Locus 2706

Sequence ID dm3.chr2L
Location 21,327,506 – 21,327,601
Length 95
Max. P 0.938239
window3708 window3709

overview

Window 8

Location 21,327,506 – 21,327,601
Length 95
Sequences 7
Columns 97
Reading direction forward
Mean pairwise identity 71.57
Shannon entropy 0.59055
G+C content 0.50702
Mean single sequence MFE -30.65
Consensus MFE -12.51
Energy contribution -13.94
Covariance contribution 1.43
Combinations/Pair 1.37
Mean z-score -1.76
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.875693
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21327506 95 + 23011544
-GCUUGGUCUAAUAAAUGUAAAUACGCCAACAGGCUGACCAACCCCCUUCCCCAGGCCAAUUGGCAAGGGGGAGAAAUUGUUGGGG-CCUGUCAACG
-...((((.((...........)).))))(((((((..(((((...(((((((..(((....)))..))))))).....)))))))-)))))..... ( -36.10, z-score =  -2.15, R)
>droSim1.chr2L 20928578 96 + 22036055
-GCUUGGUCUAAUAAAUGUAAAUACGCCAACAGGCUGACCAACCCCCUUCCCCAGCCCAAUUGGCAAGGGGGAGAAAUUGUUGGGGGCCUGUCAACG
-...((((.((...........)).))))(((((((..(((((...(((((((.(((.....)))..))))))).....))))).)))))))..... ( -34.70, z-score =  -1.55, R)
>droSec1.super_18 1257548 89 + 1342155
-------UCUAAUAAAUGUAAAUACGCCAACAGGCUGACCAACCCCCUUCCCCAGCCCAAUUGGCAAGGGGGAGAAAUUGUUGGGG-CCUGUCAACG
-------.................((...(((((((..(((((...(((((((.(((.....)))..))))))).....)))))))-)))))...)) ( -31.60, z-score =  -2.28, R)
>droYak2.chr2R 19690662 95 - 21139217
-GCAUGCCCUAAUAAAUGUAAAUACGCCAACUGGCUGACCAAUCCCCUUCCCCAGUCCUUGUGGAAAGGGGGGAAAAUUGUUGGGG-CCUGUCAACG
-(((.((((((((((..........(((....)))............((((((..(((....)))...))))))...)))))))))-).)))..... ( -35.20, z-score =  -2.65, R)
>droEre2.scaffold_4845 19419634 95 - 22589142
-GCUCGCUCUAAUAAAUGUAAAUACGUCAACUGGCUGACCAACCCCCUUUCCCAGUCCGAGUGGAAACGGGGGGAAAUUGUUGGGG-CCUGUCAACG
-((..((((((((((..........((((......))))...(((((((((((.......).))))).)))))....)))))))))-)..))..... ( -30.60, z-score =  -1.43, R)
>droAna3.scaffold_12916 5278048 79 - 16180835
-GCUUGCAAUAAUAAAUGUAAAUACAAGAG-----UGACCAACACCCUUCUCCCGAC------AACAUUGGGGGAA-----UGGGG-CUUGUCAACA
-..(((((........))))).........-----((((.((..((((((((((((.------....)))))))))-----.))).-.))))))... ( -22.80, z-score =  -2.07, R)
>droWil1.scaffold_181071 823290 96 + 1211509
GGCUCGCA-UAAUAAAUGUAAAUAUGCCAACUAACUGACCUGACCCCCAACCUCAUGUGGGCGGUUGCAGGAGAUGCGUGGAAAGGAGAUGCGAAAA
...(((((-(............(((((((......)).(((((((((((........)))).)))..))))....)))))........))))))... ( -23.55, z-score =  -0.22, R)
>consensus
_GCUUGCUCUAAUAAAUGUAAAUACGCCAACAGGCUGACCAACCCCCUUCCCCAGUCCAAGUGGAAAGGGGGGGAAAUUGUUGGGG_CCUGUCAACG
.........................(((....)))((((....((((((((((...((....))....))))))........))))....))))... (-12.51 = -13.94 +   1.43)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,327,506 – 21,327,601
Length 95
Sequences 7
Columns 97
Reading direction reverse
Mean pairwise identity 71.57
Shannon entropy 0.59055
G+C content 0.50702
Mean single sequence MFE -32.46
Consensus MFE -14.10
Energy contribution -14.14
Covariance contribution 0.05
Combinations/Pair 1.50
Mean z-score -1.87
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.44
SVM RNA-class probability 0.938239
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21327506 95 - 23011544
CGUUGACAGG-CCCCAACAAUUUCUCCCCCUUGCCAAUUGGCCUGGGGAAGGGGGUUGGUCAGCCUGUUGGCGUAUUUACAUUUAUUAGACCAAGC-
(((..(((((-(.(((((..(..((.((((..(((....)))..)))).))..))))))...))))))..))).......................- ( -40.80, z-score =  -3.21, R)
>droSim1.chr2L 20928578 96 - 22036055
CGUUGACAGGCCCCCAACAAUUUCUCCCCCUUGCCAAUUGGGCUGGGGAAGGGGGUUGGUCAGCCUGUUGGCGUAUUUACAUUUAUUAGACCAAGC-
(((..((((((..(((((..(..((.((((..(((.....))).)))).))..))))))...))))))..))).......................- ( -40.10, z-score =  -2.58, R)
>droSec1.super_18 1257548 89 - 1342155
CGUUGACAGG-CCCCAACAAUUUCUCCCCCUUGCCAAUUGGGCUGGGGAAGGGGGUUGGUCAGCCUGUUGGCGUAUUUACAUUUAUUAGA-------
(((..(((((-(.(((((..(..((.((((..(((.....))).)))).))..))))))...))))))..))).................------- ( -39.70, z-score =  -3.26, R)
>droYak2.chr2R 19690662 95 + 21139217
CGUUGACAGG-CCCCAACAAUUUUCCCCCCUUUCCACAAGGACUGGGGAAGGGGAUUGGUCAGCCAGUUGGCGUAUUUACAUUUAUUAGGGCAUGC-
......((.(-(((...(((((..(.((((..(((....)))..))))..)..)))))....(((....)))................)))).)).- ( -32.10, z-score =  -1.20, R)
>droEre2.scaffold_4845 19419634 95 + 22589142
CGUUGACAGG-CCCCAACAAUUUCCCCCCGUUUCCACUCGGACUGGGAAAGGGGGUUGGUCAGCCAGUUGACGUAUUUACAUUUAUUAGAGCGAGC-
.((((((..(-((((.....((((((.(((........)))...)))))).)))))..)))))).......(((.((((.......)))))))...- ( -31.30, z-score =  -1.64, R)
>droAna3.scaffold_12916 5278048 79 + 16180835
UGUUGACAAG-CCCCA-----UUCCCCCAAUGUU------GUCGGGAGAAGGGUGUUGGUCA-----CUCUUGUAUUUACAUUUAUUAUUGCAAGC-
...((((.((-((((.-----(((.(((......------...))).)))))).))).))))-----..((((((..............)))))).- ( -21.34, z-score =  -1.27, R)
>droWil1.scaffold_181071 823290 96 - 1211509
UUUUCGCAUCUCCUUUCCACGCAUCUCCUGCAACCGCCCACAUGAGGUUGGGGGUCAGGUCAGUUAGUUGGCAUAUUUACAUUUAUUA-UGCGAGCC
..(((((((.................(((.(((((..........))))).)))....(((((....)))))...............)-)))))).. ( -21.90, z-score =   0.06, R)
>consensus
CGUUGACAGG_CCCCAACAAUUUCCCCCCCUUGCCAAUUGGACUGGGGAAGGGGGUUGGUCAGCCAGUUGGCGUAUUUACAUUUAUUAGAGCAAGC_
.((((((....((((......((((((.................))))))))))....))))))................................. (-14.10 = -14.14 +   0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:14 2011