Locus 4296

Sequence ID dm3.chr2R
Location 12,002,624 – 12,002,737
Length 113
Max. P 0.999056
window5889 window5890

overview

Window 9

Location 12,002,624 – 12,002,737
Length 113
Sequences 8
Columns 116
Reading direction forward
Mean pairwise identity 63.11
Shannon entropy 0.73318
G+C content 0.51990
Mean single sequence MFE -37.56
Consensus MFE -11.65
Energy contribution -11.24
Covariance contribution -0.41
Combinations/Pair 1.46
Mean z-score -3.24
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.62
SVM RNA-class probability 0.999056
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12002624 113 + 21146708
GCUCAUUUCAAGAGACCCAUAUAUGAUUGGGAUGAACCCACGACCAGUUACUCCAAGAACU-ACACACCCACUUGGAGUAAACUUUGAUCGCGGGCUCAUCCUUGGAACUCCUU--
.....(((((((.((((((........)))).(((.(((.(((.(((((((((((((....-.........))))))))))...))).))).))).))))))))))))......-- ( -37.12, z-score =  -4.89, R)
>droSim1.chr2R 10740122 111 + 19596830
GCUCUUAUCAGGAGAC--GCAUAUUGUUGGGAUGAACCCACGACCAGUUACUCCAAAAACU-ACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAUCUCCUG--
........(((((((.--.((.......(((((((.(((.(((((((((.((((((.....-..........))))))..)))..)))))).))).)))))))))..)))))))-- ( -43.57, z-score =  -5.33, R)
>droSec1.super_1 9498116 111 + 14215200
GCUCUUUUCAGGAGAC--ACAUAUGGUUUGGAUGAACCCACGACCACUUACUCCAAAAACU-ACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAACUCCUG--
........((((((.(--(....))....((((((.(((.((((((....((((((.....-..........)))))).......)))))).))).))))))......))))))-- ( -38.96, z-score =  -5.04, R)
>droYak2.chr2R 4158087 111 - 21139217
GCUCUUUUCAGGAAAU--GCAUUUGACUGGGAUGAACCCACGAUCAGCUACUCCAAAAACU-ACACACCCACCAGGAGGUAGCUUUGGUCGCGGGCUCAUCCUUGGAACUCCUG--
........(((((..(--.((.......(((((((.(((.((((((((((((((.......-............))).)))))..)))))).))).))))))))).)..)))))-- ( -38.02, z-score =  -3.33, R)
>droEre2.scaffold_4845 8734110 111 - 22589142
GCUCUUUUCAGGAGAU--GUAUAUGGUUGGGAUGAACCCACGACGAGCUACUCCAAAAUUU-ACACACCCACUAGGAGGAAGCUUUGGUCGCGGGCUCAUCCUUAGAACUCCUG--
........((((((.(--.((.......(((((((.(((.(((((((((.((((.......-............))))..)))))..)))).))).))))))))).).))))))-- ( -39.32, z-score =  -3.46, R)
>dp4.chr3 18619673 108 + 19779522
CCUCUUGUCAAAGCUU-----UUCAAUUGGGCGCAACCAAAGGCGGCCUCCUCCAGCCAG--ACACACCCACU-GGAGGGGUCCUCCUCGAUGGGAUGUUCCCCUGAAGUCCUCUG
........((.((..(-----((((...(((.(((.(((.(((.((.(((((((((....--.........))-))))))).)).)))...)))..))).))).)))))..)).)) ( -35.52, z-score =  -0.57, R)
>droPer1.super_34 566149 108 + 916997
CCUCUUGUCAAAGCUU-----UUCAAUUGGGCGCAACCAAAGGCGGCCUCCUCCAGCCAG--ACACACCCACU-GGAGGGGUCCUCCUCGAUGGGAUGUCCCCCUGAAGUCCUCUG
........((.((..(-----((((...(((.(((.(((.(((.((.(((((((((....--.........))-))))))).)).)))...)))..))).))).)))))..)).)) ( -35.52, z-score =  -0.48, R)
>droGri2.scaffold_15245 16979493 95 + 18325388
----------AAACAU--AUUUACUAUUGGGCUCAGGCUGGUCCCUGUUGCAUCAGAAUCAGAAGCACCCACCCGAUCUUUGCCACAGUUGACGGGCCUGCCCAAUA---------
----------......--......((((((((..(((((.(((.((((.(((..(((.((..............))))).))).))))..))).)))))))))))))--------- ( -32.44, z-score =  -2.80, R)
>consensus
GCUCUUUUCAAGAGAU__ACAUAUGAUUGGGAUGAACCCACGACCAGCUACUCCAAAAACU_ACACACCCACUUGGAGGAAACUUUGGUCGCGGGCUCAUCCUUGGAACUCCUG__
............................(((((((.((............((((....................))))...............)).)))))))............. (-11.65 = -11.24 +  -0.41)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,002,624 – 12,002,737
Length 113
Sequences 8
Columns 116
Reading direction reverse
Mean pairwise identity 63.11
Shannon entropy 0.73318
G+C content 0.51990
Mean single sequence MFE -45.25
Consensus MFE -7.58
Energy contribution -8.14
Covariance contribution 0.56
Combinations/Pair 1.59
Mean z-score -4.07
Structure conservation index 0.17
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.23
SVM RNA-class probability 0.998007
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12002624 113 - 21146708
--AAGGAGUUCCAAGGAUGAGCCCGCGAUCAAAGUUUACUCCAAGUGGGUGUGU-AGUUCUUGGAGUAACUGGUCGUGGGUUCAUCCCAAUCAUAUAUGGGUCUCUUGAAAUGAGC
--.(((((..(((.(((((((((((((((((....((((((((((.........-....)))))))))).)))))))))))))))))..........)))..)))))......... ( -49.32, z-score =  -6.05, R)
>droSim1.chr2R 10740122 111 - 19596830
--CAGGAGAUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGU-AGUUUUUGGAGUAACUGGUCGUGGGUUCAUCCCAACAAUAUGC--GUCUCCUGAUAAGAGC
--((((((((.((.(((((((((((((((((..(((..(((((((.........-....))))))).))))))))))))))))))))........)).--))))))))........ ( -52.12, z-score =  -6.71, R)
>droSec1.super_1 9498116 111 - 14215200
--CAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGUUUCCUCCAAGUGGGUGUGU-AGUUUUUGGAGUAAGUGGUCGUGGGUUCAUCCAAACCAUAUGU--GUCUCCUGAAAAGAGC
--((((((......(((((((((((((((((.......(((((((.........-....)))))))....)))))))))))))))))....((....)--).))))))........ ( -48.42, z-score =  -6.55, R)
>droYak2.chr2R 4158087 111 + 21139217
--CAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGCUACCUCCUGGUGGGUGUGU-AGUUUUUGGAGUAGCUGAUCGUGGGUUCAUCCCAGUCAAAUGC--AUUUCCUGAAAAGAGC
--((((((......((((((((((((((....((((((.(((............-.......)))))))))..))))))))))))))..((.....))--..))))))........ ( -43.41, z-score =  -3.61, R)
>droEre2.scaffold_4845 8734110 111 + 22589142
--CAGGAGUUCUAAGGAUGAGCCCGCGACCAAAGCUUCCUCCUAGUGGGUGUGU-AAAUUUUGGAGUAGCUCGUCGUGGGUUCAUCCCAACCAUAUAC--AUCUCCUGAAAAGAGC
--((((((......(((((((((((((((...((((..((((....((((....-..)))).)))).)))).)))))))))))))))...........--..))))))........ ( -44.81, z-score =  -4.92, R)
>dp4.chr3 18619673 108 - 19779522
CAGAGGACUUCAGGGGAACAUCCCAUCGAGGAGGACCCCUCC-AGUGGGUGUGU--CUGGCUGGAGGAGGCCGCCUUUGGUUGCGCCCAAUUGAA-----AAGCUUUGACAAGAGG
(((((...((((.(((..((..(((..((((.((.(((((((-(((.((.....--)).)))))))).)))).))))))).))..)))...))))-----...)))))........ ( -44.20, z-score =  -1.45, R)
>droPer1.super_34 566149 108 - 916997
CAGAGGACUUCAGGGGGACAUCCCAUCGAGGAGGACCCCUCC-AGUGGGUGUGU--CUGGCUGGAGGAGGCCGCCUUUGGUUGCGCCCAAUUGAA-----AAGCUUUGACAAGAGG
(((((...(((((((.(.((..(((..((((.((.(((((((-(((.((.....--)).)))))))).)))).))))))).))).)))...))))-----...)))))........ ( -44.00, z-score =  -1.10, R)
>droGri2.scaffold_15245 16979493 95 - 18325388
---------UAUUGGGCAGGCCCGUCAACUGUGGCAAAGAUCGGGUGGGUGCUUCUGAUUCUGAUGCAACAGGGACCAGCCUGAGCCCAAUAGUAAAU--AUGUUU----------
---------((((((((((((..(((..((((.(((.((((((((........))))).)))..))).)))).)))..))))..))))))))......--......---------- ( -35.70, z-score =  -2.15, R)
>consensus
__CAGGAGUUCCAAGGAUGAGCCCGCGACCAAAGCUUCCUCCAAGUGGGUGUGU_AGUUUUUGGAGUAACUGGUCGUGGGUUCAUCCCAAUCAUAUAC__AUCUCCUGAAAAGAGC
.......((((((((((((..(((((..................)))))..)))....)))))))))................................................. ( -7.58 =  -8.14 +   0.56)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:26:27 2011