Locus 2301

Sequence ID	2R_DroMel_CAF1
Location	8,483,368 – 8,483,492
Length	124
Max. P	0.997135

overview

Window 9

Location	8,483,368 – 8,483,464
Length	96
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	92.60
Mean single sequence MFE	-37.80
Consensus MFE	-27.76
Energy contribution	-28.32
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.73
SVM decision value	0.06
SVM RNA-class probability	0.562392
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8483368 96 + 20766785
CACCAGUCGAAUUUGCCACUCCUGCAGGUCCGCCCUUGGGCGACUUGUUUUCACUGGCAGUUGGUGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
............((((((.....(((((((.(((....))))))))))......))))))..(((((((..((((((....))))))..))))))) ( -41.40)
>DroSec_CAF1 7647 96 + 1
CCCCAGCCGAAUUUGCCACUCCUGCAGCUCCUCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGUGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
....(((((.(((..(((...((((.((.((......))))((.......))....)))).)))..)))..((((((....))))))))))).... ( -33.40)
>DroSim_CAF1 7666 96 + 1
CCCCAGCCGAAUUUGCCACUCCUGCAGCUCCUCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGUGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
....(((((.(((..(((...((((.((.((......))))((.......))....)))).)))..)))..((((((....))))))))))).... ( -33.40)
>DroEre_CAF1 7882 96 + 1
CCGCCACCGAAUUCGCAACUCCGGCAGCGCUGCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGCGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
(((((.....((((((((((((((.((((.((((....))))...))))....)))).)))).))))))....((((....)))))))))...... ( -39.70)
>DroYak_CAF1 8097 96 + 1
CCGCCGCCGAAUUUGCCACUCCAGCUGCUCCUCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGCGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
..((((((..((((((((((((((..((.((......))))((.......)).)))).)).))))))))....((((....))))))))))..... ( -41.10)
>consensus
CCCCAGCCGAAUUUGCCACUCCUGCAGCUCCUCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGUGAAUGACUGCCCAUCUGGGCGGCGGUUCGCU
............((((((.....((((.((..((....)).)).))))......))))))..(((((((..((((((....))))))..))))))) (-27.76 = -28.32 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	8,483,384 – 8,483,492
Length	108
Sequences	3
Columns	108
Reading direction	forward
Mean pairwise identity	66.36
Mean single sequence MFE	-39.07
Consensus MFE	-24.31
Energy contribution	-25.73
Covariance contribution	1.43
Combinations/Pair	1.17
Mean z-score	-1.76
Structure conservation index	0.62
SVM decision value	2.80
SVM RNA-class probability	0.997135
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8483384 108 + 20766785
CACUCCUGCAGGUCCGCCCUUGGGCGACUUGUUUUCACUGGCAGUUGGUGAAUGACUGCCCAUCUGGGCGGCGGUUCGCUUCUCCGGGCUGGGUGUCUUCUUAUCCAC
.......(((((((.(((....)))))))))).....((((.((..(((((((..((((((....))))))..))))))).))))))..((((((......)))))). ( -45.90)
>DroGri_CAF1 10560 84 + 1
---------CUGCGUUGCUUUCGGUGAUUUAUUCUCACCAGAAUUGGGCGAAUGG---------------GCGCUACGCUUCUCGGGACUGGGCGUCUUCUUGUCCGA
---------..........((((((((.......))))).)))((((((((..((---------------(((((...((.....))....)))))))..)))))))) ( -27.20)
>DroEre_CAF1 7898 108 + 1
AACUCCGGCAGCGCUGCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGCGAAUGACUGCCCAUCUGGGCGGCGGUUCGCUUCUCCGGACUGGGUGUCUUCUUAUCCGC
...(((((((((((((((....)))((.......))...))).))))((((((..((((((....))))))..))))))....)))))..(((((......))))).. ( -44.10)
>consensus
_ACUCC_GCAGGCCUGCCCUUGGGCGAUUUGUUUUCACUGGCAGUUGGCGAAUGACUGCCCAUCUGGGCGGCGGUUCGCUUCUCCGGACUGGGUGUCUUCUUAUCCGC
..............((((....))))...........((((.((..(((((((..((((((....))))))..))))))).))))))..((((((......)))))). (-24.31 = -25.73 +   1.43)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:15 2006