Locus 1399

Sequence ID	X_DroMel_CAF1
Location	4,217,364 – 4,217,459
Length	95
Max. P	0.914151

overview

Window 4

Location	4,217,364 – 4,217,459
Length	95
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	87.33
Mean single sequence MFE	-27.36
Consensus MFE	-20.99
Energy contribution	-20.87
Covariance contribution	-0.12
Combinations/Pair	1.10
Mean z-score	-1.67
Structure conservation index	0.77
SVM decision value	0.29
SVM RNA-class probability	0.670474
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4217364 95 + 22224390
CCAUGGCAUCC---------CAGACCGGCGUGGACUUCUGAUUCUGAUU------CCGAUUGAGAAUCAGAUUUUGAUUUCGGUUGCCAUCGUCUUCGCAAUUCUUGCAC
..((((((...---------...(((((.((.((..(((((((((.(..------.....).)))))))))..)).)).))))))))))).......(((.....))).. ( -29.20)
>DroSec_CAF1 5160 95 + 1
CCAUGGCAUCC---------CAGCCCGGCGUGGACUCCUGAUUCUGAUU------CCGAUUGAGAAUCAGAUUUUGAUUUCGGUUGCCAUCGUCUUCGCAAUUCUUGCAC
....(((....---------..))).(((((((.(..((((.(((((((------(.......))))))))........))))..)))).))))...(((.....))).. ( -26.00)
>DroSim_CAF1 5174 95 + 1
CCAUGGCAUCC---------CAGCCCGGCGUGGACUCCUGAUUCUGAUU------CCGAUUGAGAAUCAGAUUUUGAUUUCGGUUGCCAUCGUCUUCGCAAUUCUUGCAC
....(((....---------..))).(((((((.(..((((.(((((((------(.......))))))))........))))..)))).))))...(((.....))).. ( -26.00)
>DroEre_CAF1 5196 95 + 1
CCAUGGCAUCC---------CAGGCCGACGUGGACUCCUGAUUCAGAUU------CUGAUUCAGAAUCAGAUUUUGAUUUCGGUUGCCGUCGUCUUCGCAGUUCCUGCAC
....(((....---------...)))(((((((.(..((((.(((((.(------(((((.....)))))).)))))..))))..)))).))))...((((...)))).. ( -32.40)
>DroYak_CAF1 4905 110 + 1
UCAUGGCAUCCCAGCCAUCCCAGCCCGACGUGGACUCCUGAUUCCGAUUCUACUUCUGAUUCCGAAUAAGAUUUUGAUUUCGGUUGCCAUAGUCUUUGCAAUUCUUGCAC
..(((((......)))))........(((((((.(..((((.((.((.(((..(((.......)))..))).)).))..))))..))))).)))..((((.....)))). ( -23.20)
>consensus
CCAUGGCAUCC_________CAGCCCGGCGUGGACUCCUGAUUCUGAUU______CCGAUUGAGAAUCAGAUUUUGAUUUCGGUUGCCAUCGUCUUCGCAAUUCUUGCAC
..((((((................((((.((.((...((((((((((((........)))).))))))))...)).)).)))).)))))).......((((...)))).. (-20.99 = -20.87 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	4,217,364 – 4,217,459
Length	95
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	87.33
Mean single sequence MFE	-29.72
Consensus MFE	-24.85
Energy contribution	-25.01
Covariance contribution	0.16
Combinations/Pair	1.12
Mean z-score	-1.87
Structure conservation index	0.84
SVM decision value	1.09
SVM RNA-class probability	0.914151
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4217364 95 - 22224390
GUGCAAGAAUUGCGAAGACGAUGGCAACCGAAAUCAAAAUCUGAUUCUCAAUCGG------AAUCAGAAUCAGAAGUCCACGCCGGUCUG---------GGAUGCCAUGG
.((((.....))))....(.((((((.((..........(((((((((.....))------)))))))..((((...((.....))))))---------)).)))))).) ( -29.00)
>DroSec_CAF1 5160 95 - 1
GUGCAAGAAUUGCGAAGACGAUGGCAACCGAAAUCAAAAUCUGAUUCUCAAUCGG------AAUCAGAAUCAGGAGUCCACGCCGGGCUG---------GGAUGCCAUGG
.((((.....))))....(.((((((.((..........(((((((((.....))------)))))))......(((((.....))))).---------)).)))))).) ( -31.40)
>DroSim_CAF1 5174 95 - 1
GUGCAAGAAUUGCGAAGACGAUGGCAACCGAAAUCAAAAUCUGAUUCUCAAUCGG------AAUCAGAAUCAGGAGUCCACGCCGGGCUG---------GGAUGCCAUGG
.((((.....))))....(.((((((.((..........(((((((((.....))------)))))))......(((((.....))))).---------)).)))))).) ( -31.40)
>DroEre_CAF1 5196 95 - 1
GUGCAGGAACUGCGAAGACGACGGCAACCGAAAUCAAAAUCUGAUUCUGAAUCAG------AAUCUGAAUCAGGAGUCCACGUCGGCCUG---------GGAUGCCAUGG
.(((((...)))))........((((.((..........((.(((((((...)))------)))).))..((((...((.....))))))---------)).)))).... ( -26.70)
>DroYak_CAF1 4905 110 - 1
GUGCAAGAAUUGCAAAGACUAUGGCAACCGAAAUCAAAAUCUUAUUCGGAAUCAGAAGUAGAAUCGGAAUCAGGAGUCCACGUCGGGCUGGGAUGGCUGGGAUGCCAUGA
.((((.....)))).....(((((((.(((..(((....(((.((((.((.((.......)).)).)))).)))(((((.....)))))..)))..).))..))))))). ( -30.10)
>consensus
GUGCAAGAAUUGCGAAGACGAUGGCAACCGAAAUCAAAAUCUGAUUCUCAAUCGG______AAUCAGAAUCAGGAGUCCACGCCGGGCUG_________GGAUGCCAUGG
.(((((...)))))......((((((.((..........((((((((...................))))))))(((((.....)))))..........)).)))))).. (-24.85 = -25.01 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:31 2006