Locus 9682

Sequence ID dm3.chr3R
Location 8,185,023 – 8,185,297
Length 274
Max. P 0.945766
window13282 window13283 window13284

overview

Window 2

Location 8,185,023 – 8,185,190
Length 167
Sequences 6
Columns 178
Reading direction forward
Mean pairwise identity 75.43
Shannon entropy 0.46719
G+C content 0.48934
Mean single sequence MFE -43.82
Consensus MFE -21.94
Energy contribution -23.63
Covariance contribution 1.70
Combinations/Pair 1.18
Mean z-score -2.05
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.916814
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8185023 167 + 27905053
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCCAAAGAAACGCCACCCAUCGCCCACCGAUCGUCCCCCCCUCC----------CCUUUUUUUGCACCACUUU-GGCCACUUAUCAUUCACGGUUGCUGGUUAAACAGCCACUGAAGAUUAGGCCAUUCUCCCCGUGCUCCAAUU
......(((((((((((((((((....((....))................((((.....)))).............----------.....))))))))))))))-((((....(((.((((..((.((((......)))).)))))))))..))))...........)))...... ( -46.10, z-score =  -3.02, R)
>droSim1.chr3R 14313496 178 - 27517382
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCCAAAGAAACGCCACCCAUCACCCACCGAUCGCCCCUGUUUUUUUUUUUUUUUUGUAUUUUUGCACCACUUUUGGCCACUUAACAUUCACGGUGGCUGGUUAAACAGGCGCUGAAGAUUAGGCCAUUCUCCCAGUGCUCCCAUU
......(((((((((((((((((....((....)).(((((((((....(.(((.......))).)....))))))))).............))))))))))))))(((((...(((..((((..(((.(((......))).)))))))..))))))))..........)))...... ( -49.20, z-score =  -1.65, R)
>droSec1.super_0 7358029 172 - 21120651
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCCAAAGAAACGCCACCCAUCACCCACCGAUCGCCCCUGUUUUU------UUUUUGUUUUUUUGCACCACUUUUGGCCACUUAACAUUCACGGUGGCUGGUUAAACAGGCGCUGAAGAUUAGGCCAUUCUCCCCGUGCUCCCAUU
......(((((((((((((((((.(((((....)).(((((((((....(.(((.......))).)....)))))))------))...))).))))))))))))))(((((...(((..((((..(((.(((......))).)))))))..))))))))..........)))...... ( -50.30, z-score =  -2.02, R)
>droYak2.chr3R 12503436 158 + 28832112
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCUAAAGAAACGCCACCCAUCACCCACCGAUCGCCCCU-------------------UUUUCUGCACCACUUU-AACCACUUAACAUUCAUGGUUGCUGGUUAAGCGGGCUCUGAAGAUUAGUCCAUUUUCCCCGCGCUCCAAUU
......(((((((((((((........((....))...(((((........(((.......))).......-------------------.)))))))))))))))-(((((...........))))))))((....(((((....((((((......)))))))))))...)).... ( -42.29, z-score =  -2.24, R)
>droEre2.scaffold_4770 4316800 157 - 17746568
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCCAAAGAAACGCCACCCAUCACCCACCAAUCGCCCCU--------------------UUUUUGCACCACUUU-GGCCACUUAACAUUCAUGGUUGCUGGUUAAGCAGGCGCCGAAGAUUAGUCCAUUUUCCCCGUGCUCCCAUU
........(((((((((((((((....((....)).........((...................))....--------------------.))))))))))))))-)..............((((.((((.....))))(((((.((((((......))))))...))))).)))). ( -39.21, z-score =  -0.84, R)
>droAna3.scaffold_13340 19485939 148 - 23697760
AUUCAAACCAAAGUGGUGCAAAAAAAAAGAUGAGC--AAGACCCACCAACAAUGCCUCCCCACCCACCCGACCAGCU--------CCCUUUUCCGUGCAUCGCUUUUGCCCACUUAACAUUCAAGAUUGCAUGUUAAGUUGGCCCAAACGCAGCGGCC--------------------
.......(((((((((((((....(((((..((((--.....................................)))--------).)))))...))))))))))).(((.(((((((((.((....)).))))))))).)))...........))..-------------------- ( -35.79, z-score =  -2.54, R)
>consensus
AUUCAAAGCGAAGUGGUGCAAAAUGAUGCGCAAGCCAAAGAAACGCCACCCAUCACCCACCGAUCGCCCCU___U_U____________UUUUUUUGCACCACUUU_GGCCACUUAACAUUCACGGUUGCUGGUUAAACAGGCGCUGAAGAUUAGGCCAUUCUCCCCGUGCUCCCAUU
......(((((((((((((((((....((....))....(......).............................................)))))))))))))).((((......(......)....(((......))).............))))...........)))...... (-21.94 = -23.63 +   1.70)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,185,190 – 8,185,297
Length 107
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 72.86
Shannon entropy 0.36150
G+C content 0.33180
Mean single sequence MFE -20.20
Consensus MFE -15.00
Energy contribution -14.79
Covariance contribution -0.21
Combinations/Pair 1.22
Mean z-score -1.64
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886470
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8185190 107 + 27905053
UAUAAAUGGGUUACAGAUUGCUCUUAAAAUAUAUACAUACAUAGGUGCAAAUUCACGAGUAUCUACUUAAAUCAAAAAUUCUAGCAA-----------GUCGCUAGAAUUCUACUAAU
......(((((...((((.((((........(((......))).(((......)))))))))))))))).......(((((((((..-----------...)))))))))........ ( -17.90, z-score =  -1.74, R)
>droSec1.super_0 7358201 94 - 21120651
UAUAAAUGGGCUACAGAUUGCUCCUAAAAUGUGUAUGUACUUAGGUGCAAAUUCUCGAGUACGUACUCAAAUCAAAAA--------------------GCAGCCGCAAUUAAGA----
..(((.((((((.......(((.......((.(((((((((..((........))..))))))))).))........)--------------------)))))).)).)))...---- ( -22.07, z-score =  -1.85, R)
>droSim1.chr3R 14313674 114 - 27517382
UAUAAAUGGGCUACAGAUUGCUCCUAAAAUAUGUAUUUACUUAGGUGCAAAUUCUCGAGUACGUACUCAAAUCAUAAAUUCUAGUAAGUCACUUCAAAGCAGCCGCAAUUAAAA----
..(((.((((((.(...((((.(((((.............))))).))))......((((((.((((..(((.....)))..)))).)).))))....).)))).)).)))...---- ( -20.62, z-score =  -1.32, R)
>consensus
UAUAAAUGGGCUACAGAUUGCUCCUAAAAUAUGUAUAUACUUAGGUGCAAAUUCUCGAGUACGUACUCAAAUCAAAAAUUCUAG_AA___________GCAGCCGCAAUUAAAA____
........((((.(...((((.(((((.............))))).))))......((((....))))..............................).)))).............. (-15.00 = -14.79 +  -0.21)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,185,190 – 8,185,297
Length 107
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 72.86
Shannon entropy 0.36150
G+C content 0.33180
Mean single sequence MFE -25.17
Consensus MFE -13.49
Energy contribution -15.60
Covariance contribution 2.11
Combinations/Pair 1.04
Mean z-score -2.57
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.51
SVM RNA-class probability 0.945766
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8185190 107 - 27905053
AUUAGUAGAAUUCUAGCGAC-----------UUGCUAGAAUUUUUGAUUUAAGUAGAUACUCGUGAAUUUGCACCUAUGUAUGUAUAUAUUUUAAGAGCAAUCUGUAACCCAUUUAUA
......(((((((((((...-----------..)))))))))))(((..((.(((.((((..(((......)))....)))).))).))..)))(((....))).............. ( -20.80, z-score =  -1.51, R)
>droSec1.super_0 7358201 94 + 21120651
----UCUUAAUUGCGGCUGC--------------------UUUUUGAUUUGAGUACGUACUCGAGAAUUUGCACCUAAGUACAUACACAUUUUAGGAGCAAUCUGUAGCCCAUUUAUA
----...(((.((.((((((--------------------.......(((((((....)))))))...((((.((((((...........)))))).))))...)))))))).))).. ( -26.30, z-score =  -3.45, R)
>droSim1.chr3R 14313674 114 + 27517382
----UUUUAAUUGCGGCUGCUUUGAAGUGACUUACUAGAAUUUAUGAUUUGAGUACGUACUCGAGAAUUUGCACCUAAGUAAAUACAUAUUUUAGGAGCAAUCUGUAGCCCAUUUAUA
----...(((.((.((((((...((..((.(((.((((((..((((.(((((((....))))))).((((((......)))))).))))))))))))))).)).)))))))).))).. ( -28.40, z-score =  -2.76, R)
>consensus
____UUUUAAUUGCGGCUGC___________UU_CUAGAAUUUUUGAUUUGAGUACGUACUCGAGAAUUUGCACCUAAGUAAAUACAUAUUUUAGGAGCAAUCUGUAGCCCAUUUAUA
..............((((((...........................(((((((....)))))))...((((.((((((...........)))))).))))...))))))........ (-13.49 = -15.60 +   2.11)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:09:05 2011