Locus 6647

Sequence ID	3R_DroMel_CAF1
Location	17,460,517 – 17,460,734
Length	217
Max. P	0.831958

overview

Window 8

Location	17,460,517 – 17,460,614
Length	97
Sequences	4
Columns	110
Reading direction	reverse
Mean pairwise identity	83.00
Mean single sequence MFE	-47.23
Consensus MFE	-29.66
Energy contribution	-35.10
Covariance contribution	5.44
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.63
SVM decision value	0.72
SVM RNA-class probability	0.831958
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17460517 97 - 27905053
UGUGUUGGGCAAGGGAUGGGAAG-------------GGGGAAGGGGCAGGCGCAGGGGCCAAAGUUCUUCCUCUCUUUCUGCGUCCGUGAGGGGUGAUUCUCGCCCCUCU
.............((((((((((-------------((((.((((((.(((......)))...)))))).)))))))))..)))))..((((((((.....)))))))). ( -42.70)
>DroSec_CAF1 12890 110 - 1
UGUGUCGGGCGAGGGAUGGGAAGGGGCAGUGGAAGGGGGGAAGGGGCAGGCUCAGGGGCCAAAGUUCUUCCUCUCUUUCUGCGUCCGUGAGGGGUGAUUCUCGCCCCGCU
...((.(((((((((..........((((..((((((((((((((...((((....))))....)))))))))))))))))).(((....)))....))))))))).)). ( -52.10)
>DroSim_CAF1 14020 110 - 1
UGUGUCGGGCGAGGGGUGGGAAGGGGCAGUGGAAAGGGGGAAGGGGCAGGCUCAGGGGCCAAAGUUCUUCCUCUCUUUCUGCGUCCGUGAGGGGUGAUUCUCGCCCCGCU
.......(((..((((((((((...((.(..(((((((((.((((((.((((....))))...)))))).)))))))))..).(((....)))))..))))))))))))) ( -53.30)
>DroEre_CAF1 13108 97 - 1
U--GCCGGGUAAGGGGUGGGAAGGGGCAGGGGCUG--GGGAAGGG------GCAGGGGCCAAAGUU---CCUCUCUUUCUGCGUCCGUGAGGGGUGAUUCUCGUCCCUCU
.--........((((..(((((...((((..(..(--(((((..(------((....)))....))---))))..)..)))).(((....)))....)))))..)))).. ( -40.80)
>consensus
UGUGUCGGGCAAGGGAUGGGAAGGGGCAGUGGAAG_GGGGAAGGGGCAGGCGCAGGGGCCAAAGUUCUUCCUCUCUUUCUGCGUCCGUGAGGGGUGAUUCUCGCCCCGCU
............((((((((((...((((..((((((((((((((...(((......)))....)))))))))))))))))).(((....)))....))))))))))... (-29.66 = -35.10 +   5.44)

alignment

secondary structure

dotplot

Window 9

Location	17,460,614 – 17,460,734
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-27.32
Consensus MFE	-23.26
Energy contribution	-23.54
Covariance contribution	0.28
Combinations/Pair	1.09
Mean z-score	-1.46
Structure conservation index	0.85
SVM decision value	0.66
SVM RNA-class probability	0.813398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17460614 120 - 27905053
CCACCCAAGGAUCGUGGGAAGUUCCCGCUUGCGCUCUUCUAUCUGGUAGGCGAAAAAAAAAAACCAUCUUGCAGAAAAUGGUUGAAAAAAAAUCAAGCAUAGAGAUACUCUAAUUGCAUA
........((...(((((.....)))))...((((..((.....))..))))...........))....(((((....((.((((.......)))).))(((((...))))).))))).. ( -27.20)
>DroSec_CAF1 13000 116 - 1
CCACCCAAGGAUCGUGGGAAGUUCCCGCUUGCGCUCUUCUAUCUGGCAGGCGAAAA---AAAACCAUCUUGCAGAAAAUGGUUGGAA-AAAAUCAAGCAUAGAGAUACUCUAAUUGCAUA
...((((.......))))...(((((((((((.(..........))))))))....---..((((((.((....)).))))))))))-........((((((((...)))))..)))... ( -28.60)
>DroSim_CAF1 14130 116 - 1
CCACCCAAGGAUCGUGGGAAGUUCCCGCUUGCGCUCUUCUAUCUGGCAGGCGAAAA---AAAACCAUCUUGCAGAAAAUGGUUGGAA-AAAAUCAAGCAUAGAGAUACUCUAAUUGCAUA
...((((.......))))...(((((((((((.(..........))))))))....---..((((((.((....)).))))))))))-........((((((((...)))))..)))... ( -28.60)
>DroEre_CAF1 13205 118 - 1
CCACCCAAGGAUCGUGGGAAGUUCCCGCCUGCUCUCCUCUAUCUGGCAAGCGAAUAAA-AAAACCAUCUUGCAGAAAAUGGUCGGAA-AAAAUCAAGCAUAGAUAUACUCUAAUUGCAUA
((..(((((((..(((((.....)))))......))))...((((.((((........-........))))))))...)))..))..-........(((((((.....))))..)))... ( -24.49)
>DroYak_CAF1 13219 117 - 1
CCACCCAAGGAUCGUGGGAAGUUCCCGCUUGCUCUAUUCUAUCUGGCAAGCAAAAAAA-AA-AACAUCUUGCAGAAAAUGGUUGAAA-AAAAUCAAGCAUAGAGAUACUCUAAUUGCAUA
.......(((((.(((((.....)))(((((((...........))))))).......-..-.)))))))((((....((.((((..-....)))).))(((((...))))).))))... ( -27.70)
>consensus
CCACCCAAGGAUCGUGGGAAGUUCCCGCUUGCGCUCUUCUAUCUGGCAGGCGAAAAAA_AAAACCAUCUUGCAGAAAAUGGUUGGAA_AAAAUCAAGCAUAGAGAUACUCUAAUUGCAUA
.......(((((.(((((.....)))((((((.(..........)))))))...........)).)))))((((....((.((((.......)))).))(((((...))))).))))... (-23.26 = -23.54 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:44 2006