Locus 12463

Sequence ID dm3.chrX
Location 352,240 – 352,392
Length 152
Max. P 0.996633
window17131 window17132 window17133 window17134

overview

Window 1

Location 352,240 – 352,352
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Shannon entropy 0.20998
G+C content 0.38504
Mean single sequence MFE -29.00
Consensus MFE -23.29
Energy contribution -23.49
Covariance contribution 0.20
Combinations/Pair 1.13
Mean z-score -3.06
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.55
SVM RNA-class probability 0.992601
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 352240 112 + 22422827
UGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGUUUUUAAAUAGAAACUCGCUAUUUCCCCAUGU-AUUGUUUAAAAGAGGUAU-
...........((((.((------.....((((((((((.(((((((((..(((((((.(.......).)))))))..))))))))).)))....)))))-..))......)).)))).- ( -21.40, z-score =  -1.38, R)
>droSim1.chrX 259267 109 + 17042790
UGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUC----AUUUCAAAGCGGCAU-
((((((((((((((..((------......)).)))))))))(((((((..(((((((((.......)))))))))..)))))))...............----.))))).........- ( -28.20, z-score =  -3.25, R)
>droSec1.super_10 209908 109 + 3036183
UGAAAACAAUUUACCACU------CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUC----AUUUCAAAGCGGCAU-
((((((((((((((..((------......)).)))))))))(((((((..(((((((((.......)))))))))..)))))))...............----.))))).........- ( -28.20, z-score =  -3.25, R)
>droYak2.chrX 279494 114 + 21770863
UGAAAACAAUUUACCACU------CCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAGAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUCAAAGCGAACGA
(((((.((((......((------((.....).)))(((.(((((((((.((((((((((.......)))))))))).))))))))).)))..........))))))))).......... ( -32.00, z-score =  -3.46, R)
>droEre2.scaffold_4644 300009 119 + 2521924
UGAAAACAAUUUACCACUGCGAUCCCGAUCAGCGAGAAUUGUGAGUUUCACUUUAAAGUCGAACGCAGACUUUGAAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUUAAAACGGCAU-
..((((((((........(((((....))).))(..(((.(((((((((.((((((((((.......)))))))))).))))))))).)))..).......))))))))..........- ( -35.20, z-score =  -3.96, R)
>consensus
UGAAAACAAUUUACCACU______CCGAUCAGCGUGAAUUGUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAUUU_AUUGUUUCAAAGCGGCAU_
(((((((((((((((................).)))))))))(((((((..(((((((((.......)))))))))..)))))))....................))))).......... (-23.29 = -23.49 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 352,240 – 352,352
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.50
Shannon entropy 0.20998
G+C content 0.38504
Mean single sequence MFE -31.20
Consensus MFE -22.87
Energy contribution -23.83
Covariance contribution 0.96
Combinations/Pair 1.10
Mean z-score -2.43
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.23
SVM RNA-class probability 0.912607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 352240 112 - 22422827
-AUACCUCUUUUAAACAAU-ACAUGGGGAAAUAGCGAGUUUCUAUUUAAAAACUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCA
-...........(((((((-......((((((.....))))))........((..(.(((((..(((..(((((........)))))..)))))))------))..))..)))))))... ( -19.90, z-score =  -0.52, R)
>droSim1.chrX 259267 109 - 17042790
-AUGCCGCUUUGAAAU----GAAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCA
-.(((((((((((...----....(.(..(((.(.(((((((..(((((((((.......)))))))))..))))))).).)))..).)...))))------)))))))........... ( -34.00, z-score =  -3.39, R)
>droSec1.super_10 209908 109 - 3036183
-AUGCCGCUUUGAAAU----GAAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG------AGUGGUAAAUUGUUUUCA
-.(((((((((((...----....(.(..(((.(.(((((((..(((((((((.......)))))))))..))))))).).)))..).)...))))------)))))))........... ( -34.00, z-score =  -3.39, R)
>droYak2.chrX 279494 114 - 21770863
UCGUUCGCUUUGAAACAAUGAAAUGGGGAAAUGGCGAGUUUCCCUCUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCUCGCUGAUCGG------AGUGGUAAAUUGUUUUCA
....(((((((((..((......))(((((.((..(((((((.((.(((((((.......))))))).)).))))))).)).))))).....))))------)))))............. ( -32.70, z-score =  -2.38, R)
>droEre2.scaffold_4644 300009 119 - 2521924
-AUGCCGUUUUAAAACAAUGAAAUGGGGAAAUGGCGAGUUUCCCUUCAAAGUCUGCGUUCGACUUUAAAGUGAAACUCACAAUUCUCGCUGAUCGGGAUCGCAGUGGUAAAUUGUUUUCA
-..((((((((....((......))..))))))))(((((((.(((.((((((.......)))))).))).)))))))((((((.((((((..((....))))))))..))))))..... ( -35.40, z-score =  -2.47, R)
>consensus
_AUGCCGCUUUGAAACAAU_AAAUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCACAAUUCACGCUGAUCGG______AGUGGUAAAUUGUUUUCA
..(((((((...............(.(..(((.(.(((((((..(((((((((.......)))))))))..))))))).).)))..).).............)))))))........... (-22.87 = -23.83 +   0.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 352,274 – 352,392
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.11
Shannon entropy 0.43232
G+C content 0.41268
Mean single sequence MFE -28.51
Consensus MFE -20.90
Energy contribution -20.62
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -2.55
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.96
SVM RNA-class probability 0.996633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 352274 118 + 22422827
GUGAGUUUCACUUUAAAGUCGAAUGCAGUUUUUAAAUAGAAACUCGCUAUUUCCCCAUGU-AUUGUUUAAAAGAGG-UAUUAAAACAGCCCGCACCCGCUCAUUUUUGCUGCAAGGACGG
(((((((((..(((((((.(.......).)))))))..))))))))).......((.(((-(..((..(((.((((-(.........))).((....)))).)))..)))))).)).... ( -22.30, z-score =  -0.03, R)
>droSim1.chrX 259301 106 + 17042790
GUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAU----UCAUUUCAAAGCGG-CAUUACAACUG---------GCUCGCUUUUGCUGCAAGGACAG
(((((((((..(((((((((.......)))))))))..)))))))))...........----..........((((-((.........---------.........))))))........ ( -30.47, z-score =  -2.94, R)
>droSec1.super_10 209942 106 + 3036183
GUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAU----UCAUUUCAAAGCGG-CAUUACAACUG---------GCUCGCUUUUGCUGCAAGGACAG
(((((((((..(((((((((.......)))))))))..)))))))))...........----..........((((-((.........---------.........))))))........ ( -30.47, z-score =  -2.94, R)
>droYak2.chrX 279528 101 + 21770863
GUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAGAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUCAAAGCGAACGACAGGAUUAGUC-------AUUACUUUUA------------
(((((((((.((((((((((.......)))))))))).)))))))))...............(((((....)))))..(((.......)))-------..........------------ ( -28.60, z-score =  -3.71, R)
>droEre2.scaffold_4644 300049 107 + 2521924
GUGAGUUUCACUUUAAAGUCGAACGCAGACUUUGAAGGGAAACUCGCCAUUUCCCCAUUUCAUUGUUUUAAAACGG-CAUUAGAACUGGUCGCAGCCACUCACUUUUG------------
(((((((((.((((((((((.......)))))))))).))))))))).................(((((((.....-..)))))))((((....))))..........------------ ( -30.70, z-score =  -3.15, R)
>consensus
GUGAGUUUCACUUUAAAGUCGAAUGCAGACUUUAAAUGGAAACUCGCUAUUUCCCCAU_U_AUUGUUUCAAAGCGG_CAUUACAACUG__C______GCUCACUUUUGCUGCAAGGAC_G
(((((((((..(((((((((.......)))))))))..)))))))))......................................................................... (-20.90 = -20.62 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 352,274 – 352,392
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.11
Shannon entropy 0.43232
G+C content 0.41268
Mean single sequence MFE -30.25
Consensus MFE -15.31
Energy contribution -15.79
Covariance contribution 0.48
Combinations/Pair 1.11
Mean z-score -2.52
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972299
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 352274 118 - 22422827
CCGUCCUUGCAGCAAAAAUGAGCGGGUGCGGGCUGUUUUAAUA-CCUCUUUUAAACAAU-ACAUGGGGAAAUAGCGAGUUUCUAUUUAAAAACUGCAUUCGACUUUAAAGUGAAACUCAC
(((..(((((...........)))))..)))((((((((....-((.............-....)).))))))))(((((((..((((((.............))))))..))))))).. ( -30.05, z-score =  -1.88, R)
>droSim1.chrX 259301 106 - 17042790
CUGUCCUUGCAGCAAAAGCGAGC---------CAGUUGUAAUG-CCGCUUUGAAAUGA----AUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCAC
...(((((.((...((((((.((---------..........)-)))))))....)).----..)))))......(((((((..(((((((((.......)))))))))..))))))).. ( -31.80, z-score =  -2.64, R)
>droSec1.super_10 209942 106 - 3036183
CUGUCCUUGCAGCAAAAGCGAGC---------CAGUUGUAAUG-CCGCUUUGAAAUGA----AUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCAC
...(((((.((...((((((.((---------..........)-)))))))....)).----..)))))......(((((((..(((((((((.......)))))))))..))))))).. ( -31.80, z-score =  -2.64, R)
>droYak2.chrX 279528 101 - 21770863
------------UAAAAGUAAU-------GACUAAUCCUGUCGUUCGCUUUGAAACAAUGAAAUGGGGAAAUGGCGAGUUUCCCUCUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCAC
------------..((((((((-------(((.......)))))).)))))........................(((((((.((.(((((((.......))))))).)).))))))).. ( -26.60, z-score =  -3.02, R)
>droEre2.scaffold_4644 300049 107 - 2521924
------------CAAAAGUGAGUGGCUGCGACCAGUUCUAAUG-CCGUUUUAAAACAAUGAAAUGGGGAAAUGGCGAGUUUCCCUUCAAAGUCUGCGUUCGACUUUAAAGUGAAACUCAC
------------.....((((((.(((.((.(((.((((....-((((((((......)))))))))))).))))))))(((.(((.((((((.......)))))).))).))))))))) ( -31.00, z-score =  -2.39, R)
>consensus
C_GUCCUUGCAGCAAAAGUGAGC______G__CAGUUCUAAUG_CCGCUUUGAAACAAU_A_AUGGGGAAAUAGCGAGUUUCCAUUUAAAGUCUGCAUUCGACUUUAAAGUGAAACUCAC
............................................((.(................).)).......(((((((..(((((((((.......)))))))))..))))))).. (-15.31 = -15.79 +   0.48)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:02:43 2011