Locus 7556

Sequence ID dm3.chr3L
Location 15,536,385 – 15,536,482
Length 97
Max. P 0.979936
window10403 window10404

overview

Window 3

Location 15,536,385 – 15,536,482
Length 97
Sequences 9
Columns 103
Reading direction forward
Mean pairwise identity 90.84
Shannon entropy 0.18060
G+C content 0.31544
Mean single sequence MFE -21.24
Consensus MFE -17.49
Energy contribution -17.60
Covariance contribution 0.11
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.53
SVM RNA-class probability 0.947831
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15536385 97 + 24543557
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAAAA--GCAAAAUCGAAAAAAUGUAUAGACA-
...(((......((((((((((((.((---.((...................)))).))))))))))))......--)))......................- ( -22.31, z-score =  -2.77, R)
>droSim1.chr3L 14877600 99 + 22553184
AAAUGUGAAAGGGUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAAAAAAGCAAAAUCGAAAAAAUGUAUAGACA-
...(((.......(((((((((((.((---.((...................)))).))))))))))).........)))......................- ( -20.10, z-score =  -1.92, R)
>droSec1.super_0 7645874 96 + 21120651
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAAA---GCAAAAUCGAAAAAAUGUAUAGACA-
...(((......((((((((((((.((---.((...................)))).)))))))))))).....---)))......................- ( -21.91, z-score =  -2.59, R)
>droYak2.chr3L 18052281 96 + 24197627
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAAA---GCAAAAUCGAAAAAAAGUAUAGACA-
...(((......((((((((((((.((---.((...................)))).)))))))))))).....---)))......................- ( -21.91, z-score =  -2.75, R)
>droEre2.scaffold_4784 17794083 95 + 25762168
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAA----GCAAAAUCGAAAAAAUGUAUAGACA-
...(((......((((((((((((.((---.((...................)))).))))))))))))....----)))......................- ( -21.51, z-score =  -2.42, R)
>droWil1.scaffold_181136 1873707 96 + 2313701
AAAUGUGAAAGGUUUUCGCUUGCUGCAGCAACAUUAUUUAAUCAAUCCAAUUUGUGGAGCAAGCGAAAAAACA-------AAAUCGAAAAACUGUAUAUACAU
..(((((.....((((((((((((.((.(((....................))))).)))))))))))).(((-------............)))...))))) ( -20.25, z-score =  -1.78, R)
>droVir3.scaffold_13049 20313579 91 + 25233164
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAUUUGUGGAGCAAGCGAAAAA-------GCCAAAUCGAAAUA-UCUAUAGACA-
..........((((((((((((((.((---.((...................)))).)))))))))))..-------)))...........-..........- ( -22.01, z-score =  -2.44, R)
>droMoj3.scaffold_6680 8026775 92 + 24764193
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAUUUGUGGAGCAAGCGAAAAAAAAC------AAAUCGAAAUA-UAUACAUAUA-
...(((......((((((((((((.((---.((...................)))).))))))))))))...))------)..........-..........- ( -20.81, z-score =  -2.70, R)
>droGri2.scaffold_15110 7978280 91 - 24565398
AAAUGUGAAAGGUUUUCGCUUGCUGCA---ACAUUAUUUAAUCAAUCCAAUUUGUGGAGCAAGCGAAAAA-------GCAAAAUCGAAAUA-UAUGUAUACA-
...(((......((((((((((((.((---.((...................)))).)))))))))))).-------)))...........-..........- ( -20.31, z-score =  -1.84, R)
>consensus
AAAUGUGAAAGGUUUUCGCUUGCUGCA___ACAUUAUUUAAUCAAUCCAAAUUGUGGAGCAAGCGAAAAAAAA____GCAAAAUCGAAAAAAUGUAUAGACA_
............((((((((((((.((........(((.....)))........)).)))))))))))).................................. (-17.49 = -17.60 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,536,385 – 15,536,482
Length 97
Sequences 9
Columns 103
Reading direction reverse
Mean pairwise identity 90.84
Shannon entropy 0.18060
G+C content 0.31544
Mean single sequence MFE -18.49
Consensus MFE -18.40
Energy contribution -18.51
Covariance contribution 0.11
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 1.00
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.03
SVM RNA-class probability 0.979936
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 15536385 97 - 24543557
-UGUCUAUACAUUUUUUCGAUUUUGC--UUUUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-.........................--......(((((((((((((.(((((((((.....))))))..)))---.).))))))))))))............ ( -18.30, z-score =  -1.91, R)
>droSim1.chr3L 14877600 99 - 22553184
-UGUCUAUACAUUUUUUCGAUUUUGCUUUUUUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAACCCUUUCACAUUU
-..................................((((((((((((.(((((((((.....))))))..)))---.).)))))))))))............. ( -17.40, z-score =  -1.78, R)
>droSec1.super_0 7645874 96 - 21120651
-UGUCUAUACAUUUUUUCGAUUUUGC---UUUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-.........................---.....(((((((((((((.(((((((((.....))))))..)))---.).))))))))))))............ ( -18.30, z-score =  -1.88, R)
>droYak2.chr3L 18052281 96 - 24197627
-UGUCUAUACUUUUUUUCGAUUUUGC---UUUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-.........................---.....(((((((((((((.(((((((((.....))))))..)))---.).))))))))))))............ ( -18.30, z-score =  -2.00, R)
>droEre2.scaffold_4784 17794083 95 - 25762168
-UGUCUAUACAUUUUUUCGAUUUUGC----UUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-.........................----....(((((((((((((.(((((((((.....))))))..)))---.).))))))))))))............ ( -18.30, z-score =  -1.88, R)
>droWil1.scaffold_181136 1873707 96 - 2313701
AUGUAUAUACAGUUUUUCGAUUU-------UGUUUUUUCGCUUGCUCCACAAAUUGGAUUGAUUAAAUAAUGUUGCUGCAGCAAGCGAAAACCUUUCACAUUU
((((....((((..........)-------))).((((((((((((.(((((.....(((.....)))....))).)).))))))))))))......)))).. ( -20.00, z-score =  -1.58, R)
>droVir3.scaffold_13049 20313579 91 - 25233164
-UGUCUAUAGA-UAUUUCGAUUUGGC-------UUUUUCGCUUGCUCCACAAAUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-((((....))-))....((...((.-------.((((((((((((.((...((((...........))))..---)).))))))))))))))..))...... ( -21.00, z-score =  -2.11, R)
>droMoj3.scaffold_6680 8026775 92 - 24764193
-UAUAUGUAUA-UAUUUCGAUUU------GUUUUUUUUCGCUUGCUCCACAAAUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-..........-...........------.....((((((((((((.((...((((...........))))..---)).))))))))))))............ ( -17.40, z-score =  -1.43, R)
>droGri2.scaffold_15110 7978280 91 + 24565398
-UGUAUACAUA-UAUUUCGAUUUUGC-------UUUUUCGCUUGCUCCACAAAUUGGAUUGAUUAAAUAAUGU---UGCAGCAAGCGAAAACCUUUCACAUUU
-..........-..............-------.((((((((((((.((...((((...........))))..---)).))))))))))))............ ( -17.40, z-score =  -1.49, R)
>consensus
_UGUCUAUACAUUUUUUCGAUUUUGC____UUUUUUUUCGCUUGCUCCACAAUUUGGAUUGAUUAAAUAAUGU___UGCAGCAAGCGAAAACCUUUCACAUUU
..................................(((((((((((((((.....))))............(((....))))))))))))))............ (-18.40 = -18.51 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:29:09 2011