Locus 6243

Sequence ID	dm3.chr3L
Location	4,947,279 – 4,947,418
Length	139
Max. P	0.994261

overview

Window 7

Location	4,947,279 – 4,947,392
Length	113
Sequences	7
Columns	117
Reading direction	reverse
Mean pairwise identity	71.04
Shannon entropy	0.54217
G+C content	0.42092
Mean single sequence MFE	-33.68
Consensus MFE	-14.50
Energy contribution	-15.43
Covariance contribution	0.92
Combinations/Pair	1.45
Mean z-score	-2.80
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.68
SVM RNA-class probability	0.994261
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4947279 113 - 24543557
-UUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGCCACUUAGUUUUAGUUAGC---UAGCAUGCCACCCAAAACUUAAUCCAAUCUCUGGCUCAGUUGACAAUAGAGCCGGA
-(((((((((((((((((((...((((.......)))).)))))))))))).((((((---(.(...((((.....................)))).))))))))....))))))). ( -39.40, z-score =  -4.43, R)
>droSim1.chr3L 4485578 114 - 22553184
-UUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGCCACUUAGUUUUAGUUAGCAGCUAGCGUGCCACCCAAAACUUAAUCCAA--UCUGGCUCAGCUGACAAUAGAGCCGGA
-(((((((((((((((((((...((((.......)))).)))))))))))).((((((((((((..((.................)).--.))))))..))))))....))))))). ( -43.13, z-score =  -4.72, R)
>droSec1.super_2 4927896 114 - 7591821
-UUGGCUCGAAAUUAAGUGGAAAAGUCUUUCCUUGACUGCCACUUAGUUUUAGUUAGCAGCUUGCGUGCCACCCAAAACUUAAUCCAA--UCUGGCUCAGCUGACAAUAGAGCCGGA
-(((((((((((((((((((...((((.......)))).)))))))))))).((((((.(....)(.((((.................--..)))).).))))))....))))))). ( -41.81, z-score =  -4.46, R)
>droYak2.chr3L 5529524 112 - 24197627
UUUGGCUCGAAAUGAAGUGGAAAAGUCUUUCGUUGACUGCCACUUAGUUUUAGUUAGC---UAGCAUGCUACCGAAAACUUAAUCCAA--UCUGGCUUAGCCGACAAUAGAGCCGGA
(((((((((((((.((((((...((((.......)))).)))))).))))).((..((---((((........((........))...--....)).))))..))....)))))))) ( -34.96, z-score =  -2.77, R)
>droEre2.scaffold_4784 7659919 113 - 25762168
-UUGGCUGGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGCCACUUAGUUUUAGUCAGC-UGUAGCAUGCCACCGAAAACUUAAUCCAA--UCUGGCUCAGCCGACAAUAGAGCCGGA
-((((((.((((((((((((...((((.......)))).)))))))))))).(((.((-((.(((........((........))...--....))))))).))).....)))))). ( -38.76, z-score =  -3.36, R)
>dp4.chrXR_group8 3104385 97 - 9212921
-UUCAAAUUGAAUCGAGUGGAAAAGUCUUUGGCUG--UGU-GCUUUGCUUUGCUU----------UUGCCUUUCGAAACUUAAUCUAAAUGCGGAUUAC-AAGAGGGUAAGU-----
-.((...(((..(((((.((((((((....(((..--...-.....)))..))))----------)).)).)))))....((((((......)))))))-))...)).....----- ( -18.00, z-score =   0.79, R)
>droPer1.super_8066 74 93 + 1396
-UUCAAAUUGAAUCGAGUGUAAAAGUCGUUCGAUG--UGA------GCUUUGCUU----------UUGCCUUUCGAAACUUAAUCUAAAUGCGGAUUACAAAGAGGGUAAGU-----
-((((.((((((.(((.(.....).))))))))).--)))------).......(----------((((((((.......((((((......))))))....))))))))).----- ( -19.70, z-score =  -0.64, R)
>consensus
_UUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGCCACUUAGUUUUAGUUAGC___UAGCAUGCCACCCAAAACUUAAUCCAA__UCUGGCUCAGCUGACAAUAGAGCCGGA
...((((((((((.((((((...((((.......)))).)))))).))))).(((.((.........((((.....................))))...)).)))....)))))... (-14.50 = -15.43 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	4,947,318 – 4,947,418
Length	100
Sequences	7
Columns	108
Reading direction	reverse
Mean pairwise identity	68.56
Shannon entropy	0.58177
G+C content	0.40004
Mean single sequence MFE	-28.20
Consensus MFE	-8.95
Energy contribution	-9.71
Covariance contribution	0.76
Combinations/Pair	1.38
Mean z-score	-2.28
Structure conservation index	0.32
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.95
SVM RNA-class probability	0.859932
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4947318 100 - 24543557
UUAAACGAAGAGCGAAGGAAAA---UCGCUUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGC--CACUUAGUUUUAGUU---AGCUAGCAUGCCACCCAAAA
...(((...((((.((((....---.).))).))))((((((((((((...((((.......)))).)--))))))))))).)))---.((......))......... ( -30.80, z-score =  -3.02, R)
>droSim1.chr3L 4485615 103 - 22553184
UUAAACGAAGAGCGAAGGAAAA---UCGCUUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGC--CACUUAGUUUUAGUUAGCAGCUAGCGUGCCACCCAAAA
.........((((((.......---))))))(((.(((((((((((((...((((.......)))).)--))))))))))).(((((...)))))).)))........ ( -34.40, z-score =  -3.37, R)
>droSec1.super_2 4927933 103 - 7591821
UUAAACGAAGAGCGAAGGAAAA---UCGCUUGGCUCGAAAUUAAGUGGAAAAGUCUUUCCUUGACUGC--CACUUAGUUUUAGUUAGCAGCUUGCGUGCCACCCAAAA
.........((((((.......---))))))(((.(((((((((((((...((((.......)))).)--))))))))))).....((.....))).)))........ ( -33.20, z-score =  -3.06, R)
>droYak2.chr3L 5529561 103 - 24197627
UUAAAUGAAAAGCAAAGGAAAAUCGUCGUUUGGCUCGAAAUGAAGUGGAAAAGUCUUUCGUUGACUGC--CACUUAGUUUUAGUU---AGCUAGCAUGCUACCGAAAA
............((((.((......)).))))(((.(((((.((((((...((((.......)))).)--))))).))))))))(---(((......))))....... ( -24.10, z-score =  -1.07, R)
>droEre2.scaffold_4784 7659956 102 - 25762168
UUAAACGAAGAGCGAAGGAAAA---GCGCUUGGCUGGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGC--CACUUAGUUUUAGUCAGCUG-UAGCAUGCCACCGAAAA
.....((....((.........---))(((((((((((((((((((((...((((.......)))).)--)))))))))))...))))))-.))).......)).... ( -31.20, z-score =  -2.13, R)
>dp4.chrXR_group8 3104418 92 - 9212921
UUAAACCAAAUUGAAGAGGGAAAAGUACUUCAAAUUG-AAUCGAGUGGAAAAGUCUUUGGCUGUGUGCUUUGCUUUGCUUUUGCCUUUCGAAA---------------
......(((.((((((...........)))))).)))-..(((((.((((((((....(((..........)))..)))))).)).)))))..--------------- ( -19.40, z-score =  -0.25, R)
>droPer1.super_8066 108 87 + 1396
UUAAACCAAAUUGAAGAGGGAAAAGUACUUCAAAUUG-AAUCGAGUGUAAAAGUCGUUCGAUGUG-----AGCUUUGCUUUUGCCUUUCGAAA---------------
..........((((.((((.(((((((.((((.((((-((.(((.(.....).))))))))).))-----))...))))))).))))))))..--------------- ( -24.30, z-score =  -3.06, R)
>consensus
UUAAACGAAGAGCGAAGGAAAA___UCGCUUGGCUCGAAAUUAAGUGGAAAAGUCUUUCGUUGACUGC__CACUUAGUUUUAGUUAGCAGCUAGCAUGCCACCCAAAA
.........((((.(((...........))).))))(((((.(((((....((((.......))))....))))).)))))........................... ( -8.95 =  -9.71 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:03:51 2011