Locus 7665

Sequence ID	3L_DroMel_CAF1
Location	20,573,147 – 20,573,316
Length	169
Max. P	0.633825

overview

Window 7

Location	20,573,147 – 20,573,256
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	93.27
Mean single sequence MFE	-33.97
Consensus MFE	-28.01
Energy contribution	-27.57
Covariance contribution	-0.44
Combinations/Pair	1.07
Mean z-score	-2.21
Structure conservation index	0.82
SVM decision value	0.21
SVM RNA-class probability	0.633825
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20573147 109 - 23771897
UGGAGGUGCACCACGUGGUGUAUUCGAUGUCUCUUCCUCUUGGGAUGGCGGCUCUACUGCCCCAGAUUUUUCCUCCGCAUCUUCUUCCUCCUCCACGGAUUGAACUCUA
((((((((((((....))))))...(((((...((((....))))(((.(((......))))))............)))))........)))))).............. ( -33.30)
>DroSec_CAF1 18063 109 - 1
UGGAGGUGCACCACGUGGUGUAUUCGAUGUUCCUUCCUCUUGGGAUGGUGGCUCUACUGCCGCAGGUUUUUCCUCCUCAUCUUCUUCCUCCUCCAUGGAUUGAACUCUC
..(((.((((((....)))))))))((.((((..(((....((((.((((((......)))))(((.....)))............).))))....)))..)))))).. ( -33.30)
>DroSim_CAF1 11560 109 - 1
UGGAGGUGCACCACGUGGUGUAUUCGAUGUUCCUUCCUCUUGGGAAGGUGGAUCUACUGCAGCAGGUUUUUCCUCCGCAUCUUCUUCCUCCUCCACGGAUUGAACUCUC
((((((((((((....))))))...(((((.((((((.....)))))).(((...(((......)))...)))...)))))........)))))).............. ( -35.30)
>consensus
UGGAGGUGCACCACGUGGUGUAUUCGAUGUUCCUUCCUCUUGGGAUGGUGGCUCUACUGCCGCAGGUUUUUCCUCCGCAUCUUCUUCCUCCUCCACGGAUUGAACUCUC
((((((((((((....))))))...((((((((........)))).((.((.....(((...)))......)).)).))))........)))))).............. (-28.01 = -27.57 +  -0.44)

alignment

secondary structure

dotplot

Window 8

Location	20,573,226 – 20,573,316
Length	90
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	76.96
Mean single sequence MFE	-33.11
Consensus MFE	-19.21
Energy contribution	-19.41
Covariance contribution	0.20
Combinations/Pair	1.22
Mean z-score	-1.65
Structure conservation index	0.58
SVM decision value	-0.00
SVM RNA-class probability	0.532840
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20573226 90 - 23771897
CGUGAUGGUGCGCCGAAGGUUGAUGGGGGUACCUAUAAGAACUUUUUCCUCUGACAUAAC------------------------------UGGAGGUGCACCACGUGGUGUAUUCGAUGU
......(((((((((((((((.(((((....)))))...)))))))(((...........------------------------------.)))))))))))((((.(......).)))) ( -29.80)
>DroSec_CAF1 18142 90 - 1
CGUGAUGGUGCGUCGAAGGUUGAUAGGGGUACCUAUAAGAACUUUUUCCUCUGUCAUAAC------------------------------UGGAGGUGCACCACGUGGUGUAUUCGAUGU
.........(((((((((..(((((((((..................)))))))))...)------------------------------)....(((((((....)))))))))))))) ( -28.47)
>DroAna_CAF1 39792 120 - 1
GGUGAUGGUGCGGCGAAGAUUGAUGGGCGUGCCUAUCAGGACUUUCUCCUCGGACACCACAGUGGGCUGGGAUUGUGGCUGGGGCUGUGUUGGUGGAGCAGCCCUUGGGGUGUUGGAGGG
..((((((..((.(.(.......).).))..)).)))).........((((.((((((.((...((((........))))((((((((.........)))))))))).)))))).)))). ( -47.70)
>DroSim_CAF1 11639 90 - 1
CGUGAUGGUGCGUCGAAGGUUGAUAGGGGUACCUAUAAGAACUUUUUCCUCUGUCAUAAC------------------------------UGGAGGUGCACCACGUGGUGUAUUCGAUGU
.........(((((((((..(((((((((..................)))))))))...)------------------------------)....(((((((....)))))))))))))) ( -28.47)
>DroEre_CAF1 11367 90 - 1
CGUAAUGGUGCGUCGAAGGUUGAUGGGGGUGCCUAUCAGCACUUUUUCCUCUGUCAUAAC------------------------------UGGAGGUGCACCACGUGGUGUAUUUGAUGG
..........(((((((.(((((((((....))))))))).......(((((((....))------------------------------.)))))((((((....))))))))))))). ( -31.10)
>consensus
CGUGAUGGUGCGUCGAAGGUUGAUGGGGGUACCUAUAAGAACUUUUUCCUCUGUCAUAAC______________________________UGGAGGUGCACCACGUGGUGUAUUCGAUGU
......(((((...(((((((.(((((....)))))...))))))).(((((.......................................))))).)))))((((.(......).)))) (-19.21 = -19.41 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:53:10 2006