Locus 10004

Sequence ID dm3.chr3R
Location 10,496,466 – 10,496,567
Length 101
Max. P 0.998275
window13750 window13751

overview

Window 0

Location 10,496,466 – 10,496,567
Length 101
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 59.64
Shannon entropy 0.69377
G+C content 0.54275
Mean single sequence MFE -31.88
Consensus MFE -18.60
Energy contribution -17.92
Covariance contribution -0.68
Combinations/Pair 1.44
Mean z-score -1.82
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.31
SVM RNA-class probability 0.998275
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10496466 101 + 27905053
--GUCCGUUAUCCCCGUCAGCCUUUUCGUAGUCGUGACU---AUGGUCGUCCCUGUGGUUAUCAUAGCCACAGGUGGCGUUCGUCGGAUGCAUGUCUGCCUGCCUG--------
--(((((........(((((.((......)).).)))).---(((..((((((((((((((...)))))))))).))))..))))))))(((.(....).)))...-------- ( -33.50, z-score =  -2.54, R)
>droEre2.scaffold_4770 10030777 101 + 17746568
--GUCCGUUAUCCUCGUCAGCCUUUUCGUAGUCGUGGCU---GUGGUCGUCCCUGUGGCUAUCAUAGCCACAGGUGGCGUUCGUUGGAUGCAUGUCAGUCUGCCUG--------
--...((((((((....(((((....((....)).))))---).(..((((((((((((((...)))))))))).))))..)...))))).)))............-------- ( -37.40, z-score =  -3.42, R)
>droWil1.scaffold_181130 1283304 79 - 16660200
------------------------UUCCCUGUCAUGGUU---GUGGUUGUCCUUGUGGCUGUCAUAGCCACAGGUGGCAUUCUUUUGCACCAUAUCUGCGUGACUG--------
------------------------......((((((..(---(((((((((((((((((((...)))))))))).)))).........))))))....))))))..-------- ( -30.20, z-score =  -3.19, R)
>droMoj3.scaffold_6540 31210151 106 + 34148556
UUCCACCUCAUCCUCCUCCAGAUUCUCGCCGGGCCAAUUUUCAUAACUGCCUUUGUGGCUGUCGUAGCCACAGGUGGCAUUCUGCUGCAGCAUAUCGGCGUGCCUA--------
........................(.((((((...............((((((((((((((...)))))))))).))))...(((....)))..)))))).)....-------- ( -30.00, z-score =  -0.73, R)
>droGri2.scaffold_14906 11928927 111 - 14172833
CUCCUGCUUAUGUUCCAUCCCGCUCUGCUCGUGUGGACU---GUGGUUGUCAGUAUGGCUAUCGUAGCCACAGGUGGCAUUCUGCUGCAAGAUGUCCGCGUGUCUGUUAUCCAA
........(((((..((((((((.(.....).)))).((---(((((((.(.(((....))).))))))))))(..((.....))..)..))))...)))))............ ( -28.30, z-score =   0.80, R)
>consensus
__CCCCCUUAUCCUCCUCAGCCUUUUCGUAGUCGUGACU___GUGGUUGUCCCUGUGGCUAUCAUAGCCACAGGUGGCAUUCUUCUGCAGCAUGUCUGCGUGCCUG________
............................................((.((((((((((((((...)))))))))).)))).))................................ (-18.60 = -17.92 +  -0.68)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,496,466 – 10,496,567
Length 101
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 59.64
Shannon entropy 0.69377
G+C content 0.54275
Mean single sequence MFE -28.23
Consensus MFE -10.32
Energy contribution -9.92
Covariance contribution -0.40
Combinations/Pair 1.29
Mean z-score -1.63
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.904872
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10496466 101 - 27905053
--------CAGGCAGGCAGACAUGCAUCCGACGAACGCCACCUGUGGCUAUGAUAACCACAGGGACGACCAU---AGUCACGACUACGAAAAGGCUGACGGGGAUAACGGAC--
--------.......(((....)))((((..((...(((.(((((((.........)))))))(((......---.))).............)))...)).)))).......-- ( -27.80, z-score =  -1.53, R)
>droEre2.scaffold_4770 10030777 101 - 17746568
--------CAGGCAGACUGACAUGCAUCCAACGAACGCCACCUGUGGCUAUGAUAGCCACAGGGACGACCAC---AGCCACGACUACGAAAAGGCUGACGAGGAUAACGGAC--
--------...(((........)))((((......((.(.((((((((((...))))))))))).))....(---((((.............)))))....)))).......-- ( -33.32, z-score =  -4.42, R)
>droWil1.scaffold_181130 1283304 79 + 16660200
--------CAGUCACGCAGAUAUGGUGCAAAAGAAUGCCACCUGUGGCUAUGACAGCCACAAGGACAACCAC---AACCAUGACAGGGAA------------------------
--------..((((........(((((((......)))..(((((((((.....)))))).)))...)))).---.....))))......------------------------ ( -21.14, z-score =  -1.25, R)
>droMoj3.scaffold_6540 31210151 106 - 34148556
--------UAGGCACGCCGAUAUGCUGCAGCAGAAUGCCACCUGUGGCUACGACAGCCACAAAGGCAGUUAUGAAAAUUGGCCCGGCGAGAAUCUGGAGGAGGAUGAGGUGGAA
--------......((((..(((.((.(..((((.((((...(((((((.....)))))))..(((....((....))..))).))))....))))..).)).))).))))... ( -34.30, z-score =  -1.09, R)
>droGri2.scaffold_14906 11928927 111 + 14172833
UUGGAUAACAGACACGCGGACAUCUUGCAGCAGAAUGCCACCUGUGGCUACGAUAGCCAUACUGACAACCAC---AGUCCACACGAGCAGAGCGGGAUGGAACAUAAGCAGGAG
...............((.(.((((((((.((.....))...(((((((((...)))))..((((.......)---)))........)))).))))))))...)....))..... ( -24.60, z-score =   0.15, R)
>consensus
________CAGGCACGCAGACAUGCUGCAGAAGAAUGCCACCUGUGGCUAUGAUAGCCACAAGGACAACCAC___AGUCACGACGACGAAAAGGCGGACGAGGAUAACGGAC__
...........(((........)))..........((((...(((((((.....))))))).)).))............................................... (-10.32 =  -9.92 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:15:34 2011