Locus 5673

Sequence ID	3R_DroMel_CAF1
Location	14,895,376 – 14,895,480
Length	104
Max. P	0.923285

overview

Window 2

Location	14,895,376 – 14,895,480
Length	104
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	82.69
Mean single sequence MFE	-37.97
Consensus MFE	-19.07
Energy contribution	-20.39
Covariance contribution	1.32
Combinations/Pair	1.11
Mean z-score	-2.26
Structure conservation index	0.50
SVM decision value	0.09
SVM RNA-class probability	0.576616
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14895376 104 + 27905053
CAUUGGCCCAAAGACCAAACAGUCCAAGCCGAUCCAAUCAAGACGACUUGGGUCGCUUCGGAUCG-----GAUUGGA-------UCGGUGUCCGUUGCAUGGUGACCAUUAAAGGG
......(((............((((((.(((((((....(((.((((....))))))).))))))-----).)))))-------).(((..((((...))))..)))......))) ( -35.60)
>DroSec_CAF1 22947 109 + 1
CAUUGGCCCAAAGACCAAACAGGCCAAGCCGAUCCAAUCAAGACGACUUGGGUCGCUUCGGAUCGGAGCGGAUUGGA-------UCGGUGCCCGUUGCAUGGUGACCAUAAAAGGG
..((((((.............))))))((((((((((((.....(((....)))((((((...)))))).)))))))-------))))).(((.((..((((...)))).)).))) ( -44.42)
>DroSim_CAF1 22841 88 + 1
CAUUGGCCCAAAGACC---------AAGCCGAUCCAAUCAAGACGACUUGGGUCGCUUCGGAUCG-----GAUUGGA-------UC-------GUUGCAUGGUGACCAUAAAAGGG
......(((...((((---------((.(((((((....(((.((((....))))))).))))))-----).)))).-------))-------((..(...)..)).......))) ( -30.20)
>DroEre_CAF1 22448 109 + 1
--UUGGCCCAAAGACCAAACAGGCCAAGCCGAUCCAAUCAAGCCGACUUGGGUCGCUUCGGAUCG-----UAUCGGAGCGCUGCCCGGUGCCCGUUGCAUGGCGACCAUAAAAGGG
--((((((.............))))))((((((((....((((.(((....))))))).)))))(-----((.(((.(((((....)))))))).)))..)))..((......)). ( -42.12)
>DroYak_CAF1 28482 97 + 1
--UUGGCCCAAAGACCAAACAGGGCAAGCCGAUCCAAUCAAGACGACUUGGGUCUCUUCGGAUAG-----GAUC------------GGUGCCCGUUGCAUGGCGACCAUAAAAGGG
--....(((............((((..((((((((.(((.(((.(((....))))))...))).)-----))))------------)))))))(((((...))))).......))) ( -37.50)
>consensus
CAUUGGCCCAAAGACCAAACAGGCCAAGCCGAUCCAAUCAAGACGACUUGGGUCGCUUCGGAUCG_____GAUUGGA_______UCGGUGCCCGUUGCAUGGUGACCAUAAAAGGG
..(((((....................))))).((...((((....))))(((((((((.((((......)))).))..........((((.....)))))))))))......)). (-19.07 = -20.39 +   1.32)

alignment

secondary structure

dotplot

Window 3

Location	14,895,376 – 14,895,480
Length	104
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	82.69
Mean single sequence MFE	-39.08
Consensus MFE	-22.90
Energy contribution	-24.64
Covariance contribution	1.74
Combinations/Pair	1.06
Mean z-score	-2.65
Structure conservation index	0.59
SVM decision value	1.15
SVM RNA-class probability	0.923285
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14895376 104 - 27905053
CCCUUUAAUGGUCACCAUGCAACGGACACCGA-------UCCAAUC-----CGAUCCGAAGCGACCCAAGUCGUCUUGAUUGGAUCGGCUUGGACUGUUUGGUCUUUGGGCCAAUG
........(((((((((.(((.(((...))).-------(((((.(-----((((((((((((((....)))).))...))))))))).))))).))).)))).....)))))... ( -38.80)
>DroSec_CAF1 22947 109 - 1
CCCUUUUAUGGUCACCAUGCAACGGGCACCGA-------UCCAAUCCGCUCCGAUCCGAAGCGACCCAAGUCGUCUUGAUUGGAUCGGCUUGGCCUGUUUGGUCUUUGGGCCAAUG
........(((((((((...(((((((.((((-------(((((((.(((.((...)).)))(((....))).....)))))))))))....))))))))))).....)))))... ( -42.70)
>DroSim_CAF1 22841 88 - 1
CCCUUUUAUGGUCACCAUGCAAC-------GA-------UCCAAUC-----CGAUCCGAAGCGACCCAAGUCGUCUUGAUUGGAUCGGCUU---------GGUCUUUGGGCCAAUG
........(((((......(((.-------((-------.((((.(-----((((((((((((((....)))).))...))))))))).))---------)))).))))))))... ( -31.00)
>DroEre_CAF1 22448 109 - 1
CCCUUUUAUGGUCGCCAUGCAACGGGCACCGGGCAGCGCUCCGAUA-----CGAUCCGAAGCGACCCAAGUCGGCUUGAUUGGAUCGGCUUGGCCUGUUUGGUCUUUGGGCCAA--
........((((((((........)))(((((((((.((((((((.-----(((((..(((((((....))).))))))))).)))))...)))))))))))).....))))).-- ( -43.40)
>DroYak_CAF1 28482 97 - 1
CCCUUUUAUGGUCGCCAUGCAACGGGCACC------------GAUC-----CUAUCCGAAGAGACCCAAGUCGUCUUGAUUGGAUCGGCUUGCCCUGUUUGGUCUUUGGGCCAA--
........(((((((((.(((..(((((((------------((((-----(.(((..(((((((....))).))))))).)))))))..)))))))).)))).....))))).-- ( -39.50)
>consensus
CCCUUUUAUGGUCACCAUGCAACGGGCACCGA_______UCCAAUC_____CGAUCCGAAGCGACCCAAGUCGUCUUGAUUGGAUCGGCUUGGCCUGUUUGGUCUUUGGGCCAAUG
........(((((((((...(((((((...(((.....)))..........((((((((((((((....)))).))...)))))))).....))))))))))).....)))))... (-22.90 = -24.64 +   1.74)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:22 2006