Locus 12435

Sequence ID	dm3.chrXHet
Location	160,605 – 160,738
Length	133
Max. P	0.975541

overview

Window 0

Location	160,605 – 160,738
Length	133
Sequences	3
Columns	133
Reading direction	forward
Mean pairwise identity	61.71
Shannon entropy	0.55283
G+C content	0.58241
Mean single sequence MFE	-54.40
Consensus MFE	-19.56
Energy contribution	-23.23
Covariance contribution	3.68
Combinations/Pair	1.21
Mean z-score	-1.96
Structure conservation index	0.36
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.52
SVM RNA-class probability	0.728871
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 160605 133 + 204112
UCUUAUCCAGAGACAGAGUUUCUGCGGGUGACUUGCCCUGCUAAAGGUAACGAAGAUGCCACUUCGUUCUGGACCCGCUCAGCCCCUUACGGUUAGGGUCAUCCCGGGACCCAGGCUGACCAAGUUGCGGUAA
.....(((((((.(..(((....((((((.....)))).))....((((.......)))))))..)))))))).((((((((((((....))...(((((.......))))).)))))).......))))... ( -45.61, z-score =  -0.56, R)
>droMoj3.scaffold_6496 1647639 131 + 26866924
--UUAGCCAUGCGAAAGGCCUCGUCGGCCGGGAAGCCUUUCUCUAGAUACCGCAUAUACCACUUGGUACGUGAGCCGCUCAGGACUCUCCGAUUCGGAUCAUCCCGAGCGCCGGGCUGUCCGAGUGGAGGCAA
--...((((((((...((((.....))))(((((....))))).......)))))...((((((((.((((..(.(((((.(((...((((...))))...))).))))).)..)).)))))))))).))).. ( -55.50, z-score =  -2.29, R)
>droGri2.scaffold_14822 968639 131 + 1097346
--UUGGCCUUUUUCAGGGCUUCAUCGGGGUUGAGUCCCUGCUGGAGGUACCGGAGGUACCACUUGACCCUUGAACCGCAGAGAUUUCUCCGGUUCGGGUCAUCCAGCCCACCGGGUUGACCCCUUGGUGGCAG
--..(((((......)))))((((((((((..(..(((.((((((((((((...))))))...((((((..((((((..(((....))))))))))))))))))))).....))))..)))))..)))))... ( -62.10, z-score =  -3.04, R)
>consensus
__UUAGCCAUACACAGGGCUUCAUCGGGCGAGAAGCCCUGCUAAAGGUACCGAAGAUACCACUUGGUACUUGAACCGCUCAGAACUCUCCGGUUCGGGUCAUCCCGAGCACCGGGCUGACCAAGUGGAGGCAA
.....(((.....((((((.(((.......))).)))))).................(((((((.......((((((............)))))).(((((.((.(.....).)).))))))))))))))).. (-19.56 = -23.23 +   3.68)

alignment

secondary structure

dotplot

Window 1

Location	160,605 – 160,738
Length	133
Sequences	3
Columns	133
Reading direction	reverse
Mean pairwise identity	61.71
Shannon entropy	0.55283
G+C content	0.58241
Mean single sequence MFE	-55.94
Consensus MFE	-24.30
Energy contribution	-23.76
Covariance contribution	-0.54
Combinations/Pair	1.34
Mean z-score	-2.31
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.93
SVM RNA-class probability	0.975541
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrXHet 160605 133 - 204112
UUACCGCAACUUGGUCAGCCUGGGUCCCGGGAUGACCCUAACCGUAAGGGGCUGAGCGGGUCCAGAACGAAGUGGCAUCUUCGUUACCUUUAGCAGGGCAAGUCACCCGCAGAAACUCUGUCUCUGGAUAAGA
...((((.......((((((.(((((.......)))))...((....))))))))))))(((((((((((((......))))))...........(((.......)))((((.....)))).))))))).... ( -49.21, z-score =  -1.05, R)
>droMoj3.scaffold_6496 1647639 131 - 26866924
UUGCCUCCACUCGGACAGCCCGGCGCUCGGGAUGAUCCGAAUCGGAGAGUCCUGAGCGGCUCACGUACCAAGUGGUAUAUGCGGUAUCUAGAGAAAGGCUUCCCGGCCGACGAGGCCUUUCGCAUGGCUAA--
..((((((....)))..(((((.((((((((((..((((...))))..)))))))))).).((..((((....))))..)).))........((((((((((.........))))))))))))..)))...-- ( -56.00, z-score =  -2.11, R)
>droGri2.scaffold_14822 968639 131 - 1097346
CUGCCACCAAGGGGUCAACCCGGUGGGCUGGAUGACCCGAACCGGAGAAAUCUCUGCGGUUCAAGGGUCAAGUGGUACCUCCGGUACCUCCAGCAGGGACUCAACCCCGAUGAAGCCCUGAAAAAGGCCAA--
..(((.(((..(((....)))..)))((((((((((((((((((.(((....))).))))))..))))))...((((((...))))))))))))((((..(((.......)))..))))......)))...-- ( -62.60, z-score =  -3.78, R)
>consensus
UUGCCACCACUCGGUCAGCCCGGCGCCCGGGAUGACCCGAACCGGAGAGACCUGAGCGGCUCAAGAACCAAGUGGUAUCUCCGGUACCUACAGCAGGGCAUCACACCCGAAGAAGCCCUGAAAAUGGCUAA__
.((((((.....(((((.((((.....)))).))))).((.(((............))).)).........)))))).....(((.......((((((.................)))))).....))).... (-24.30 = -23.76 +  -0.54)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:08 2011