Locus 14222

Sequence ID dm3.chrX
Location 12,014,656 – 12,014,710
Length 54
Max. P 0.978454
window19582 window19583

overview

Window 2

Location 12,014,656 – 12,014,710
Length 54
Sequences 7
Columns 54
Reading direction forward
Mean pairwise identity 81.66
Shannon entropy 0.33289
G+C content 0.49471
Mean single sequence MFE -16.66
Consensus MFE -11.05
Energy contribution -11.40
Covariance contribution 0.35
Combinations/Pair 1.19
Mean z-score -2.20
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12014656 54 + 22422827
UAGCAGAGCGGCCACAUGGAAUAGAAUGCUGUCAUGUGUCCAUACUGCUUUUCC
.(((((...((.((((((..((((....)))))))))).))...)))))..... ( -16.90, z-score =  -1.97, R)
>droSim1.chrU 2687590 54 - 15797150
UAGCAGAGCGGCCACAUGGAAUAGAAUGCUGUCAUGUGUCCAUACUGCUUUUCC
.(((((...((.((((((..((((....)))))))))).))...)))))..... ( -16.90, z-score =  -1.97, R)
>droSec1.super_45 241590 54 - 245362
UAGCAGAGCGUCCACAUGGAAUAGAAUGCUGUCAUGUGUCCAUACUGCUUUUCC
.(((((...(..((((((..((((....))))))))))..)...)))))..... ( -15.00, z-score =  -1.85, R)
>droYak2.chrX 19933445 54 - 21770863
UAGCAGAGCGGCCACAUGGAAUAGAAUGCUGUCAUGUGUCCGUACUGCUUUUCC
.(((((.((((.((((((..((((....)))))))))).)))).)))))..... ( -22.70, z-score =  -4.14, R)
>droEre2.scaffold_4690 3932963 54 - 18748788
UAGCAGAGCGGCCACAUGGAAUAGAAUGCUGUCAUGUGUCCGUACUGCUUUUCC
.(((((.((((.((((((..((((....)))))))))).)))).)))))..... ( -22.70, z-score =  -4.14, R)
>dp4.chrXL_group1a 6416327 54 - 9151740
AAGCAGAGCAGCCAGAUAGAAUUUCACCAUGUGCCCUGUCUGAAGUGCCUCUCC
....((((((..(((((((.....(((...)))..)))))))...)).)))).. ( -11.20, z-score =  -0.65, R)
>droPer1.super_12 575008 54 + 2414086
AAGCAGAGCAGCCAGAUAGAAUUUCACCAUGUGCCCUGUCUGAAGUGCCUCUCC
....((((((..(((((((.....(((...)))..)))))))...)).)))).. ( -11.20, z-score =  -0.65, R)
>consensus
UAGCAGAGCGGCCACAUGGAAUAGAAUGCUGUCAUGUGUCCGUACUGCUUUUCC
..((((...((.((((((..((((....)))))))))).))...))))...... (-11.05 = -11.40 +   0.35)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,014,656 – 12,014,710
Length 54
Sequences 7
Columns 54
Reading direction reverse
Mean pairwise identity 81.66
Shannon entropy 0.33289
G+C content 0.49471
Mean single sequence MFE -16.99
Consensus MFE -15.05
Energy contribution -14.58
Covariance contribution -0.46
Combinations/Pair 1.36
Mean z-score -1.89
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.00
SVM RNA-class probability 0.978454
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 12014656 54 - 22422827
GGAAAAGCAGUAUGGACACAUGACAGCAUUCUAUUCCAUGUGGCCGCUCUGCUA
.....(((((..(((.((((((..............)))))).)))..))))). ( -17.84, z-score =  -2.26, R)
>droSim1.chrU 2687590 54 + 15797150
GGAAAAGCAGUAUGGACACAUGACAGCAUUCUAUUCCAUGUGGCCGCUCUGCUA
.....(((((..(((.((((((..............)))))).)))..))))). ( -17.84, z-score =  -2.26, R)
>droSec1.super_45 241590 54 + 245362
GGAAAAGCAGUAUGGACACAUGACAGCAUUCUAUUCCAUGUGGACGCUCUGCUA
.....(((((..((..((((((..............))))))..))..))))). ( -17.54, z-score =  -2.67, R)
>droYak2.chrX 19933445 54 + 21770863
GGAAAAGCAGUACGGACACAUGACAGCAUUCUAUUCCAUGUGGCCGCUCUGCUA
.....(((((..(((.((((((..............)))))).)))..))))). ( -19.54, z-score =  -3.16, R)
>droEre2.scaffold_4690 3932963 54 + 18748788
GGAAAAGCAGUACGGACACAUGACAGCAUUCUAUUCCAUGUGGCCGCUCUGCUA
.....(((((..(((.((((((..............)))))).)))..))))). ( -19.54, z-score =  -3.16, R)
>dp4.chrXL_group1a 6416327 54 + 9151740
GGAGAGGCACUUCAGACAGGGCACAUGGUGAAAUUCUAUCUGGCUGCUCUGCUU
((((.....))))((.(((((((...((((......))))....))))))))). ( -13.30, z-score =   0.16, R)
>droPer1.super_12 575008 54 - 2414086
GGAGAGGCACUUCAGACAGGGCACAUGGUGAAAUUCUAUCUGGCUGCUCUGCUU
((((.....))))((.(((((((...((((......))))....))))))))). ( -13.30, z-score =   0.16, R)
>consensus
GGAAAAGCAGUACGGACACAUGACAGCAUUCUAUUCCAUGUGGCCGCUCUGCUA
.....(((((..(((.((((((..............)))))).)))..))))). (-15.05 = -14.58 +  -0.46)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:36:13 2011