Locus 4375

Sequence ID dm3.chr2R
Location 12,619,645 – 12,619,746
Length 101
Max. P 0.732864
window5998 window5999

overview

Window 8

Location 12,619,645 – 12,619,745
Length 100
Sequences 7
Columns 101
Reading direction forward
Mean pairwise identity 72.59
Shannon entropy 0.49926
G+C content 0.50580
Mean single sequence MFE -25.85
Consensus MFE -15.58
Energy contribution -15.79
Covariance contribution 0.21
Combinations/Pair 1.11
Mean z-score -0.89
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.05
SVM RNA-class probability 0.520600
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12619645 100 + 21146708
CAACUGCAACUCGAACUGCAAGUCUAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAGUU
.((((.(((.....((((((((((.....((.(((((((.((....)).).))))))....))....)))))))).)).((.-.....))...))).)))) ( -27.10, z-score =  -0.75, R)
>droAna3.scaffold_13266 5907284 86 - 19884421
-----------CAACAUCAGACUCGAACCUGUUGGCCACUGCACUUGUCGUUUUAGCCAACU----CGCCAUGCACGUGGCUAUAGUUUCAUACAAGUGCC
-----------...((.(((........))).))......((((((((.....((((((...----.((...))...)))))).........)))))))). ( -20.84, z-score =  -0.71, R)
>droEre2.scaffold_4845 9356073 100 - 22589142
CAACGGCAACUCGAACUGCAAGCCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAAUU
(((..((((.....((((((((((((...((.(((((((.((....)).).))))))....))..)))))))))).))....-...))))...)))..... ( -34.30, z-score =  -2.59, R)
>droYak2.chr2R 4779434 100 - 21139217
CGACGGCAACUCGAACUGCAAGUUGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAGUU
(((.(....)))).((((((((((((...((.(((((((.((....)).).))))))....))..)))))))))).)).((.-.....))........... ( -30.70, z-score =  -0.92, R)
>droSec1.super_1 10125499 88 + 14215200
------------CAACUGCAACUCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUUCACGUGGCU-CAUUUGCAUAUUGAAGUU
------------.((((.(((...........(((((((.((....)).).))))))....(((((.((((.......))))-.)))))....))).)))) ( -19.40, z-score =   0.31, R)
>droPer1.super_37 660474 84 - 760358
------------CAACUCGAACACGCACAUGUUGGCCGCUGCACUUGUCGCUCGAACUCCUC----CGGCAUGCACGUGGCU-CAUUUGCAUUUUGUGGUU
------------.((((((((...(((.(((..((((((((((..(((((...(....)...----))))))))).))))))-))).)))..)))).)))) ( -24.80, z-score =  -0.74, R)
>dp4.chr3 680632 84 - 19779522
------------CAACUCGAACACGCACAUGUUGGCCGCUGCACUUGUCGCUCGAACUCCUC----CGGCAUGCACGUGGCU-CAUUUGCAUUUUGUUGUU
------------.(((.((((...(((.(((..((((((((((..(((((...(....)...----))))))))).))))))-))).)))..))))..))) ( -23.80, z-score =  -0.81, R)
>consensus
___________CCAACUGCAACUCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU_CAUUUGCAUAUUGAAGUU
............................((((.((((((((((...((((................)))).)))).))))))......))))......... (-15.58 = -15.79 +   0.21)

alignment

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secondary structure

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dotplot

Postscript

Window 9

Location 12,619,646 – 12,619,746
Length 100
Sequences 7
Columns 101
Reading direction forward
Mean pairwise identity 72.89
Shannon entropy 0.49536
G+C content 0.50414
Mean single sequence MFE -26.78
Consensus MFE -15.58
Energy contribution -15.79
Covariance contribution 0.21
Combinations/Pair 1.11
Mean z-score -1.22
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.732864
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12619646 100 + 21146708
AACUGCAACUCGAACUGCAAGUCUAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAGUUG
.....((((((((((((((((((.....((.(((((((.((....)).).))))))....))....)))))))).)).((.-.....))...))).))))) ( -29.30, z-score =  -1.51, R)
>droAna3.scaffold_13266 5907285 86 - 19884421
-----------AACAUCAGACUCGAACCUGUUGGCCACUGCACUUGUCGUUUUAGCCAACU----CGCCAUGCACGUGGCUAUAGUUUCAUACAAGUGCCA
-----------..((.(((........))).))......((((((((.....((((((...----.((...))...)))))).........)))))))).. ( -20.84, z-score =  -0.65, R)
>droEre2.scaffold_4845 9356074 100 - 22589142
AACGGCAACUCGAACUGCAAGCCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAAUUG
...(....)((((((((((((((((...((.(((((((.((....)).).))))))....))..)))))))))).)).((.-.....))...))))..... ( -34.20, z-score =  -2.58, R)
>droYak2.chr2R 4779435 100 - 21139217
GACGGCAACUCGAACUGCAAGUUGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU-CAUUUGCAUAUUGAAGUUG
.....((((((((((((((((((((...((.(((((((.((....)).).))))))....))..)))))))))).)).((.-.....))...))).))))) ( -32.00, z-score =  -1.42, R)
>droSec1.super_1 10125500 88 + 14215200
------------AACUGCAACUCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUUCACGUGGCU-CAUUUGCAUAUUGAAGUUG
------------.....(((((..((..((.(((((((.((....)).).))))))....(((((.((((.......))))-.)))))))..))..))))) ( -21.70, z-score =  -0.50, R)
>droPer1.super_37 660475 84 - 760358
------------AACUCGAACACGCACAUGUUGGCCGCUGCACUUGUCGCUCGAACUCCUC----CGGCAUGCACGUGGCU-CAUUUGCAUUUUGUGGUUG
------------((((((((...(((.(((..((((((((((..(((((...(....)...----))))))))).))))))-))).)))..)))).)))). ( -25.20, z-score =  -0.90, R)
>dp4.chr3 680633 84 - 19779522
------------AACUCGAACACGCACAUGUUGGCCGCUGCACUUGUCGCUCGAACUCCUC----CGGCAUGCACGUGGCU-CAUUUGCAUUUUGUUGUUG
------------(((.((((...(((.(((..((((((((((..(((((...(....)...----))))))))).))))))-))).)))..))))..))). ( -24.20, z-score =  -0.97, R)
>consensus
____________AACUGCAACUCGAACGUGUUGGCCACUGCACUUGUCGUUGGCCAUCUUCAAAUCGGCUUGCACGUGGCU_CAUUUGCAUAUUGAAGUUG
...........................((((.((((((((((...((((................)))).)))).))))))......)))).......... (-15.58 = -15.79 +   0.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:28:00 2011