Locus 13024

Sequence ID dm3.chrX
Location 3,909,302 – 3,909,367
Length 65
Max. P 0.999072
window17898 window17899

overview

Window 8

Location 3,909,302 – 3,909,367
Length 65
Sequences 9
Columns 77
Reading direction forward
Mean pairwise identity 84.58
Shannon entropy 0.29640
G+C content 0.49528
Mean single sequence MFE -19.59
Consensus MFE -16.76
Energy contribution -16.76
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964710
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3909302 65 + 22422827
-----GACUUCAAUGAA--GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG-----
-----..((((...)))--).((((((((....)))))))).((((((....))))))(((.....)))...----- ( -19.20, z-score =  -1.79, R)
>droPer1.super_14 1831436 65 + 2168203
-----GGCUUCAACGAA--UGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUCCGG-----
-----((...((((...--..((((((((....)))))))).((((((....))))))..))))....))..----- ( -21.50, z-score =  -2.43, R)
>dp4.chrXL_group1e 737711 65 - 12523060
-----GGCUUCAACGAA--UGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUCCGG-----
-----((...((((...--..((((((((....)))))))).((((((....))))))..))))....))..----- ( -21.50, z-score =  -2.43, R)
>droAna3.scaffold_13117 40960 61 - 5790199
---------ACAAUGAA--GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG-----
---------.((((...--..((((((((....)))))))).((((((....))))))..))))........----- ( -17.90, z-score =  -1.70, R)
>droEre2.scaffold_4690 1279878 65 + 18748788
-----GACUUCAAUGAA--GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG-----
-----..((((...)))--).((((((((....)))))))).((((((....))))))(((.....)))...----- ( -19.20, z-score =  -1.79, R)
>droYak2.chrX 17249252 65 - 21770863
-----GACUUCAAUGAA--GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG-----
-----..((((...)))--).((((((((....)))))))).((((((....))))))(((.....)))...----- ( -19.20, z-score =  -1.79, R)
>droSec1.super_4 3368157 65 - 6179234
-----GACUUCAAUGAA--GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG-----
-----..((((...)))--).((((((((....)))))))).((((((....))))))(((.....)))...----- ( -19.20, z-score =  -1.79, R)
>droGri2.scaffold_14853 2789851 77 - 10151454
GACGACACUAGAGUAGACGUGGACAGCCGACGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCAUGGAAAUUAUG
.................((((((((((((....)))))))).((((((....))))))......))))......... ( -20.80, z-score =  -1.79, R)
>droWil1.scaffold_180588 91579 58 - 1294757
------------AGGAA--CGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCGGUUGUACUGUAA-----
------------.(.((--(.((((((((....)))))))).((((((....))))))..))).).......----- ( -17.80, z-score =  -1.74, R)
>consensus
_____GACUUCAAUGAA__GGGACAGCCGUCGCCGGCUGUCAAUAUGGAAAUUCAUAUCAGUUGCACUGCAG_____
.....................((((((((....)))))))).((((((....))))))................... (-16.76 = -16.76 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 3,909,302 – 3,909,367
Length 65
Sequences 9
Columns 77
Reading direction reverse
Mean pairwise identity 84.58
Shannon entropy 0.29640
G+C content 0.49528
Mean single sequence MFE -23.59
Consensus MFE -20.11
Energy contribution -20.11
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.79
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.63
SVM RNA-class probability 0.999072
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3909302 65 - 22422827
-----CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC--UUCAUUGAAGUC-----
-----((.(((((.....((((((......))))))((((((((....))))))))..--..))))).))..----- ( -24.10, z-score =  -3.88, R)
>droPer1.super_14 1831436 65 - 2168203
-----CCGGAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCA--UUCGUUGAAGCC-----
-----..((....((((.((((((......))))))((((((((....))))))))..--...))))...))----- ( -25.60, z-score =  -3.90, R)
>dp4.chrXL_group1e 737711 65 + 12523060
-----CCGGAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCA--UUCGUUGAAGCC-----
-----..((....((((.((((((......))))))((((((((....))))))))..--...))))...))----- ( -25.60, z-score =  -3.90, R)
>droAna3.scaffold_13117 40960 61 + 5790199
-----CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC--UUCAUUGU---------
-----..((((((.....((((((......))))))((((((((....))))))))..--..))))))--------- ( -24.70, z-score =  -4.54, R)
>droEre2.scaffold_4690 1279878 65 - 18748788
-----CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC--UUCAUUGAAGUC-----
-----((.(((((.....((((((......))))))((((((((....))))))))..--..))))).))..----- ( -24.10, z-score =  -3.88, R)
>droYak2.chrX 17249252 65 + 21770863
-----CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC--UUCAUUGAAGUC-----
-----((.(((((.....((((((......))))))((((((((....))))))))..--..))))).))..----- ( -24.10, z-score =  -3.88, R)
>droSec1.super_4 3368157 65 + 6179234
-----CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC--UUCAUUGAAGUC-----
-----((.(((((.....((((((......))))))((((((((....))))))))..--..))))).))..----- ( -24.10, z-score =  -3.88, R)
>droGri2.scaffold_14853 2789851 77 + 10151454
CAUAAUUUCCAUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGUCGGCUGUCCACGUCUACUCUAGUGUCGUC
..................((((((......))))))((((((((....)))))))).(((.(.((....))).))). ( -19.50, z-score =  -1.89, R)
>droWil1.scaffold_180588 91579 58 + 1294757
-----UUACAGUACAACCGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCG--UUCCU------------
-----.............((((((......))))))((((((((....))))))))..--.....------------ ( -20.50, z-score =  -4.36, R)
>consensus
_____CUGCAGUGCAACUGAUAUGAAUUUCCAUAUUGACAGCCGGCGACGGCUGUCCC__UUCAUUGAAGUC_____
..................((((((......))))))((((((((....))))))))..................... (-20.11 = -20.11 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:13:10 2011