Locus 15314

Sequence ID dm3.chrX
Location 18,371,504 – 18,371,647
Length 143
Max. P 0.880217
window21096 window21097 window21098

overview

Window 6

Location 18,371,504 – 18,371,574
Length 70
Sequences 4
Columns 70
Reading direction forward
Mean pairwise identity 86.91
Shannon entropy 0.20686
G+C content 0.50046
Mean single sequence MFE -15.50
Consensus MFE -12.94
Energy contribution -12.88
Covariance contribution -0.06
Combinations/Pair 1.18
Mean z-score -1.80
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.85
SVM RNA-class probability 0.834353
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18371504 70 + 22422827
CCAUUCGGCAUUCGGCCAAAUGAGCCAUCAUUUAUUUCUCUCCGUGUGGCCGUAUCGUCACAUCGUUGUU
......(((.....)))((((((....)))))).........((((((((......)))))).))..... ( -15.50, z-score =  -1.42, R)
>droSim1.chrX 14162842 65 + 17042790
-----CGGCAUUCGGCCAAAUGAGCCAUCAUUUAUUUCUCUCCGUGUUGCCCUAUCGCCACAUCGUUGUU
-----.(((.....)))((((((....)))))).........(((((.((......)).))).))..... ( -11.70, z-score =  -0.57, R)
>droSec1.super_8 677462 65 + 3762037
-----CGGCAUUCGGCCAAAUGAGCCAUCAUUUAUUUCUCUCCGUGUGGCCCUAUCGCCACAUCGUUGUU
-----.(((.....)))((((((....)))))).........((((((((......)))))).))..... ( -18.20, z-score =  -2.45, R)
>droEre2.scaffold_4690 8687762 62 + 18748788
-------CCAUUCGGCCAAAUGAGCUAUAAUUUAUUUCUCUCCGUGUGGCC-CAUCGCCACAUCGCCGCU
-------.....((((.....(((..(((...)))..)))...(((((((.-....))))))).)))).. ( -16.60, z-score =  -2.74, R)
>consensus
_____CGGCAUUCGGCCAAAUGAGCCAUCAUUUAUUUCUCUCCGUGUGGCCCUAUCGCCACAUCGUUGUU
............((((.((((((....))))))..........(((((((......))))))).)))).. (-12.94 = -12.88 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,371,574 – 18,371,647
Length 73
Sequences 7
Columns 92
Reading direction forward
Mean pairwise identity 70.75
Shannon entropy 0.51857
G+C content 0.56981
Mean single sequence MFE -22.65
Consensus MFE -14.78
Energy contribution -15.47
Covariance contribution 0.69
Combinations/Pair 1.07
Mean z-score -0.93
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.777644
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18371574 73 + 22422827
GUUGCCCCAUCAUUCAGGCUGAUGGAAAUGGAAA------UGGCCUGGGAAAUGGGGAAAUGGGGCGAA--GGCGAUGGCG-----------
(((.((((((..((((((((..............------.))))))))..)))))).......((...--.))...))).----------- ( -24.96, z-score =  -1.85, R)
>droSim1.chrX 14162907 67 + 17042790
GUGGCCCCAUCAUUCAGGCUGAUGGAAAUGGAAA------UGGCCUGGGAAAUGGGGAUGUGGGGCGACGGCG-------------------
((.((((((.(((((...((.(.((..((....)------)..))).))......))))))))))).))....------------------- ( -25.80, z-score =  -2.32, R)
>droSec1.super_8 677527 67 + 3762037
GUGGCCCCAUCAUUCAGGCUGAUGGAAAUGGAAA------UGGCCUGGGAAAUGGGGAAGUGGGGCGACGGCG-------------------
((.(((((((..((((..((.(.((..((....)------)..))).))...))))...))))))).))....------------------- ( -25.20, z-score =  -2.21, R)
>droYak2.chrX 17002430 75 + 21770863
GUAGCACCAUCAUUCAGGCUGAUGGAAAUGGAAA------UGGCCUGGGAAAUGGUGAAAUGGGGAAAUGCGGCGCUGGCG-----------
....((((((..((((((((..............------.))))))))..))))))...............((....)).----------- ( -19.66, z-score =  -0.56, R)
>droEre2.scaffold_4690 8687824 59 + 18748788
GUAGCCCCAUCAUUCUGGCUGAUGGACAUGGAAA------UGGCCUGGGAAAUGGGGCGAUGGCG---------------------------
((.(((((((..(((.(((.......(((....)------))))).)))..)))))))....)).--------------------------- ( -20.81, z-score =  -1.27, R)
>dp4.chrXL_group3a 318868 92 + 2690836
GUCGCGCCAUCAUUCAGGCUGAUGGAAAUGGAAAUGGAAACGGCAUGGGAAAUGGGGCCAUGGGACGAGGGAGAUGGGUCACAGAGCAGCCA
((.((.(((((.(((.(.((.((((.........((....)).(((.....)))...)))).)).)...)))))))))).)).......... ( -21.30, z-score =   1.06, R)
>droPer1.super_39 333326 86 - 745454
GUCGCGCCAUCAUUCAAGCUGAUGGAAAUGGAAA------CGGCAUAGGAAAUGGGGCCAUGGGACGAGGGAGAUGGGUCACAGAGCAGCCA
((.((.(((((.(((..(((.((((...((....------)).(((.....)))...)))).)).)...)))))))))).)).......... ( -20.80, z-score =   0.60, R)
>consensus
GUAGCCCCAUCAUUCAGGCUGAUGGAAAUGGAAA______UGGCCUGGGAAAUGGGGAAAUGGGGCGACGGAG____G_C____________
....((((((..((((((((.....................))))))))..))))))................................... (-14.78 = -15.47 +   0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,371,574 – 18,371,647
Length 73
Sequences 7
Columns 92
Reading direction reverse
Mean pairwise identity 70.75
Shannon entropy 0.51857
G+C content 0.56981
Mean single sequence MFE -16.70
Consensus MFE -12.40
Energy contribution -12.83
Covariance contribution 0.43
Combinations/Pair 1.17
Mean z-score -0.90
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.04
SVM RNA-class probability 0.880217
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 18371574 73 - 22422827
-----------CGCCAUCGCC--UUCGCCCCAUUUCCCCAUUUCCCAGGCCA------UUUCCAUUUCCAUCAGCCUGAAUGAUGGGGCAAC
-----------..........--...(((((((.....((((...(((((..------...............))))))))))))))))... ( -19.23, z-score =  -1.98, R)
>droSim1.chrX 14162907 67 - 17042790
-------------------CGCCGUCGCCCCACAUCCCCAUUUCCCAGGCCA------UUUCCAUUUCCAUCAGCCUGAAUGAUGGGGCCAC
-------------------................(((((((...(((((..------...............)))))...))))))).... ( -17.73, z-score =  -1.64, R)
>droSec1.super_8 677527 67 - 3762037
-------------------CGCCGUCGCCCCACUUCCCCAUUUCCCAGGCCA------UUUCCAUUUCCAUCAGCCUGAAUGAUGGGGCCAC
-------------------................(((((((...(((((..------...............)))))...))))))).... ( -17.73, z-score =  -1.72, R)
>droYak2.chrX 17002430 75 - 21770863
-----------CGCCAGCGCCGCAUUUCCCCAUUUCACCAUUUCCCAGGCCA------UUUCCAUUUCCAUCAGCCUGAAUGAUGGUGCUAC
-----------....(((((((((((...................(((((..------...............))))))))).))))))).. ( -16.13, z-score =  -1.95, R)
>droEre2.scaffold_4690 8687824 59 - 18748788
---------------------------CGCCAUCGCCCCAUUUCCCAGGCCA------UUUCCAUGUCCAUCAGCCAGAAUGAUGGGGCUAC
---------------------------.......((((((((.....(((..------...............))).....))))))))... ( -17.43, z-score =  -1.64, R)
>dp4.chrXL_group3a 318868 92 - 2690836
UGGCUGCUCUGUGACCCAUCUCCCUCGUCCCAUGGCCCCAUUUCCCAUGCCGUUUCCAUUUCCAUUUCCAUCAGCCUGAAUGAUGGCGCGAC
.(((.(((.((.(((...........))).)).)))............)))................((((((.......))))))...... ( -14.32, z-score =   1.47, R)
>droPer1.super_39 333326 86 + 745454
UGGCUGCUCUGUGACCCAUCUCCCUCGUCCCAUGGCCCCAUUUCCUAUGCCG------UUUCCAUUUCCAUCAGCUUGAAUGAUGGCGCGAC
.(((.(((.((.(((...........))).)).)))............))).------.........((((((.......))))))...... ( -14.32, z-score =   1.19, R)
>consensus
____________G_C____CCCCCUCGCCCCAUUUCCCCAUUUCCCAGGCCA______UUUCCAUUUCCAUCAGCCUGAAUGAUGGGGCCAC
...................................(((((((...(((((.......................)))))...))))))).... (-12.40 = -12.83 +   0.43)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:56:57 2011