Locus 11704

Sequence ID	dm3.chr3R
Location	23,238,594 – 23,238,689
Length	95
Max. P	0.991646

overview

Window 8

Location	23,238,594 – 23,238,689
Length	95
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	67.21
Shannon entropy	0.61182
G+C content	0.50166
Mean single sequence MFE	-24.80
Consensus MFE	-13.53
Energy contribution	-14.04
Covariance contribution	0.51
Combinations/Pair	1.21
Mean z-score	-0.95
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.90
SVM RNA-class probability	0.848845
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23238594 95 + 27905053
-----------CUAUGGUGGGGCACGA--UGGG--GUAUGCCAAGGGGUAA-UGAGGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUAAAA--
-----------((((.(((...))).)--)))(--((.((((....)))).-......(((((((..(((((......))))).....((....))))))))).)))....-- ( -26.20, z-score =  -0.81, R)
>droSim1.chr3R 22972035 98 + 27517382
-----------CGGUGGUGGGGCACGACAUGGG--GGAUGCCAAGGGGGAAAUGAGGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUAAAA--
-----------...((((..((((...(....)--...))))................(((((((..(((((......))))).....((....))))))))).))))...-- ( -23.50, z-score =   0.30, R)
>droSec1.super_13 1982287 98 + 2104621
-----------CGAUGGUGGGGCACGACAUGGG--GGAUGCCAAGGGGGAAAUGAGGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUAAAA--
-----------...((((..((((...(....)--...))))................(((((((..(((((......))))).....((....))))))))).))))...-- ( -23.60, z-score =   0.07, R)
>droYak2.chr3R 5574341 111 - 28832112
CGAUGCUAUUUGGGGAGUUGGGGAUACCCAAGGAUGGAUGGGUGUGGGUAAUGAAAGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUAAAA--
....(((((((((....(((((....))))).......(((((((..((...(((....))).))..))))))).))))))((..(((((....)))))..))))).....-- ( -30.00, z-score =  -1.14, R)
>droEre2.scaffold_4820 5676726 92 - 10470090
--------------CGAUGGGGGAAAA--UUGG--GGAAGCCAGGGGUUGA-UGCGGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCGGCUAAAA--
--------------((((........)--))).--...((((....((...-.))...(((((((..(((((......))))).....((....)))))))))))))....-- ( -23.80, z-score =  -0.46, R)
>droAna3.scaffold_13340 4257999 86 - 23697760
--------------------AUAAAAAAGUUUUUAGAGGACGGCAGGAUG-----GGAGCUCGGCGAGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCUGCUAAAA--
--------------------........((((.....)))).......((-----(.((((((((..(((((......))))).....((....)))))))))).)))...-- ( -25.20, z-score =  -1.99, R)
>droWil1.scaffold_181089 3473208 79 + 12369635
-----------------------------UGAGGAGGGGACUUGUAGGUG-----GGAAGUGAAAAAGGUCUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUCUAAAA
-----------------------------...((((...(((((....((-----(((..(....)...)))))..)))))((..(((((....)))))..))..)))).... ( -21.30, z-score =  -2.64, R)
>consensus
______________UGGUGGGGCACAA__UGGG__GGAUGCCAAGGGGUAA_UGAGGAGUUCGGCGGGCACUCAAUCAAGUGCAAAAUGCAAAUGCGUUGAGCAGCUAAAA__
..........................................................(((((((..(((((......))))).....((....))))))))).......... (-13.53 = -14.04 +   0.51)

alignment

secondary structure

dotplot

Window 9

Location	23,238,594 – 23,238,689
Length	95
Sequences	7
Columns	113
Reading direction	reverse
Mean pairwise identity	67.21
Shannon entropy	0.61182
G+C content	0.50166
Mean single sequence MFE	-16.77
Consensus MFE	-10.79
Energy contribution	-11.07
Covariance contribution	0.29
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.64
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.49
SVM RNA-class probability	0.991646
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 23238594 95 - 27905053
--UUUUAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCCUCA-UUACCCCUUGGCAUAC--CCCA--UCGUGCCCCACCAUAG-----------
--.....((.((((((..((..(((.....)))..)).))))))))...............-.........(((((..--....--..))))).........----------- ( -17.70, z-score =  -1.66, R)
>droSim1.chr3R 22972035 98 - 27517382
--UUUUAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCCUCAUUUCCCCCUUGGCAUCC--CCCAUGUCGUGCCCCACCACCG-----------
--.....((.((((((..((..(((.....)))..)).))))))))..(((((................)))))....--........(((......)))..----------- ( -17.59, z-score =  -1.37, R)
>droSec1.super_13 1982287 98 - 2104621
--UUUUAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCCUCAUUUCCCCCUUGGCAUCC--CCCAUGUCGUGCCCCACCAUCG-----------
--.....((.((((((..((..(((.....)))..)).)))))))).........................(((((..--(....)..))))).........----------- ( -17.30, z-score =  -1.11, R)
>droYak2.chr3R 5574341 111 + 28832112
--UUUUAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCUUUCAUUACCCACACCCAUCCAUCCUUGGGUAUCCCCAACUCCCCAAAUAGCAUCG
--.....((.((((((..((..(((.....)))..)).))))))))..((.(((....))).........(((((........)))))...................)).... ( -20.60, z-score =  -2.26, R)
>droEre2.scaffold_4820 5676726 92 + 10470090
--UUUUAGCCGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCCGCA-UCAACCCCUGGCUUCC--CCAA--UUUUCCCCCAUCG--------------
--....((((((((((..((..(((.....)))..)).))))))....((.(....).)).-.........))))...--....--.............-------------- ( -17.70, z-score =  -2.14, R)
>droAna3.scaffold_13340 4257999 86 + 23697760
--UUUUAGCAGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCUCGCCGAGCUCC-----CAUCCUGCCGUCCUCUAAAAACUUUUUUAU--------------------
--.....(((((((((..((..(((.....)))..)).))))).((((...))))...-----....))))......................-------------------- ( -16.40, z-score =  -0.96, R)
>droWil1.scaffold_181089 3473208 79 - 12369635
UUUUAGAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGACCUUUUUCACUUCC-----CACCUACAAGUCCCCUCCUCA-----------------------------
....((((...(((((..((..(((.....)))..)).)))))..)))).........-----.....................----------------------------- ( -10.10, z-score =  -1.16, R)
>consensus
__UUUUAGCUGCUCAACGCAUUUGCAUUUUGCACUUGAUUGAGUGCCCGCCGAACUCCUCA_UUACCCCCUGGCAUCC__CCCA__UCGUGCCCCACCA______________
.......((.((((((..((..(((.....)))..)).))))))))................................................................... (-10.79 = -11.07 +   0.29)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:47:58 2011