Locus 13122

Sequence ID dm3.chrX
Location 4,428,229 – 4,428,339
Length 110
Max. P 0.928176
window18035 window18036

overview

Window 5

Location 4,428,229 – 4,428,339
Length 110
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 80.47
Shannon entropy 0.38655
G+C content 0.41079
Mean single sequence MFE -29.20
Consensus MFE -16.22
Energy contribution -17.25
Covariance contribution 1.03
Combinations/Pair 1.15
Mean z-score -1.71
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.24
SVM RNA-class probability 0.608115
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4428229 110 + 22422827
AUGCUUCGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAGUC-UCGGUAAUCGAGCCAUAAUCGAAAAUAUCGUUUGUGCGAUAAGCGAUAACUAUUUCGUUGCCCAUUU
.....((((((((((.(...(((((.((.((((((((...(.(-(((.....))))).)))))))).)))))))...))))))..)))))((((......))))....... ( -29.30, z-score =  -1.65, R)
>droSim1.chrX 3427812 110 + 17042790
AAGCUUCGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAGUC-UCGGUAAUCGAGCCAUAAUCGAAAAAAUCGUUUGUGCGAUAAGCGAUAACUCUUUCGUUGCCCAUUU
..((.((((((((((.(...((((..((.((((((((...(.(-(((.....))))).)))))))).)).))))...))))))..))))).(((......)))))...... ( -28.70, z-score =  -1.64, R)
>droSec1.super_4 3879932 98 - 6179234
AUGCUUCGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAGUC-UCGGUAAUCGAGCCAUAAUCGAAAAAAUCGUUUGUGCGAUAAGCGUUGCCCAUUU------------
..((..(((((((((.(...((((..((.((((((((...(.(-(((.....))))).)))))))).)).))))...))))))..))))..))......------------ ( -29.10, z-score =  -2.37, R)
>droYak2.chrX 17761408 110 - 21770863
AUGCUUUGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAAUC-UCGGUAAUCGAGGCAUAAUCGGAAAAAUCGUUUGUGCGAUAAGCGAUAACUAUUUGGUUGCCUAUUU
............(((((((..((((.((((((.((((.....(-(((.....))))((((((.(((.....))).)))))).)))).)))))).)))))))))))...... ( -28.50, z-score =  -1.16, R)
>droEre2.scaffold_4690 1806907 110 + 18748788
AUGCUUCGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAGUC-UCGGUAAUCGAGGCAUAAUCGAAAAAAUCGUUUGUGCGAUAAGCGAUAACUAUUUCGUUGCCCAUUU
.....((((((((((.(...((((..((.((((((((...(((-(((.....)))))))))))))).)).))))...))))))..)))))((((......))))....... ( -32.70, z-score =  -2.45, R)
>droAna3.scaffold_13335 3323354 101 - 3335858
GUGCUUCGCUU-GCAGCUAACGGU---UAUCGAUUAUCGAUUAAUCGGCCAUCGCCAUAAAACGGCAAAG-----UUGUGCGAUAAGUUUUCGUUGCUCAGUUGAACACC-
(((.((((((.-(((((.((((((---...((((((.....)))))))))(((((.....(((......)-----))..)))))..)))...)))))..)).))))))).- ( -26.90, z-score =  -0.99, R)
>consensus
AUGCUUCGCUUCGCAGCUAUCGAUGCUUAUCGAUUAUAUAGUC_UCGGUAAUCGAGCCAUAAUCGAAAAAAUCGUUUGUGCGAUAAGCGAUAACUAUUUCGUUGCCCAUUU
.....((((((((((....(((((.....((((((((..........))))))))......)))))(((.....))).)))))..)))))..................... (-16.22 = -17.25 +   1.03)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,428,229 – 4,428,339
Length 110
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 80.47
Shannon entropy 0.38655
G+C content 0.41079
Mean single sequence MFE -30.10
Consensus MFE -14.81
Energy contribution -16.67
Covariance contribution 1.86
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928176
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 4428229 110 - 22422827
AAAUGGGCAACGAAAUAGUUAUCGCUUAUCGCACAAACGAUAUUUUCGAUUAUGGCUCGAUUACCGA-GACUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCGAAGCAU
......(((((......))).(((((..((((((...((((.((.(((((((((.((((.....)))-)....))))))))).))..))))...).)))))))))).)).. ( -33.40, z-score =  -3.20, R)
>droSim1.chrX 3427812 110 - 17042790
AAAUGGGCAACGAAAGAGUUAUCGCUUAUCGCACAAACGAUUUUUUCGAUUAUGGCUCGAUUACCGA-GACUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCGAAGCUU
....((((..(....).....(((((..((((((...(((((((.(((((((((.((((.....)))-)....))))))))).))).))))...).)))))))))).)))) ( -35.00, z-score =  -3.40, R)
>droSec1.super_4 3879932 98 + 6179234
------------AAAUGGGCAACGCUUAUCGCACAAACGAUUUUUUCGAUUAUGGCUCGAUUACCGA-GACUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCGAAGCAU
------------......((..((((..((((((...(((((((.(((((((((.((((.....)))-)....))))))))).))).))))...).)))))))))..)).. ( -32.40, z-score =  -3.89, R)
>droYak2.chrX 17761408 110 + 21770863
AAAUAGGCAACCAAAUAGUUAUCGCUUAUCGCACAAACGAUUUUUCCGAUUAUGCCUCGAUUACCGA-GAUUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCAAAGCAU
.....(....).....((((((((((((((........((....)).(((((((.((((.....)))-)....))))))))))))))...)))))))((........)).. ( -25.40, z-score =  -2.01, R)
>droEre2.scaffold_4690 1806907 110 - 18748788
AAAUGGGCAACGAAAUAGUUAUCGCUUAUCGCACAAACGAUUUUUUCGAUUAUGCCUCGAUUACCGA-GACUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCGAAGCAU
......(((((......))).(((((..((((((...(((((((.(((((((((.((((.....)))-)....))))))))).))).))))...).)))))))))).)).. ( -31.40, z-score =  -2.72, R)
>droAna3.scaffold_13335 3323354 101 + 3335858
-GGUGUUCAACUGAGCAACGAAAACUUAUCGCACAA-----CUUUGCCGUUUUAUGGCGAUGGCCGAUUAAUCGAUAAUCGAUA---ACCGUUAGCUGC-AAGCGAAGCAC
-(.(((((....))))).).........((((....-----..(((((((...))))))).(((..((..((((.....)))).---...))..)))..-..))))..... ( -23.00, z-score =  -0.06, R)
>consensus
AAAUGGGCAACGAAAUAGUUAUCGCUUAUCGCACAAACGAUUUUUUCGAUUAUGGCUCGAUUACCGA_GACUAUAUAAUCGAUAAGCAUCGAUAGCUGCGAAGCGAAGCAU
.......................((((.((((((...((((....(((((((((..(((.....)))......))))))))).....))))...).)))))....)))).. (-14.81 = -16.67 +   1.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:15:02 2011