Locus 12944

Sequence ID	dm3.chrX
Location	3,484,418 – 3,484,522
Length	104
Max. P	0.989888

overview

Window 7

Location	3,484,418 – 3,484,522
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.06
Shannon entropy	0.39795
G+C content	0.38299
Mean single sequence MFE	-24.34
Consensus MFE	-11.24
Energy contribution	-13.00
Covariance contribution	1.76
Combinations/Pair	1.05
Mean z-score	-2.09
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.28
SVM RNA-class probability	0.627754
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3484418 104 + 22422827
GGCAUUUUUGAACAAUAAUUACAC---------------ACAGAUUUUUCCAGUGCAGAAAUAAGCAUGACGUAUACGUGAUAUA-GUCUCCAUUUGGACCAUAUCACACAUACGCCACC
(((.....................---------------.............((((........))))...((((..(((((((.-((((......)))).)))))))..)))))))... ( -23.70, z-score =  -3.49, R)
>droEre2.scaffold_4690 899016 107 + 18748788
GACAUUUUGGAACACUAAUUAAAUGCUUAUGGUAUUUUCACAUACUUCUCCUGUGCAGAA-------------AUACGUGUUAUACGUCUCCAUUUGAGCCAUAUCACGCAUACGCCACC
.......(((.....................(((((((..((((.......))))..)))-------------))))((((.(((.(.(((.....))).).))).)))).....))).. ( -16.10, z-score =   0.05, R)
>droYak2.chrX 16868190 119 - 21770863
GACAUUUUUGAACACUAAUUUAACUCUUAUGAUAUUUUCACAUAUUUUUGCAGUGCAGAAAUAACCAUGAUGUAUACGUGAUAUA-GUCUCCAUUCGGACCAUAUCACACAUACGCCACC
.(((((..((...................(((.....)))..(((((((((...)))))))))..)).)))))....(((((((.-((((......)))).)))))))............ ( -22.80, z-score =  -2.68, R)
>droSec1.super_4 2989645 118 - 6179234
GGCAUUUU-GAACAAUAAUUAAAAGCUUAUGAUAUUUGCACAUAUUGGUACAGUGCAUAAGUAACCAAGUCGUAUACGUGAUAUA-GUCUCCAAUCGGGCCAUAUCACGCACACGCCACC
(((.....-...............(((((((.(((((((........))).))))))))))).........((...((((((((.-((((......)))).))))))))...)))))... ( -28.20, z-score =  -1.81, R)
>droSim1.chrX 2553095 119 + 17042790
GGCAUUUUUGAACAAUAAUUAAAAGCUUAUGAUAUUUACACAUGUUGGCACAGUGCAUAAGUAACCAUGACGUAUACGUGAUAUA-GUCUCCAAUCGGGCCAUAUCACGCAUACGCCACC
(((.....................(((((((.......(((.(((....))))))))))))).........((((.((((((((.-((((......)))).)))))))).)))))))... ( -30.91, z-score =  -2.51, R)
>consensus
GGCAUUUUUGAACAAUAAUUAAAAGCUUAUGAUAUUUUCACAUAUUUGUACAGUGCAGAAAUAACCAUGACGUAUACGUGAUAUA_GUCUCCAUUCGGGCCAUAUCACGCAUACGCCACC
(((...................................(((...........)))................((((.(((((((...((((......))))..))))))).)))))))... (-11.24 = -13.00 +   1.76)

alignment

secondary structure

dotplot

Window 8

Location	3,484,418 – 3,484,522
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.06
Shannon entropy	0.39795
G+C content	0.38299
Mean single sequence MFE	-33.74
Consensus MFE	-18.04
Energy contribution	-19.44
Covariance contribution	1.40
Combinations/Pair	1.18
Mean z-score	-2.93
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.39
SVM RNA-class probability	0.989888
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3484418 104 - 22422827
GGUGGCGUAUGUGUGAUAUGGUCCAAAUGGAGAC-UAUAUCACGUAUACGUCAUGCUUAUUUCUGCACUGGAAAAAUCUGU---------------GUGUAAUUAUUGUUCAAAAAUGCC
.((((((((((((((((((((((........)))-))))))))))))))))))).........(((((((((....)))).---------------)))))................... ( -34.90, z-score =  -4.51, R)
>droEre2.scaffold_4690 899016 107 - 18748788
GGUGGCGUAUGCGUGAUAUGGCUCAAAUGGAGACGUAUAACACGUAU-------------UUCUGCACAGGAGAAGUAUGUGAAAAUACCAUAAGCAUUUAAUUAGUGUUCCAAAAUGUC
(((((((....))).(((((.(((.....))).)))))..(((((((-------------((((.(...).)))))))))))....))))...((((((.....)))))).......... ( -26.60, z-score =  -1.34, R)
>droYak2.chrX 16868190 119 + 21770863
GGUGGCGUAUGUGUGAUAUGGUCCGAAUGGAGAC-UAUAUCACGUAUACAUCAUGGUUAUUUCUGCACUGCAAAAAUAUGUGAAAAUAUCAUAAGAGUUAAAUUAGUGUUCAAAAAUGUC
.(((..((((((((((((((((((.....).)))-))))))))))))))..))).....(((..((((((....(((.(((((.....)))))...)))....))))))..)))...... ( -30.30, z-score =  -2.32, R)
>droSec1.super_4 2989645 118 + 6179234
GGUGGCGUGUGCGUGAUAUGGCCCGAUUGGAGAC-UAUAUCACGUAUACGACUUGGUUACUUAUGCACUGUACCAAUAUGUGCAAAUAUCAUAAGCUUUUAAUUAUUGUUC-AAAAUGCC
...(((((((((((((((((((((....)).).)-))))))))))))))(((.((((((((((((...(((((......))))).....))))))....))))))..))).-.....))) ( -36.60, z-score =  -2.79, R)
>droSim1.chrX 2553095 119 - 17042790
GGUGGCGUAUGCGUGAUAUGGCCCGAUUGGAGAC-UAUAUCACGUAUACGUCAUGGUUACUUAUGCACUGUGCCAACAUGUGUAAAUAUCAUAAGCUUUUAAUUAUUGUUCAAAAAUGCC
((((((((((((((((((((((((....)).).)-)))))))))))))))))(((((...(((((((.(((....))))))))))..))))).........................))) ( -40.30, z-score =  -3.66, R)
>consensus
GGUGGCGUAUGCGUGAUAUGGCCCGAAUGGAGAC_UAUAUCACGUAUACGUCAUGGUUACUUCUGCACUGGAAAAAUAUGUGAAAAUAUCAUAAGCGUUUAAUUAUUGUUCAAAAAUGCC
.(((((((((((((((((((.(((....)).)...))))))))))))))))))).................................................................. (-18.04 = -19.44 +   1.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:46 2011