Locus 1219

Sequence ID	dm3.chr2L
Location	9,234,095 – 9,234,209
Length	114
Max. P	0.905947

overview

Window 3

Location	9,234,095 – 9,234,209
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	73.42
Shannon entropy	0.42161
G+C content	0.63986
Mean single sequence MFE	-41.25
Consensus MFE	-26.79
Energy contribution	-26.60
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-1.15
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.13
SVM RNA-class probability	0.558959
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9234095 114 + 23011544
CAACAAAUACAACAGCGGCAACAUAUCGGUCUGCAACCUGCCGCGCUCAUCGCCGGCCGCUGCAACAGCAGCCGUUACACUAUCGUCGGCCGCCGGCGGUAUUGGCAGCAACUU------
..............((((((.......(((.....)))))))))(((.(((((((((.((((...)))).((((..((......)))))).)))))))))...)))........------ ( -41.51, z-score =  -1.72, R)
>droWil1.scaffold_180708 236350 117 + 12563649
UACCAGCCACAGAGAUAGCAACA---CAGUUUGCAAUCUGCCGCGCUCAUCGCCGGCUGCGGCCACUGCAGCCGUUACAAUCUCAUCAGCCGCUGGCGGCAUCGGCAGCAAUAAUUUAUU
.....(((...(((((.((((..---....))))........(((.....)))(((((((((...))))))))).....)))))....((((....))))...))).............. ( -39.50, z-score =  -1.62, R)
>droPer1.super_5 5960248 108 + 6813705
CGGCAAGUACAACAGCAGCAACAUCUCCGUGUGCAACCUGCCACGCUCCUCGCCGGCCGCCGCCACAGCAGCCGUCACCCUCUCUGCGGCCGCGGGCGGCAGCAGCCU------------
.(((..((......)).((........((((.((.....))))))......((((.((((.(((.(((.((..........))))).))).)))).)))).)).))).------------ ( -42.00, z-score =  -0.64, R)
>dp4.chr4_group5 1552188 108 + 2436548
CGGCAAGUACAACAGCAGCAACAUCUCCGUGUGCAACCUGCCACGCUCCUCGCCGGCCGCCGCCACAGCAGCCGUCACCCUCUCUGCGGCCGCGGGCGGCAGCAGCCU------------
.(((..((......)).((........((((.((.....))))))......((((.((((.(((.(((.((..........))))).))).)))).)))).)).))).------------ ( -42.00, z-score =  -0.64, R)
>consensus
CAGCAAGUACAACAGCAGCAACAUCUCCGUGUGCAACCUGCCACGCUCAUCGCCGGCCGCCGCCACAGCAGCCGUCACACUCUCUGCGGCCGCGGGCGGCAGCAGCAG____________
.................(((((......)).)))..........(((.((.((((.((((.((....)).((((............)))).)))).)))))).))).............. (-26.79 = -26.60 +  -0.19)

alignment

secondary structure

dotplot

Window 4

Location	9,234,095 – 9,234,209
Length	114
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.42
Shannon entropy	0.42161
G+C content	0.63986
Mean single sequence MFE	-52.70
Consensus MFE	-37.65
Energy contribution	-39.40
Covariance contribution	1.75
Combinations/Pair	1.27
Mean z-score	-1.51
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.18
SVM RNA-class probability	0.905947
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 9234095 114 - 23011544
------AAGUUGCUGCCAAUACCGCCGGCGGCCGACGAUAGUGUAACGGCUGCUGUUGCAGCGGCCGGCGAUGAGCGCGGCAGGUUGCAGACCGAUAUGUUGCCGCUGUUGUAUUUGUUG
------.....((((((.........))))))..(((((((((...(((((((((...)))))))))((.....))((((((.((((.....)))).)))))))))))))))........ ( -45.80, z-score =  -0.47, R)
>droWil1.scaffold_180708 236350 117 - 12563649
AAUAAAUUAUUGCUGCCGAUGCCGCCAGCGGCUGAUGAGAUUGUAACGGCUGCAGUGGCCGCAGCCGGCGAUGAGCGCGGCAGAUUGCAAACUG---UGUUGCUAUCUCUGUGGCUGGUA
........(((((.((((..((((....))))..((......))..)))).)))))(((((((((((((.....)).))))((((.((((....---..)))).)))).))))))).... ( -45.20, z-score =  -0.66, R)
>droPer1.super_5 5960248 108 - 6813705
------------AGGCUGCUGCCGCCCGCGGCCGCAGAGAGGGUGACGGCUGCUGUGGCGGCGGCCGGCGAGGAGCGUGGCAGGUUGCACACGGAGAUGUUGCUGCUGUUGUACUUGCCG
------------..(((.((((((.((((.(((((((((..(....)..)).))))))).)))).)))).)).)))..(((((((.(((.((((((......)).)))))))))))))). ( -59.90, z-score =  -2.45, R)
>dp4.chr4_group5 1552188 108 - 2436548
------------AGGCUGCUGCCGCCCGCGGCCGCAGAGAGGGUGACGGCUGCUGUGGCGGCGGCCGGCGAGGAGCGUGGCAGGUUGCACACGGAGAUGUUGCUGCUGUUGUACUUGCCG
------------..(((.((((((.((((.(((((((((..(....)..)).))))))).)))).)))).)).)))..(((((((.(((.((((((......)).)))))))))))))). ( -59.90, z-score =  -2.45, R)
>consensus
____________AGGCCGAUGCCGCCCGCGGCCGAAGAGAGGGUAACGGCUGCUGUGGCGGCGGCCGGCGAGGAGCGCGGCAGGUUGCACACGGAGAUGUUGCUGCUGUUGUACUUGCCG
.............((((((((((((..(((((((............))))))).))))))))))))((((((.(((((((((....(((........))))))))).)))...)))))). (-37.65 = -39.40 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:27:49 2011