Locus 2364

Sequence ID dm3.chr2L
Location 18,364,447 – 18,364,545
Length 98
Max. P 0.561106
window3257 window3258

overview

Window 7

Location 18,364,447 – 18,364,545
Length 98
Sequences 7
Columns 113
Reading direction forward
Mean pairwise identity 63.27
Shannon entropy 0.68663
G+C content 0.41753
Mean single sequence MFE -26.22
Consensus MFE -7.59
Energy contribution -8.92
Covariance contribution 1.33
Combinations/Pair 1.27
Mean z-score -1.59
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.02
SVM RNA-class probability 0.507188
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18364447 98 + 23011544
---------GUUGUAACUAUU--GCACCAU-UGUUGCGAAACAUUGUUGUCGCUGCAACAUUUGGCUUAGAUACAUGUGUAAGGGUGCAAAAUCACCCCUUAAAAUGUUG---
---------..((((.(((..--((.....-(((((((..(((....)))..).))))))....)).))).)))).......(((((......)))))............--- ( -23.60, z-score =  -0.52, R)
>droPer1.super_1 4355295 86 - 10282868
---------GCAGAAGUUGCA--GCAGCAUUUGUUCCUUCCAAAAGU---UGCAGCAGCAU---------AGAAAAGUGUCUGA-AACAUGGCCCUUCCUGCAGCCAGCA---
---------((((..(((((.--(((((.((((.......)))).))---))).)))))..---------....(((.(((...-.....))).))).))))........--- ( -24.80, z-score =  -0.99, R)
>dp4.chr4_group3 7247567 111 - 11692001
UCAAAAGUUGCAGAAACAUUUAAGCAACAUGUCUCGCAAGGCAACAUAGUUGUUGCAACAUAUCCCUUU-AGACAGGC-UAUAGCAACAUAUCCUCCAGCAGAAGUUGCAGCA
......(((((((.........(((....((((((....)((((((....)))))).............-))))).))-)...((.............)).....))))))). ( -26.22, z-score =  -1.91, R)
>droEre2.scaffold_4845 16684725 94 - 22589142
---------GCUGAAACUAUU--GCACCAA-UGUUGCGAAACAUUGU---CGCUGCAACAUUUGGCUUAGAUACAUAUGUAAGGGUGCAAAUUCACCC-UAAAAUUGUUG---
---------((..((....((--(((.(((-((((....))))))).---...)))))..))..)).....(((....)))((((((......)))))-)..........--- ( -23.10, z-score =  -1.39, R)
>droYak2.chr2R 4881521 98 + 21139217
---------GUUCAAGGUUUU--GCACCCA-UGUUGCGAAACAUUGUUGUCGCUGCAACAUUUUGCUUAGAUACAUUCGCAGGGGUGCAAAUUCACCCCUAAAAUUGUUU---
---------......((((((--((((((.-...((((((....(((.(((...((((....))))...)))))))))))).)))))))))...))).............--- ( -30.30, z-score =  -2.77, R)
>droSec1.super_7 1991097 100 + 3727775
---------GUACAACCUAUUUUGCACCAU-UGUUGCGAAACAUUGUUGUCGCUGCAACAUUUGGCUUAGAUACAUGUGUAAGGGUGCAAAAUCACCCCUUAACAUGUUG---
---------...........((((..(((.-(((((((..(((....)))..).))))))..)))..)))).((((((....(((((......)))))....))))))..--- ( -26.70, z-score =  -1.44, R)
>droSim1.chr2L 18052088 100 + 22036055
---------GUACAACCUAUUUUGCACCAU-UGUUGCGAAACAUUGUUGUCGCUGCAACAUUUGGUUUAGAUACAUGUGUAAGGGUGCAAAAUCACCCCUUAACAUGUUG---
---------...........((((.((((.-(((((((..(((....)))..).))))))..)))).)))).((((((....(((((......)))))....))))))..--- ( -28.80, z-score =  -2.14, R)
>consensus
_________GUAGAAACUAUU__GCACCAU_UGUUGCGAAACAUUGUUGUCGCUGCAACAUUUGGCUUAGAUACAUGUGUAAGGGUGCAAAAUCACCCCUAAAAAUGUUG___
.......................(((((...(((((((...............)))))))...........(((....)))..)))))......................... ( -7.59 =  -8.92 +   1.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,364,447 – 18,364,545
Length 98
Sequences 7
Columns 113
Reading direction reverse
Mean pairwise identity 63.27
Shannon entropy 0.68663
G+C content 0.41753
Mean single sequence MFE -27.41
Consensus MFE -8.31
Energy contribution -8.17
Covariance contribution -0.14
Combinations/Pair 1.45
Mean z-score -1.58
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.14
SVM RNA-class probability 0.561106
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18364447 98 - 23011544
---CAACAUUUUAAGGGGUGAUUUUGCACCCUUACACAUGUAUCUAAGCCAAAUGUUGCAGCGACAACAAUGUUUCGCAACA-AUGGUGC--AAUAGUUACAAC---------
---..........(((((((......))))))).....((((.(((.((((..((((((.(.((((....)))).)))))))-.))))..--..))).))))..--------- ( -27.50, z-score =  -2.49, R)
>droPer1.super_1 4355295 86 + 10282868
---UGCUGGCUGCAGGAAGGGCCAUGUU-UCAGACACUUUUCU---------AUGCUGCUGCA---ACUUUUGGAAGGAACAAAUGCUGC--UGCAACUUCUGC---------
---(((.(((.((((((((((...((((-...)))))))))))---------.))).))))))---......(((((.......(((...--.))).)))))..--------- ( -20.00, z-score =   1.45, R)
>dp4.chr4_group3 7247567 111 + 11692001
UGCUGCAACUUCUGCUGGAGGAUAUGUUGCUAUA-GCCUGUCU-AAAGGGAUAUGUUGCAACAACUAUGUUGCCUUGCGAGACAUGUUGCUUAAAUGUUUCUGCAACUUUUGA
(((.((((((((....))))((((((((.((.((-(.....))-).)).))))))))((((((....)))))).))))(((((((.........))))))).)))........ ( -29.90, z-score =  -1.29, R)
>droEre2.scaffold_4845 16684725 94 + 22589142
---CAACAAUUUUA-GGGUGAAUUUGCACCCUUACAUAUGUAUCUAAGCCAAAUGUUGCAGCG---ACAAUGUUUCGCAACA-UUGGUGC--AAUAGUUUCAGC---------
---..........(-(((((......))))))......((...(((.(((((.(((((((((.---.....)))..))))))-)))))..--..)))...))..--------- ( -22.90, z-score =  -1.16, R)
>droYak2.chr2R 4881521 98 - 21139217
---AAACAAUUUUAGGGGUGAAUUUGCACCCCUGCGAAUGUAUCUAAGCAAAAUGUUGCAGCGACAACAAUGUUUCGCAACA-UGGGUGC--AAAACCUUGAAC---------
---.......(((((((.....(((((((((.(((............)))..(((((((.(.((((....)))).)))))))-)))))))--))).))))))).--------- ( -31.70, z-score =  -3.15, R)
>droSec1.super_7 1991097 100 - 3727775
---CAACAUGUUAAGGGGUGAUUUUGCACCCUUACACAUGUAUCUAAGCCAAAUGUUGCAGCGACAACAAUGUUUCGCAACA-AUGGUGCAAAAUAGGUUGUAC---------
---..((((((..(((((((......)))))))..))))))......((((..((((((.(.((((....)))).)))))))-.))))((((......))))..--------- ( -30.10, z-score =  -2.15, R)
>droSim1.chr2L 18052088 100 - 22036055
---CAACAUGUUAAGGGGUGAUUUUGCACCCUUACACAUGUAUCUAAACCAAAUGUUGCAGCGACAACAAUGUUUCGCAACA-AUGGUGCAAAAUAGGUUGUAC---------
---..((((((..(((((((......)))))))..))))))......((((..((((((.(.((((....)))).)))))))-.))))((((......))))..--------- ( -29.80, z-score =  -2.30, R)
>consensus
___CAACAUUUUAAGGGGUGAAUUUGCACCCUUACACAUGUAUCUAAGCCAAAUGUUGCAGCGACAACAAUGUUUCGCAACA_AUGGUGC__AAUAGUUUCUAC_________
...............(((((......)))))......................((((((.................))))))............................... ( -8.31 =  -8.17 +  -0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:53 2011