUGCAAAUGUGAGGCUGCC--GGCA----GUGGGUGGCAG--------CUUGGUAUGGGGGCGUG---A---------AGGAGGAGCAGAAGG-
.(((.(((((-..((((((.....(((.(..(((..((((((((--(.(.----...).))))))--------)))..))).).))).))---)---------)))..)))))..)))- ( -39.90)
>DroSec_CAF1 16642 94 - 1
ACCUGUGCUG-AGCCUUCGAUGUGGCUGCAAAUGUGAGGCUGCC--GGCA----GUGGGUGGCAG--------CUUGGUAUGGGGGCGUGGCAA---------GGGAGGAGCAGGAGG-
.(((((....-..(((((..(((.((.((..(((..((((((((--(.(.----...).))))))--------)))..)))....)))).))).---------.))))).)))))...- ( -39.40)
>DroEre_CAF1 20457 116 - 1
ACCUGUGCUG-AGCCUUCGAUGUGGCUCCAAGUGUGAGGCUGCU--GGCAGUGGAUGGGUGGCAAGGUGGCAAGUUGGCAUGGAGGAGUCACGAUGGAUGUGGAGUAGGAGCAGGAGGU
.(((((.(((-..((.((.((((((((((...(((.((....))--.)))((.(((..((.((...)).))..))).)).....)))))))).)).))...))..)))..))))).... ( -41.70)
>DroAna_CAF1 16881 84 - 1
ACCUGUGCUGCGGCCUUCGAUGGGGCUCCAAAUACGAGGCUGUUUCUUCA----GUGGGUGGCGU---GG--------GA---GGU-------A---------GUGAGUGUUAGGGGG-
.((((..((((.((((((.(((..((.(((.....((((......)))).----.)))))..)))---.)--------))---)))-------.---------)).))..).)))...- ( -26.30)
>consensus
ACCUGUGCUG_AGCCUUCGAUGUGGCUCCAAAUGUGAGGCUGCC__GGCA____GUGGGUGGCAG________CUUGGUAUGGGGGCGUG___A_________AGGAGGAGCAGGAGG_
.(((((..((.((((........)))).))........((..((.............))..))...............................................))))).... (-15.83 = -15.77 +  -0.06)

alignment

secondary structure

dotplot

Window 2

Location	3,831,226 – 3,831,318
Length	92
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	76.71
Mean single sequence MFE	-25.66
Consensus MFE	-18.36
Energy contribution	-18.68
Covariance contribution	0.32
Combinations/Pair	1.15
Mean z-score	-1.31
Structure conservation index	0.72
SVM decision value	0.13
SVM RNA-class probability	0.598191
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3831226 92 + 22224390
ACCAAG--------CUGCCACCCAC----UGCC--GGCAGCCUCACAUUUGCAGCCACAUCGAAGGCU-AAGCACAGGUGGCAUUAUUUACGCAGUUCGC-------UUCCUGC
......--------.(((((((...----(((.--.((((........))))((((........))))-..)))..)))))))........((((.....-------...)))) ( -26.40)
>DroSec_CAF1 16672 92 + 1
ACCAAG--------CUGCCACCCAC----UGCC--GGCAGCCUCACAUUUGCAGCCACAUCGAAGGCU-CAGCACAGGUGGCAUUAUUUACGCAGUUCGC-------UUCCUGC
......--------.(((((((...----(((.--(((((........))))((((........))))-).)))..)))))))........((((.....-------...)))) ( -25.80)
>DroEre_CAF1 20497 104 + 1
GCCAACUUGCCACCUUGCCACCCAUCCACUGCC--AGCAGCCUCACACUUGGAGCCACAUCGAAGGCU-CAGCACAGGUGGCAUUAUUUACGCAGUUCGC-------UUCCUGC
.......(((((((((((..........(((..--..)))...........(((((........))))-).))).))))))))........((((.....-------...)))) ( -31.80)
>DroYak_CAF1 16430 91 + 1
---------UCAACUUGCCACCCAU----UUCC--AGCAGCCUCACAUUUGGAGCCACAUCGAAGGCU-CAGCACAGGUGGUAUUAUUUACGCAGUUCAC-------UUCCUGU
---------......(((((((...----....--..(((........)))(((((........))))-)......)))))))........((((.....-------...)))) ( -20.60)
>DroAna_CAF1 16901 99 + 1
C--------CC---ACGCCACCCAC----UGAAGAAACAGCCUCGUAUUUGGAGCCCCAUCGAAGGCCGCAGCACAGGUGGCAAUAUUUACGCAGUUCACUAGCAGCUCCUUGC
.--------..---..((((((..(----((........((((((....(((....))).)).))))..)))....)))))).........((((....)).)).......... ( -23.70)
>consensus
ACCAA_____C___CUGCCACCCAC____UGCC__AGCAGCCUCACAUUUGGAGCCACAUCGAAGGCU_CAGCACAGGUGGCAUUAUUUACGCAGUUCGC_______UUCCUGC
................((((((.......(((....))).........(((.((((........)))).)))....)))))).........((((...............)))) (-18.36 = -18.68 +   0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:48 2006