Locus 1371

Sequence ID dm3.chr2L
Location 10,658,999 – 10,659,134
Length 135
Max. P 0.653031
window1868 window1869

overview

Window 8

Location 10,658,999 – 10,659,112
Length 113
Sequences 8
Columns 119
Reading direction forward
Mean pairwise identity 69.45
Shannon entropy 0.59516
G+C content 0.55114
Mean single sequence MFE -37.31
Consensus MFE -14.19
Energy contribution -13.78
Covariance contribution -0.42
Combinations/Pair 1.56
Mean z-score -1.57
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.653031
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10658999 113 + 23011544
---GCUGGCCCCAACUU---GGGUGAUAGAAAACGCCCCACUUAAGUGGGACUUUCUGACGCCAUCGGCCUGAUUGUAGUUAUUUGGCUGCGACUUGCUAUUUGAUUUCGCUUUUGGCG
---(((((((.......---.((((.((((((..(.(((((....))))).))))))).))))...)))).....(.(((((..((((........))))..))))).)......))). ( -34.10, z-score =  -1.51, R)
>droAna3.scaffold_12916 14502818 105 + 16180835
---GCGGUCCUCCAGUUUCUGGGUGAUGGAAAACGCCCCGCC-AAUUGGGACUUGUUGCCGCCACCGGCCUGAUUAUAGUUGUUUUGGCCAAAAUGGAUGCU-GUUGGCG---------
---...(.((..((((.((((((((.(....).))))).(((-((..(.((((.(((((((....))))..)))...)))).).)))))......))).)))-)..))).--------- ( -32.30, z-score =   0.40, R)
>droPer1.super_10 1869993 103 + 3432795
GCAGUCCGCCCCCAGUC---AGGCGCUGUUCAACGCCCCUGCCA-UUGG----CGCUGUCGCCA-----CUGAUUAUAGUGGUUUGGUUCCAGUCGGCUGCCCGA---UGCUCCUGGCG
((((..((((.......---.))))))))....((((...((.(-((((----.((.(((((((-----(((....)))))))(((....)))..))).))))))---)))....)))) ( -35.90, z-score =  -0.43, R)
>dp4.chr4_group4 2857820 103 + 6586962
GCAGUCCGCCCCCAGUC---AGGCGCUGUUCAACGCCCCUGCCA-UUGG----CGCUGUCGCCA-----CUGAUUAUAGUGGUUUGGUUCCAGUCGGCUGCCCGA---UGCUCCUGGCG
((((..((((.......---.))))))))....((((...((.(-((((----.((.(((((((-----(((....)))))))(((....)))..))).))))))---)))....)))) ( -35.90, z-score =  -0.43, R)
>droSim1.chr2L 10455839 113 + 22036055
---GCUGGCCCCAACUU---GGGUGAUAGAAAACGCCCCACUUAAGUGGGACUUUCUGCCGCCAACGGCCUGAUUGUAGUUAUUUGACUGCGACUUACUAUUUGAAGUCGCUUUUGGCG
---...((((((.....---)))....(((((..(.(((((....))))).)))))))))(((((.(((......((((((....))))))(((((........)))))))).))))). ( -40.60, z-score =  -3.87, R)
>droSec1.super_3 6076842 113 + 7220098
---GCUGGCCCCAACUU---GGGUGAUAGAAAACGCCCCACUUAAGUGGGACUUUCUGCCGCCAUCAGCCUGAUUGUAGUUAUUUGGCUGCGUCUUGCUAUUUGAAGUCGCUUUUGGCG
---...((((((.....---)))....(((((..(.(((((....))))).)))))))))((((..((((.(((.......))).))))(((.(((........))).)))...)))). ( -36.10, z-score =  -1.38, R)
>droYak2.chr2L 7062689 113 + 22324452
---GCAGGCCCCCAGUU---GGGUGAUAGAAAACGCCCCACCUAACUGGGACUUUCUGCCGCCUUCGGCCUGAUUGUAGUUAUUUGGCUGGGACUUGCUAUUUGAAGUCGCCUUUAACG
---.(((((((((((((---(((((.............)))))))))))).(.....)........))))))......((((...(((...(((((........))))))))..)))). ( -40.92, z-score =  -2.61, R)
>droEre2.scaffold_4929 11867346 113 - 26641161
---GCAGGCCCCAAGUU---GGGUGAUAGAAAACGCCCCACUUAAGUGGGUCUUUCUGCAGCCGUCGGCCUGAUUGUAGUUAUUUGGCUGCGACUUGCUAUUUGCAGUCGCUUUUGUCG
---.((((((......(---((.((.((((((..(.(((((....))))).))))))))).)))..)))))).............(((.((((((.((.....))))))))....))). ( -42.70, z-score =  -2.76, R)
>consensus
___GCUGGCCCCAAGUU___GGGUGAUAGAAAACGCCCCACCUAAGUGGGACUUUCUGCCGCCAUCGGCCUGAUUGUAGUUAUUUGGCUGCGACUUGCUAUUUGAAGUCGCUUUUGGCG
...((................((((.((((((....(((((....)))))..)))))).)))).............((((.(.(((....))).).)))).........))........ (-14.19 = -13.78 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,659,033 – 10,659,134
Length 101
Sequences 8
Columns 111
Reading direction reverse
Mean pairwise identity 66.79
Shannon entropy 0.62973
G+C content 0.56811
Mean single sequence MFE -28.17
Consensus MFE -12.20
Energy contribution -11.80
Covariance contribution -0.40
Combinations/Pair 1.50
Mean z-score -1.00
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.03
SVM RNA-class probability 0.511859
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10659033 101 - 23011544
UGUGGCGCCCGCCGCACACCCACG---------CCAAAAGCGAAAUCAAAUAGCAAGUCGCAGCCAAAUAACUACAAUCAG-GCCGAUGGCGUCAGAAAGUCCCACUUAAG
((((((....)))))).....(((---------(((...((((...(.....)....)))).(((...............)-))...)))))).................. ( -24.36, z-score =  -1.44, R)
>droAna3.scaffold_12916 14502855 90 - 16180835
UGUGGCGCCUGCCACACGCCCACG---------CCAACAGC----------AUCCAUUUUGGCCAAAACAACUAUAAUCAG-GCCGGUGGCGGCAACAAGUCCCAAUUGG-
((((((....)))))).(((..((---------((....(.----------...).....((((................)-)))))))..)))................- ( -24.39, z-score =   0.54, R)
>droPer1.super_10 1870030 100 - 3432795
UGCGACGCCUGUCACAUGCCCACGGCCUCGCCCACGCCAGGAGCAUCGGGCAGCCGACUGGAACCAAACCACUAUAAUCAGUGGCGACAGCGCCAAUGGC-----------
......(((((((......(((((((...((((..((.....))...)))).))))..))).......(((((......))))).))))).)).......----------- ( -32.10, z-score =   0.06, R)
>dp4.chr4_group4 2857857 100 - 6586962
UGCGACGCCUGUCACAUUCCCACGGCCUCGCCCACGCCAGGAGCAUCGGGCAGCCGACUGGAACCAAACCACUAUAAUCAGUGGCGACAGCGCCAAUGGC-----------
......(((((((...((((..((((...((((..((.....))...)))).))))...)))).....(((((......))))).))))).)).......----------- ( -33.20, z-score =  -0.79, R)
>droSim1.chr2L 10455873 100 - 22036055
UGUGGCG-CCGCCGCACACCCACG---------CCAAAAGCGACUUCAAAUAGUAAGUCGCAGUCAAAUAACUACAAUCAG-GCCGUUGGCGGCAGAAAGUCCCACUUAAG
.((((.(-(.(((((.((...(((---------((....((((((((.....).)))))))(((......))).......)-).)))))))))).....)).))))..... ( -30.30, z-score =  -2.62, R)
>droSec1.super_3 6076876 101 - 7220098
UGUGGCGCCCGCCGCACACCCACG---------CCAAAAGCGACUUCAAAUAGCAAGACGCAGCCAAAUAACUACAAUCAG-GCUGAUGGCGGCAGAAAGUCCCACUUAAG
((((((....))))))......((---------(((...(((.(((........))).)))((((...............)-)))..)))))................... ( -26.36, z-score =  -1.01, R)
>droYak2.chr2L 7062723 101 - 22324452
UGUGGCGCCCGCCGCACACCCACG---------UUAAAGGCGACUUCAAAUAGCAAGUCCCAGCCAAAUAACUACAAUCAG-GCCGAAGGCGGCAGAAAGUCCCAGUUAGG
((((((....))))))...((...---------.....((((((((........)))))...)))...(((((((..((..-((((....)))).))..))...))))))) ( -26.20, z-score =  -0.60, R)
>droEre2.scaffold_4929 11867380 101 + 26641161
UGUGGCGCCCGUCGCACACCCACG---------ACAAAAGCGACUGCAAAUAGCAAGUCGCAGCCAAAUAACUACAAUCAG-GCCGACGGCUGCAGAAAGACCCACUUAAG
....(((.((((((..........---------......((((((((.....)).)))))).(((...............)-)))))))).)))................. ( -28.46, z-score =  -2.17, R)
>consensus
UGUGGCGCCCGCCGCACACCCACG_________CCAAAAGCGACUUCAAAUAGCAAGUCGCAGCCAAAUAACUACAAUCAG_GCCGAUGGCGGCAGAAAGUCCCACUUAAG
((((((....))))))..................................................................((((....))))................. (-12.20 = -11.80 +  -0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:30:40 2011