Locus 8062

Sequence ID dm3.chr3L
Location 19,896,702 – 19,896,801
Length 99
Max. P 0.913070
window11095 window11096

overview

Window 5

Location 19,896,702 – 19,896,801
Length 99
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.05
Shannon entropy 0.32960
G+C content 0.37265
Mean single sequence MFE -23.93
Consensus MFE -13.59
Energy contribution -14.37
Covariance contribution 0.78
Combinations/Pair 1.08
Mean z-score -2.29
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.90
SVM RNA-class probability 0.848212
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19896702 99 + 24543557
UGUAGCCGC-UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUUC-GUAUAUA-----GUAUAUGCGUGCACACAUGUAUGCAGCACACACGGACGGACAAACUUUUC-------------
....(((((-(((...(((((......)))))((((((.....-)))))).-----((...((((((((....))))))))..))..)))).))).).........------------- ( -22.80, z-score =  -1.45, R)
>droEre2.scaffold_4784 19634994 97 + 25762168
UGUAGCCGC-UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUUC-GUAUAUA-----GUAUAUGCGUGCACACAUGUAUGCAGCACAC--GGACGGACACACUUUUG-------------
(((..((((-(((...(((((......)))))((((((.....-)))))).-----((...((((((((....))))))))..))))--)).)))..)))......------------- ( -24.90, z-score =  -1.85, R)
>droYak2.chr3L 3517286 97 - 24197627
UGUAGCCGC-UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUAC-GUAUAUA-----GUAUAUGCGUGCACACAUGUAUGCAGCACAC--GGACGGACACACUUUUA-------------
(((..((((-(((...(((((......)))))((((((.....-)))))).-----((...((((((((....))))))))..))))--)).)))..)))......------------- ( -24.90, z-score =  -1.85, R)
>droSec1.super_29 542078 99 + 700605
UGUAGCCGC-UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUUC-GUAUAUA-----GUAUAUGCGUGCACACAUGUAUGCAGCACACACGGACGGACACACUUUUG-------------
(((..((((-(((...(((((......)))))((((((.....-)))))).-----((...((((((((....))))))))..))..)))).)))..)))......------------- ( -24.90, z-score =  -1.75, R)
>droSim1.chr3L 19191352 99 + 22553184
UGUAGCCGC-UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUUC-GUAUAUA-----GUAUAUGCGUGCACACAUGUAUGCAGCACACACGGACGGACACACUUUUG-------------
(((..((((-(((...(((((......)))))((((((.....-)))))).-----((...((((((((....))))))))..))..)))).)))..)))......------------- ( -24.90, z-score =  -1.75, R)
>droWil1.scaffold_180698 2809688 117 - 11422946
--UGACGGCAUGUCUUUCAUUAUACAAAAUGAAUAUACAUUUUUGUAUAUACAUUUGUAUAUAUCUUUACCCCCCUCUAUCACCCUCUCCCUCUCACUGACUAUGUCGAUCUCUUUUUU
--.(((((((((((......((((((((.((.(((((((....))))))).))))))))))((....)).............................))).)))))).))........ ( -21.20, z-score =  -5.10, R)
>consensus
UGUAGCCGC_UGUCUUUCAUUAUAAAAAAUGAAUAUACAUUUC_GUAUAUA_____GUAUAUGCGUGCACACAUGUAUGCAGCACACACGGACGGACACACUUUUG_____________
...........((((.(((((......)))))((((((......))))))......((...(((((((......)))))))..))........))))...................... (-13.59 = -14.37 +   0.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,896,702 – 19,896,801
Length 99
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 81.05
Shannon entropy 0.32960
G+C content 0.37265
Mean single sequence MFE -27.44
Consensus MFE -18.69
Energy contribution -19.33
Covariance contribution 0.64
Combinations/Pair 1.10
Mean z-score -2.07
Structure conservation index 0.68
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.913070
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19896702 99 - 24543557
-------------GAAAAGUUUGUCCGUCCGUGUGUGCUGCAUACAUGUGUGCACGCAUAUAC-----UAUAUAC-GAAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA-GCGGCUACA
-------------....((((((((..((.((((((((((((((....)))))).))))))))-----..((((.-((((((......)))))).))))..))..))))-)..)))... ( -29.70, z-score =  -2.67, R)
>droEre2.scaffold_4784 19634994 97 - 25762168
-------------CAAAAGUGUGUCCGUCC--GUGUGCUGCAUACAUGUGUGCACGCAUAUAC-----UAUAUAC-GAAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA-GCGGCUACA
-------------......((((.((((..--((((((((((((....)))))).))))))..-----.......-....(((...((((((......))))))..)))-)))).)))) ( -26.50, z-score =  -1.53, R)
>droYak2.chr3L 3517286 97 + 24197627
-------------UAAAAGUGUGUCCGUCC--GUGUGCUGCAUACAUGUGUGCACGCAUAUAC-----UAUAUAC-GUAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA-GCGGCUACA
-------------......((((.((((..--((((((((((((....)))))).))))))..-----.......-....(((...((((((......))))))..)))-)))).)))) ( -26.50, z-score =  -1.33, R)
>droSec1.super_29 542078 99 - 700605
-------------CAAAAGUGUGUCCGUCCGUGUGUGCUGCAUACAUGUGUGCACGCAUAUAC-----UAUAUAC-GAAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA-GCGGCUACA
-------------......((((.((((..((((((((((((((....)))))).))))))))-----.......-....(((...((((((......))))))..)))-)))).)))) ( -30.70, z-score =  -2.50, R)
>droSim1.chr3L 19191352 99 - 22553184
-------------CAAAAGUGUGUCCGUCCGUGUGUGCUGCAUACAUGUGUGCACGCAUAUAC-----UAUAUAC-GAAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA-GCGGCUACA
-------------......((((.((((..((((((((((((((....)))))).))))))))-----.......-....(((...((((((......))))))..)))-)))).)))) ( -30.70, z-score =  -2.50, R)
>droWil1.scaffold_180698 2809688 117 + 11422946
AAAAAAGAGAUCGACAUAGUCAGUGAGAGGGAGAGGGUGAUAGAGGGGGGUAAAGAUAUAUACAAAUGUAUAUACAAAAAUGUAUAUUCAUUUUGUAUAAUGAAAGACAUGCCGUCA--
............(((...((((.(...........).))))...((.(.((.......((((((((((.(((((((....))))))).)).)))))))).......)).).))))).-- ( -20.54, z-score =  -1.88, R)
>consensus
_____________CAAAAGUGUGUCCGUCCGUGUGUGCUGCAUACAUGUGUGCACGCAUAUAC_____UAUAUAC_GAAAUGUAUAUUCAUUUUUUAUAAUGAAAGACA_GCGGCUACA
..................((.((((.......((((((((((((....)))))).)))))).........(((((......)))))((((((......)))))).)))).))....... (-18.69 = -19.33 +   0.64)

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 23:38:43 2011