Locus 8594

Sequence ID	dm3.chr3RHet
Location	1,412,292 – 1,412,479
Length	187
Max. P	0.997337

overview

Window 2

Location	1,412,292 – 1,412,479
Length	187
Sequences	5
Columns	187
Reading direction	forward
Mean pairwise identity	87.10
Shannon entropy	0.23793
G+C content	0.46407
Mean single sequence MFE	-63.34
Consensus MFE	-50.66
Energy contribution	-52.14
Covariance contribution	1.48
Combinations/Pair	1.19
Mean z-score	-2.63
Structure conservation index	0.80
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.14
SVM RNA-class probability	0.983702
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1412292 187 + 2517507
UUUGACAUAGUCAUAUUCUUGUUGUUGUAGCUUCUAAGCGGAUGUGUCUGCAGUUGCGACAUUCGCUUAUUGGCUACAAUGUUUCCCGGUUCAAUAAAAUUCUUAGUGAACGUGAAACGAUCGAGGGGGUUUCGGUGGGGAGUGUAGGCGUGUUACCGAUGGGUCGGUAACUCGCGCACUAUAAUGA
......((((((((((((((...(((((((((..(((((((((((...(((....))))))))))))))..)))))))))(((((.((.((((.(((.....))).)))))).))))).((((((.....)))))).))))))))..(((.((((((((....)))))))).)))).)))))..... ( -68.10, z-score =  -3.85, R)
>droEre2.scaffold_4845 22547886 183 - 22589142
-UUGACAUAGU---AUUCUUGCUGAUGUAGCUUCUAAGCGGAUGUGUCUGCAGUUGCGACAUUCGCUUAUUAGCUACAAUGUUUCCCGGUUCAAUAACAUUGUUAGUGAAUUUGGAACGAUCGAGGGGGUUUCGGUGGAGAGUGUAGGCGUGGUACCGAUGGGUCGGUAACUCGUGCGUUGUUGUGA
-....((((((---(((((..(((((((((((..(((((((((((...(((....))))))))))))))..))))))).((((.((..(((((.((((...)))).)))))..))))))............))))..).)))))...(((.(.((((((....)))))).).)))......))))). ( -61.00, z-score =  -2.01, R)
>droYak2.chr2L_random 2740495 187 - 4064425
UUUGACAUAGUCAUAUUUUUGCUGAUGUAGCUUCUAAGCGGAUGUGUCUGCAGUUGCGACAUUCGCUUAUUAACUACAAUGUUUCCCGGUUCAAUAACAUUGUUAGUGAACUUGGAACGAUCGAGGGGGUUUCGGUGGGGAGUGUAGGCAUGGUACCGAUGGGUCGGUAACUCGUGCGAAAUGUGGA
..........(((((((((......(((((.(..(((((((((((...(((....))))))))))))))..).)))))(..((((((((((((.((((...)))).))))))((((((..(....)..))))))..))))))..)..((((((((((((....))))).)).)))))))))))))). ( -60.50, z-score =  -1.94, R)
>droSec1.super_81 62816 178 + 123496
UUUGACCUAGUCAUAUUCUUGCUGAUGUAGCUUCUAAGCGGAUGUGUCUGCAGUUGAGACAUUCGCUUAUUGGAUACAAUGUUUCCCGGUUCAAUAACAUUGUUAGUGAACUUGGAGCGAUCGUGGGGGUUUUGGUGGGGAGUGUAGGCGUGGUACCGAUGGGUCGGUAACGCGACCA---------
.....(((..(((.(((((..(.((((((.((..(((((((((((.((.......)).)))))))))))..)).)))..((((.((.((((((.((((...)))).)))))).))))))))))..)))))..)))..)))......((((((.((((((....)))))).)))).)).--------- ( -65.30, z-score =  -3.09, R)
>droSim1.chrU 6331469 179 - 15797150
UUUGACAUAAUCAUAUUCUUGCUGAUGUAGCUUCUAAGCGGAUGUGUCCGCAGUUGCGACAUUCGCUUAUUGGAUACAUUA------AGUUCAAUAACAUUGUUAGUGAACUUGGAGCGAUCGUGGGGGUUUCGGUGGGGAGUGUAUGCGUGGUACCGAUGGGUCGGUAACUCGCGCACCCGAAU--
..........((...((((..((((...(((((((..(((((....)))))....((((...((((((..((....)).((------((((((.((((...)))).)))))))))))))))))))))))))))))..))))..(..(((((((((((((....))))).)).))))))..)))..-- ( -61.80, z-score =  -2.23, R)
>consensus
UUUGACAUAGUCAUAUUCUUGCUGAUGUAGCUUCUAAGCGGAUGUGUCUGCAGUUGCGACAUUCGCUUAUUGGCUACAAUGUUUCCCGGUUCAAUAACAUUGUUAGUGAACUUGGAACGAUCGAGGGGGUUUCGGUGGGGAGUGUAGGCGUGGUACCGAUGGGUCGGUAACUCGCGCACUAUAAUGA
...............((((..(((((((((((..(((((((((((...(((....))))))))))))))..)))))))....((((.((((((.((((...)))).)))))).))))..............))))..))))......(((((.((((((....))))))...))))).......... (-50.66 = -52.14 +   1.48)

alignment

secondary structure

dotplot

Window 3

Location	1,412,292 – 1,412,479
Length	187
Sequences	5
Columns	187
Reading direction	reverse
Mean pairwise identity	87.10
Shannon entropy	0.23793
G+C content	0.46407
Mean single sequence MFE	-47.04
Consensus MFE	-31.72
Energy contribution	-31.96
Covariance contribution	0.24
Combinations/Pair	1.15
Mean z-score	-3.81
Structure conservation index	0.67
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.08
SVM RNA-class probability	0.997337
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1412292 187 - 2517507
UCAUUAUAGUGCGCGAGUUACCGACCCAUCGGUAACACGCCUACACUCCCCACCGAAACCCCCUCGAUCGUUUCACGUUCACUAAGAAUUUUAUUGAACCGGGAAACAUUGUAGCCAAUAAGCGAAUGUCGCAACUGCAGACACAUCCGCUUAGAAGCUACAACAACAAGAAUAUGACUAUGUCAAA
........(((.(((.((((((((....)))))))).))).)))..((((....(((((..........)))))..(((((.((((...)))).))))).))))....(((((((...((((((..((((((....)).))))....))))))...)))))))...........((((...)))).. ( -54.50, z-score =  -5.71, R)
>droEre2.scaffold_4845 22547886 183 + 22589142
UCACAACAACGCACGAGUUACCGACCCAUCGGUACCACGCCUACACUCUCCACCGAAACCCCCUCGAUCGUUCCAAAUUCACUAACAAUGUUAUUGAACCGGGAAACAUUGUAGCUAAUAAGCGAAUGUCGCAACUGCAGACACAUCCGCUUAGAAGCUACAUCAGCAAGAAU---ACUAUGUCAA-
..........((.((((.((((((....))))))............((......))......))))....((((...((((.((((...)))).))))...))))....(((((((..((((((..((((((....)).))))....))))))..)))))))...))......---..........- ( -43.40, z-score =  -3.54, R)
>droYak2.chr2L_random 2740495 187 + 4064425
UCCACAUUUCGCACGAGUUACCGACCCAUCGGUACCAUGCCUACACUCCCCACCGAAACCCCCUCGAUCGUUCCAAGUUCACUAACAAUGUUAUUGAACCGGGAAACAUUGUAGUUAAUAAGCGAAUGUCGCAACUGCAGACACAUCCGCUUAGAAGCUACAUCAGCAAAAAUAUGACUAUGUCAAA
..........(((((((.((((((....)))))).).................(((.......))).))))(((..(((((.((((...)))).)))))..))).....(((((((..((((((..((((((....)).))))....))))))..)))))))...)).......((((...)))).. ( -46.00, z-score =  -3.76, R)
>droSec1.super_81 62816 178 - 123496
---------UGGUCGCGUUACCGACCCAUCGGUACCACGCCUACACUCCCCACCAAAACCCCCACGAUCGCUCCAAGUUCACUAACAAUGUUAUUGAACCGGGAAACAUUGUAUCCAAUAAGCGAAUGUCUCAACUGCAGACACAUCCGCUUAGAAGCUACAUCAGCAAGAAUAUGACUAGGUCAAA
---------(((((((((((((((....))))))..)))).............................(((((..(((((.((((...)))).)))))..))).....((((.(...((((((.((((.((.......)).)))).))))))...).))))...))........)))))....... ( -43.10, z-score =  -2.68, R)
>droSim1.chrU 6331469 179 + 15797150
--AUUCGGGUGCGCGAGUUACCGACCCAUCGGUACCACGCAUACACUCCCCACCGAAACCCCCACGAUCGCUCCAAGUUCACUAACAAUGUUAUUGAACU------UAAUGUAUCCAAUAAGCGAAUGUCGCAACUGCGGACACAUCCGCUUAGAAGCUACAUCAGCAAGAAUAUGAUUAUGUCAAA
--(((((((((((((.(.((((((....)))))).).)))..................................(((((((.((((...)))).))))))------)...)))))).....((..((((.((..(((((((....)))))..))..)).))))..))..)))).((((...)))).. ( -48.20, z-score =  -3.35, R)
>consensus
UCAUUAUAGUGCACGAGUUACCGACCCAUCGGUACCACGCCUACACUCCCCACCGAAACCCCCUCGAUCGUUCCAAGUUCACUAACAAUGUUAUUGAACCGGGAAACAUUGUAGCCAAUAAGCGAAUGUCGCAACUGCAGACACAUCCGCUUAGAAGCUACAUCAGCAAGAAUAUGACUAUGUCAAA
.............((.(.((((((....)))))).).))..............................(((((..(((((.((((...)))).)))))..))).....((((((...((((((..((((((....)).))))....))))))...))))))...)).................... (-31.72 = -31.96 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:48:30 2011