Locus 12456

Sequence ID	dm3.chrX
Location	283,415 – 283,562
Length	147
Max. P	0.980107

overview

Window 1

Location	283,415 – 283,529
Length	114
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	80.49
Shannon entropy	0.31213
G+C content	0.40497
Mean single sequence MFE	-24.70
Consensus MFE	-17.51
Energy contribution	-20.01
Covariance contribution	2.50
Combinations/Pair	1.20
Mean z-score	-1.92
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.99
SVM RNA-class probability	0.869936
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 283415 114 - 22422827
AGACAUGCAGAAUUUGUGCAUACCUCUUCAUGAGAUCAUUUCAAGUGUUAAUCGAUCCCACUCU-AUAACCGCAAAAGAUUAAUUGGCGACUGAUCUCAGCCUCCCCUAACAUGA
....(((((.......))))).........((((((((.......(((((((..(((.......-............)))..)))))))..))))))))................ ( -18.71, z-score =   0.11, R)
>droYak2.chrX 216057 108 - 21770863
AGGCAUGCAGAAUUUUUCUUAGCCUAUGCAUCAGUUUA-------UGUUAGUCGAGCCCACACUAACGACUGCGGAAGAUUAAUUGGCGACCGAUCUCGUUUUCCCCAAACAUGA
((((.((.(((.....)))))))))..........(((-------(((((((((((......))..)))))(.(((((((..(((((...)))))...))))))).).))))))) ( -22.00, z-score =   0.03, R)
>droSec1.super_10 145206 114 - 3036183
AGGUAUGCAGAAUUUUUGCAUACCUCUUCUUGAGAUCAUUGCAAGUAUUAAUCGAUUCCACUCU-AUAACCGCAAAAGAUUAAUUAGCGACUGAUCUCGGCCUACCCAAACAUUA
(((((((((((...)))))))))))......(((((((((((....(((((((...........-............)))))))..)))).)))))))((.....))........ ( -30.40, z-score =  -4.35, R)
>droSim1.chrX 195689 114 - 17042790
AGGUAUGCAGAAUUUUAGCAUACCUCUUCUUGAGAUCAUUGCAAGUAUUAAUCGAUCCCACUCU-AUAACCGCAAAAGAUUAAUUAGCGACUGAUCUCGGCCUACCCAAACAUUA
((((((((.........))))))))......(((((((((((....(((((((...........-............)))))))..)))).)))))))((.....))........ ( -27.70, z-score =  -3.48, R)
>consensus
AGGCAUGCAGAAUUUUUGCAUACCUCUUCAUGAGAUCAUUGCAAGUAUUAAUCGAUCCCACUCU_AUAACCGCAAAAGAUUAAUUAGCGACUGAUCUCGGCCUACCCAAACAUGA
(((((((((((...))))))))))).....((((((((((((....(((((((........................)))))))..)))).))))))))................ (-17.51 = -20.01 +   2.50)

alignment

secondary structure

dotplot

Window 2

Location	283,453 – 283,562
Length	109
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	77.33
Shannon entropy	0.35514
G+C content	0.39450
Mean single sequence MFE	-32.36
Consensus MFE	-20.24
Energy contribution	-20.43
Covariance contribution	0.19
Combinations/Pair	1.36
Mean z-score	-2.58
Structure conservation index	0.63
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.04
SVM RNA-class probability	0.980107
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 283453 109 + 22422827
UUUUGCGGUUAU-AGAGUGGGAUCGAUUAACACUUGAAAUGAUCUCAUGAAGAGGUAUGCACAAAUUCUGCAUGUCUAAUCCUGUUUUAGACAGUGC------CUUCGAUCUGCAA
..((((((....-...(((((((((.((........)).)))))))))...((((((((((.......))).(((((((.......)))))))))))------)))....)))))) ( -30.50, z-score =  -1.91, R)
>droYak2.chrX 216095 109 + 21770863
UUCCGCAGUCGUUAGUGUGGGCUCGACUAACA-------UAAACUGAUGCAUAGGCUAAGAAAAAUUCUGCAUGCCUAAUACUGCAUUGGGAAGUGCUUUAGACUUCGACUUGCAA
....((((((((((((.((....)))))))).-------....(..((((((((((..(((.....)))....)))))....)))))..)(((((.......)))))))).))).. ( -33.50, z-score =  -2.43, R)
>droSec1.super_10 145244 109 + 3036183
UUUUGCGGUUAU-AGAGUGGAAUCGAUUAAUACUUGCAAUGAUCUCAAGAAGAGGUAUGCAAAAAUUCUGCAUACCUAAUACUGUUUUAGGCAGUGU------CUUCGAUCUGCGA
..((((((((((-.(((((...........)))))...))))))....(((((((((((((.......))))))))).(((((((.....)))))))------)))).....)))) ( -31.50, z-score =  -2.64, R)
>droSim1.chrX 195727 109 + 17042790
UUUUGCGGUUAU-AGAGUGGGAUCGAUUAAUACUUGCAAUGAUCUCAAGAAGAGGUAUGCUAAAAUUCUGCAUACCUAAUACUGUUUUAGGCAGUGU------CUUCGAUCUGCAA
..((((((....-....((((((((..............)))))))).((((((((((((.........)))))))).(((((((.....)))))))------))))...)))))) ( -33.94, z-score =  -3.36, R)
>consensus
UUUUGCGGUUAU_AGAGUGGGAUCGAUUAACACUUGCAAUGAUCUCAAGAAGAGGUAUGCAAAAAUUCUGCAUACCUAAUACUGUUUUAGGCAGUGC______CUUCGAUCUGCAA
................(..((.((((..........................(((((((((.......)))))))))..((((((.....)))))).........))))))..).. (-20.24 = -20.43 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:34 2011