Locus 7781

Sequence ID dm3.chr3L
Location 17,252,136 – 17,252,254
Length 118
Max. P 0.861537
window10704 window10705

overview

Window 4

Location 17,252,136 – 17,252,254
Length 118
Sequences 12
Columns 120
Reading direction forward
Mean pairwise identity 94.12
Shannon entropy 0.12678
G+C content 0.40217
Mean single sequence MFE -24.63
Consensus MFE -22.40
Energy contribution -22.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.91
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.96
SVM RNA-class probability 0.861537
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17252136 118 + 24543557
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCUACGAGG
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..(--(((...)))) ( -26.20, z-score =  -2.12, R)
>droSim1.chr3L 16587436 118 + 22553184
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCUACGAGG
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..(--(((...)))) ( -26.20, z-score =  -2.12, R)
>droSec1.super_0 9303154 118 + 21120651
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCUACGAGG
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..(--(((...)))) ( -26.20, z-score =  -2.12, R)
>droYak2.chr3L 7377098 118 - 24197627
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCUACGAGG
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..(--(((...)))) ( -26.20, z-score =  -2.12, R)
>droEre2.scaffold_4784 9165191 118 - 25762168
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCUACGAGG
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..(--(((...)))) ( -26.20, z-score =  -2.12, R)
>droAna3.scaffold_13337 8208744 118 + 23293914
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCGAAGAGU
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))...--.......... ( -23.60, z-score =  -1.34, R)
>dp4.chrXR_group6 3915215 118 - 13314419
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCGUCGAGU
.......(((((...((((.((((((((((((.((((....))))))))))............((........)).....)))))).)))).....((.....))...--...))))).. ( -24.20, z-score =  -1.19, R)
>droPer1.super_35 326652 118 + 973955
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC--CUCGUCGAGU
.......(((((...((((.((((((((((((.((((....))))))))))............((........)).....)))))).)))).....((.....))...--...))))).. ( -24.20, z-score =  -1.19, R)
>droWil1.scaffold_180955 2015656 120 + 2875958
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUAUACGCCAUGGCCCUAUAAGG
...(((((.(....)((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))..))))).....((....))......... ( -24.20, z-score =  -0.64, R)
>droVir3.scaffold_13049 19181157 106 - 25233164
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUACGCC--------------
...(((((.(....)((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))..)))))........-------------- ( -22.40, z-score =  -1.77, R)
>droMoj3.scaffold_6059 3242 107 - 6074
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUACGCCA-------------
...(((((.(....)((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))..))))).........------------- ( -22.40, z-score =  -1.71, R)
>droGri2.scaffold_15110 6655903 107 + 24565398
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCA-------------
...(((...(((((.((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))...)))))...)))..------------- ( -23.60, z-score =  -2.01, R)
>consensus
CACGCAAUCGGCAACGUGUCGCAUUUGUAGUUAGACAUAAUUGUUAAUUACCCGAAACCAUUACCACAUUAAAGGCCAUAAAAUGCAACACUAAUUGCUUUAUGCCAC__CUCUACGAGG
...(((((.(....)((((.((((((((((((.((((....))))))))))............((........)).....)))))).))))..)))))...................... (-22.40 = -22.40 +   0.00)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 17,252,136 – 17,252,254
Length 118
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 94.12
Shannon entropy 0.12678
G+C content 0.40217
Mean single sequence MFE -31.62
Consensus MFE -29.51
Energy contribution -29.33
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.30
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.711181
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 17252136 118 - 24543557
CCUCGUAGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...(((((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..))..))))).. ( -32.90, z-score =  -1.45, R)
>droSim1.chr3L 16587436 118 - 22553184
CCUCGUAGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...(((((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..))..))))).. ( -32.90, z-score =  -1.45, R)
>droSec1.super_0 9303154 118 - 21120651
CCUCGUAGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...(((((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..))..))))).. ( -32.90, z-score =  -1.45, R)
>droYak2.chr3L 7377098 118 + 24197627
CCUCGUAGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...(((((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..))..))))).. ( -32.90, z-score =  -1.45, R)
>droEre2.scaffold_4784 9165191 118 + 25762168
CCUCGUAGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...(((((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..))..))))).. ( -32.90, z-score =  -1.45, R)
>droAna3.scaffold_13337 8208744 118 - 23293914
ACUCUUCGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
.(((...)))--...(((....(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))....)))... ( -30.10, z-score =  -0.88, R)
>dp4.chrXR_group6 3915215 118 + 13314419
ACUCGACGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
.....(((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..)).....))). ( -30.90, z-score =  -0.80, R)
>droPer1.super_35 326652 118 - 973955
ACUCGACGAG--GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
.....(((.(--(..((...((....)).(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).)))))))))))))..)).....))). ( -30.90, z-score =  -0.80, R)
>droWil1.scaffold_180955 2015656 120 - 2875958
CCUUAUAGGGCCAUGGCGUAUAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
(((....))).....(((((..(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))....))))). ( -31.40, z-score =  -0.39, R)
>droVir3.scaffold_13049 19181157 106 + 25233164
--------------GGCGUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
--------------.((((((.(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))...)))))). ( -31.10, z-score =  -2.01, R)
>droMoj3.scaffold_6059 3242 107 + 6074
-------------UGGCGUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
-------------..((((((.(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))...)))))). ( -31.10, z-score =  -1.89, R)
>droGri2.scaffold_15110 6655903 107 - 24565398
-------------UGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
-------------..(((....(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))....)))... ( -29.50, z-score =  -1.56, R)
>consensus
CCUCGUAGAG__GUGGCAUAAAGCAAUUAGUGUUGCAUUUUAUGGCCUUUAAUGUGGUAAUGGUUUCGGGUAAUUAACAAUUAUGUCUAACUACAAAUGCGACACGUUGCCGAUUGCGUG
...............(((....(((((..(((((((((((....(((........)))..(((((..(.(((((.....))))).)..))))).))))))))))))))))....)))... (-29.51 = -29.33 +  -0.19)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:33:18 2011