Locus 2165

Sequence ID dm3.chr2L
Location 16,694,120 – 16,694,225
Length 105
Max. P 0.995527
window2984 window2985

overview

Window 4

Location 16,694,120 – 16,694,225
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 61.41
Shannon entropy 0.71071
G+C content 0.53307
Mean single sequence MFE -31.22
Consensus MFE -14.62
Energy contribution -15.52
Covariance contribution 0.90
Combinations/Pair 1.57
Mean z-score -1.89
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.81
SVM RNA-class probability 0.995527
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16694120 105 + 23011544
AGCGCCUGU-UGGGUUUGGCAACAAAACAUCCUUUUCCCAGCCACGAUGGGAAAUUGGUAAGGGAAGGGGUGGGGUGGUCGUGGAAUAGGCGGAGGGACAGAGGGG
..(((((((-(.....((((.((....(((((((((((..((((...........))))..)))))))))))..)).))))...)))))))).............. ( -35.30, z-score =  -1.47, R)
>droWil1.scaffold_181132 155375 94 - 1035393
GGCGCCUGU--UGGGUAUGCAGCAAAAAAAAUCUCUCUAAGCUGCU-UGGAAAAGGAGGUUAGGUUGGGUUGGUUGUGUUGUGAAGUUCAGGGGGCG---------
..(((((.(--((..(..((((((.((..(((((.(((((.((.((-(....))).)).)))))..)))))..)).))))))...)..))).)))))--------- ( -34.80, z-score =  -4.29, R)
>droAna3.scaffold_12916 311354 81 - 16180835
AGCGCCUGU--UGGU-AGGCAACGAAAAAUCCCUUUCGCAAGGAUAAUAGCAAAG-GAUGGGGGGAGAGACUGC----UAGUGAGUAGG-----------------
...(((((.--...)-)))).........((((((((....)))......((...-..)).)))))....((((----(....))))).----------------- ( -19.20, z-score =   0.23, R)
>droEre2.scaffold_4845 19763746 90 + 22589142
AGCGCCUGUGUUGGUUGGGCAACAAAGCAUCCUUUUCCCAGCCAGGAUGGCAAGUUGGCAGGGGAAGAGGAGC-----UCGUGGGAGAGAGUGGG-----------
...((...(((((......)))))..)).((((((((((.(((((.........)))))..))))))))))((-----((........))))...----------- ( -32.80, z-score =  -0.92, R)
>droYak2.chr2R 16730174 94 - 21139217
AGCGCCUGU--UGGUUUGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAGGAAAUUGGUAAGGGAAGAGGAGC-----UCGUGGGAGAGCGUUAGAGGGGG-----
..(.(((..--((.((((....)))).))((((((((((.(((((.........)))))..))))))))))((-----((......)))).....))).).----- ( -35.30, z-score =  -2.72, R)
>droSim1.chr2L 16390287 92 + 22036055
AGCGCCUGU--UGGUUGGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAUUAAAUUGGUAAGGGAAGAGGUGG-----UAGUGGAAGAUGGAGAGGGGG-------
..(.(((.(--(.(((......((..((..(((((((((.(((((.........)))))..)))))))))..)-----)..))...))).)).))).).------- ( -29.90, z-score =  -2.14, R)
>consensus
AGCGCCUGU__UGGUUAGGCAACAAAACAUCCUUUUCCCAGCCAGGAUAGCAAAUUGGUAAGGGAAGAGGUGG_____UCGUGGAAGAGAGGGAG_G_________
.(((((((.......)))))..........(((((((((.(((((.........)))))..)))))))))..........))........................ (-14.62 = -15.52 +   0.90)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 16,694,120 – 16,694,225
Length 105
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 61.41
Shannon entropy 0.71071
G+C content 0.53307
Mean single sequence MFE -19.63
Consensus MFE -6.56
Energy contribution -7.70
Covariance contribution 1.14
Combinations/Pair 1.38
Mean z-score -1.26
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.513856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16694120 105 - 23011544
CCCCUCUGUCCCUCCGCCUAUUCCACGACCACCCCACCCCUUCCCUUACCAAUUUCCCAUCGUGGCUGGGAAAAGGAUGUUUUGUUGCCAAACCCA-ACAGGCGCU
..............(((((.................((..(((((...(((...........)))..)))))..)).......((((.......))-))))))).. ( -20.00, z-score =  -0.12, R)
>droWil1.scaffold_181132 155375 94 + 1035393
---------CGCCCCCUGAACUUCACAACACAACCAACCCAACCUAACCUCCUUUUCCA-AGCAGCUUAGAGAGAUUUUUUUUGCUGCAUACCCA--ACAGGCGCC
---------((((...((.....))..................................-.(((((..(((((...)))))..))))).......--...)))).. ( -14.80, z-score =  -2.16, R)
>droAna3.scaffold_12916 311354 81 + 16180835
-----------------CCUACUCACUA----GCAGUCUCUCCCCCCAUC-CUUUGCUAUUAUCCUUGCGAAAGGGAUUUUUCGUUGCCU-ACCA--ACAGGCGCU
-----------------..........(----((.............(((-((((((..........))))..)))))........((((-....--..))))))) ( -14.60, z-score =  -0.46, R)
>droEre2.scaffold_4845 19763746 90 - 22589142
-----------CCCACUCUCUCCCACGA-----GCUCCUCUUCCCCUGCCAACUUGCCAUCCUGGCUGGGAAAAGGAUGCUUUGUUGCCCAACCAACACAGGCGCU
-----------................(-----((((((.(((((..((((...........)))).))))).)))).(((((((((......))))).))))))) ( -27.40, z-score =  -2.32, R)
>droYak2.chr2R 16730174 94 + 21139217
-----CCCCCUCUAACGCUCUCCCACGA-----GCUCCUCUUCCCUUACCAAUUUCCUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCAAACCA--ACAGGCGCU
-----..........((((.......((-----((((((.(((((...(((...........)))..))))).)))).))))(((((......))--))))))).. ( -23.50, z-score =  -1.83, R)
>droSim1.chr2L 16390287 92 - 22036055
-------CCCCCUCUCCAUCUUCCACUA-----CCACCUCUUCCCUUACCAAUUUAAUAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCCAACCA--ACAGGCGCU
-------.....................-----((.(((.(((((...(((...........)))..))))).)))......(((((......))--))))).... ( -17.50, z-score =  -0.65, R)
>consensus
_________C_CUCACCCUCUCCCACGA_____CCACCUCUUCCCUUACCAAUUUCCCAUCCUGGCUGGGAAAAGGAUGUUUUGUUGCCAAACCA__ACAGGCGCU
....................................(((.(((((...(((...........)))..))))).))).......((.(((...........))))). ( -6.56 =  -7.70 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:46:04 2011