Locus 13823

Sequence ID	dm3.chrX
Location	9,398,390 – 9,398,453
Length	63
Max. P	0.999663

overview

Window 8

Location	9,398,390 – 9,398,453
Length	63
Sequences	11
Columns	64
Reading direction	forward
Mean pairwise identity	82.26
Shannon entropy	0.38587
G+C content	0.54134
Mean single sequence MFE	-26.63
Consensus MFE	-18.85
Energy contribution	-17.93
Covariance contribution	-0.92
Combinations/Pair	1.53
Mean z-score	-2.99
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.17
SVM RNA-class probability	0.997732
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9398390 63 + 22422827
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG-CAAGCAGCCAGCCCAGUUCAAAAAUAGUU
..(((((...(((((((((.(.((((......))-)).)))))))))).))))).......... ( -29.00, z-score =  -3.25, R)
>droPer1.super_13 61064 62 - 2293547
UCGAACUAAAGACUCGCUGCUUUGCUGGGCCGGG-CAGGCAGCGAGUCAAGUUCAAAAAUAUU-
..(((((...((((((((((((.(((......))-))))))))))))).))))).........- ( -30.10, z-score =  -5.55, R)
>dp4.chrXL_group1a 1564005 62 - 9151740
UCGAACUAAAGACUCGCUGCUUUGCUGGGCCGGG-CAGGCAGCGAGUCAAGUUCAAAAAUAUU-
..(((((...((((((((((((.(((......))-))))))))))))).))))).........- ( -30.10, z-score =  -5.55, R)
>droSim1.chrX 7493173 63 + 17042790
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG-CAAGCAGCCGGCCCAGUUCAAAAAUAGUU
..(((((...(((((((((.(.((((......))-)).)))))))))).))))).......... ( -28.30, z-score =  -2.84, R)
>droSec1.super_15 164838 63 + 1954846
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG-CAAGCAGCCGGCCCAGUUCAAAAAUAGUU
..(((((...(((((((((.(.((((......))-)).)))))))))).))))).......... ( -28.30, z-score =  -2.84, R)
>droYak2.chrX 17990407 63 + 21770863
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG-CAAGCAGCAAGCCCAGUUCAAAAAUAGUU
..(((((...((((.((((.(.((((......))-)).))))).)))).))))).......... ( -22.50, z-score =  -1.32, R)
>droEre2.scaffold_4690 13032668 63 - 18748788
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG-CAAGCAGCAAGCCCAGUUCAAACAUAAUU
..(((((...((((.((((.(.((((......))-)).))))).)))).))))).......... ( -22.50, z-score =  -1.63, R)
>droWil1.scaffold_181096 9764900 63 - 12416693
UCGAACUACAG-CUGGCUGACUUGCUGGGCUGGGGCAAGCAGCUAGCCAAGUUCAAAUAUUGGC
..(((((...(-(((((((.((((((.......))))))))))))))..))))).......... ( -27.40, z-score =  -3.26, R)
>droVir3.scaffold_12970 6035220 62 + 11907090
UCGAACUGA-UGCCUGCUGACCUGCUGGGCUGGG-CAGGCAGCAAGCCGAGUUCAAUGAACAUG
..(((((..-.((.(((((.((((((......))-))))))))).))..))))).......... ( -26.10, z-score =  -2.77, R)
>droMoj3.scaffold_6473 1353792 63 - 16943266
UCGAACUACCUGCCUGCUGACCUGCUGGGCUGGG-CAGACAGCAAGCCGAGUUCAAUGAUCGUU
..(((((....((.(((((..(((((......))-))).))))).))..))))).......... ( -21.40, z-score =  -1.26, R)
>droGri2.scaffold_14853 895212 62 - 10151454
UCGAACUAA-UGCCUGCUGUCCUGCUGGGCUGGG-CAGGCAGCAAGCCGAGUUCAAUGUCCUUU
..(((((..-.((.(((((.((((((......))-))))))))).))..))))).......... ( -27.20, z-score =  -2.66, R)
>consensus
UCGAACUAAAGGCUGGCUGACCUGCUGGGCUGGG_CAAGCAGCAAGCCCAGUUCAAAAAUAGUU
..(((((....(((((((..((....))(((......))))))))))..))))).......... (-18.85 = -17.93 +  -0.92)

alignment

secondary structure

dotplot

Window 9

Location	9,398,390 – 9,398,453
Length	63
Sequences	11
Columns	64
Reading direction	reverse
Mean pairwise identity	82.26
Shannon entropy	0.38587
G+C content	0.54134
Mean single sequence MFE	-28.33
Consensus MFE	-20.44
Energy contribution	-20.31
Covariance contribution	-0.13
Combinations/Pair	1.35
Mean z-score	-4.14
Structure conservation index	0.72
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	4.15
SVM RNA-class probability	0.999663
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 9398390 63 - 22422827
AACUAUUUUUGAACUGGGCUGGCUGCUUG-CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........(((((((((((((((((((((-(........))))).))))))))))..))))))) ( -33.30, z-score =  -5.06, R)
>droPer1.super_13 61064 62 + 2293547
-AAUAUUUUUGAACUUGACUCGCUGCCUG-CCCGGCCCAGCAAAGCAGCGAGUCUUUAGUUCGA
-.......(((((((.((((((((((.((-(........)))..))))))))))...))))))) ( -28.30, z-score =  -5.88, R)
>dp4.chrXL_group1a 1564005 62 + 9151740
-AAUAUUUUUGAACUUGACUCGCUGCCUG-CCCGGCCCAGCAAAGCAGCGAGUCUUUAGUUCGA
-.......(((((((.((((((((((.((-(........)))..))))))))))...))))))) ( -28.30, z-score =  -5.88, R)
>droSim1.chrX 7493173 63 - 17042790
AACUAUUUUUGAACUGGGCCGGCUGCUUG-CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........(((((((((((.(((((((((-(........))))).))))).))))..))))))) ( -28.70, z-score =  -3.72, R)
>droSec1.super_15 164838 63 - 1954846
AACUAUUUUUGAACUGGGCCGGCUGCUUG-CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........(((((((((((.(((((((((-(........))))).))))).))))..))))))) ( -28.70, z-score =  -3.72, R)
>droYak2.chrX 17990407 63 - 21770863
AACUAUUUUUGAACUGGGCUUGCUGCUUG-CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........((((((((((((.((((((((-(........))))).)))).)))))..))))))) ( -26.80, z-score =  -3.48, R)
>droEre2.scaffold_4690 13032668 63 + 18748788
AAUUAUGUUUGAACUGGGCUUGCUGCUUG-CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........((((((((((((.((((((((-(........))))).)))).)))))..))))))) ( -26.80, z-score =  -3.32, R)
>droWil1.scaffold_181096 9764900 63 + 12416693
GCCAAUAUUUGAACUUGGCUAGCUGCUUGCCCCAGCCCAGCAAGUCAGCCAG-CUGUAGUUCGA
........((((((((((((.(((((((((.........))))).)))).))-))).))))))) ( -24.00, z-score =  -3.31, R)
>droVir3.scaffold_12970 6035220 62 - 11907090
CAUGUUCAUUGAACUCGGCUUGCUGCCUG-CCCAGCCCAGCAGGUCAGCAGGCA-UCAGUUCGA
........(((((((..((((((((((((-(........))))).)))))))).-..))))))) ( -29.90, z-score =  -4.17, R)
>droMoj3.scaffold_6473 1353792 63 + 16943266
AACGAUCAUUGAACUCGGCUUGCUGUCUG-CCCAGCCCAGCAGGUCAGCAGGCAGGUAGUUCGA
........((((((((.((((((((((((-(........))))).))))))))..).))))))) ( -26.90, z-score =  -2.85, R)
>droGri2.scaffold_14853 895212 62 + 10151454
AAAGGACAUUGAACUCGGCUUGCUGCCUG-CCCAGCCCAGCAGGACAGCAGGCA-UUAGUUCGA
........(((((((..((((((((((((-(........))))).)))))))).-..))))))) ( -29.90, z-score =  -4.17, R)
>consensus
AACUAUUUUUGAACUGGGCUUGCUGCUUG_CCCAGCCCAGCAGGUCAGCCAGCCUUUAGUUCGA
........(((((((..((((((((((((.(........))))).))))))))....))))))) (-20.44 = -20.31 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:28:29 2011