Locus 13728

Sequence ID	dm3.chrX
Location	8,725,123 – 8,725,226
Length	103
Max. P	0.741375

overview

Window 7

Location	8,725,123 – 8,725,226
Length	103
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	58.54
Shannon entropy	0.63733
G+C content	0.45293
Mean single sequence MFE	-25.53
Consensus MFE	-11.59
Energy contribution	-11.34
Covariance contribution	-0.25
Combinations/Pair	1.50
Mean z-score	-0.93
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.17
SVM RNA-class probability	0.577418
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8725123 103 + 22422827
CGAGGUGCGAAAAUGUUGGGUUGCAACGUGGCGGCCGGGGAAUUAUGUAUGUCUGUAGCCCCUUGGAAAAAAUGUGGGCGAAAACAAAGGGCGCACUAAGCAC-
...((((((....((((...((((.((((.....((((((..((((........))))..)))))).....))))..)))).)))).....))))))......- ( -29.80, z-score =  -0.29, R)
>droSec1.super_34 98179 89 + 457129
CGAGGUGCGAAAAUGUCCGGGUUUGGAACGG--GCCGGGGAAUUAUGAA--------GCCCCCUAGGAA----GUGGGCGAAAACAAAGGGCGCACUAAGCAC-
...((((((..(((..((.((((((...)))--))).))..))).....--------((((.((....)----).))))............))))))......- ( -27.40, z-score =  -0.50, R)
>droMoj3.scaffold_6473 5936987 88 + 16943266
AGAGGUGCGAAAAUGUCAA--UGCAACAAAAGUGUUGUAAAAGUUUUGUUGUU----GCAUUUUGUGUG----AUAUGCGAAAA------GCGCAUUAAACAUU
.(((((((((.....))..--.(((((((((.(........).))))))))).----)))))))((((.----..(((((....------.)))))...)))). ( -23.10, z-score =  -1.68, R)
>droVir3.scaffold_12726 281500 83 - 2840439
AGAGGUGCGAAAACGUCAA--UGUAACAAAUAUGCUGU-----UGUUCUUGUU----GCACUUUGUGUG----AUAUGCGAAAA------GCGCAUUAAACAUU
.(((((((((......(((--((((.......))).))-----))......))----)))))))((((.----..(((((....------.)))))...)))). ( -21.80, z-score =  -1.24, R)
>consensus
AGAGGUGCGAAAAUGUCAA__UGCAACAAAG_UGCCGGGGAAUUAUGAAUGUU____GCACCUUGGGAA____AUAGGCGAAAA______GCGCACUAAACAC_
...((((((............((((((......))))))..................((((..............))))............))))))....... (-11.59 = -11.34 +  -0.25)

alignment

secondary structure

dotplot

Window 8

Location	8,725,123 – 8,725,226
Length	103
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	58.54
Shannon entropy	0.63733
G+C content	0.45293
Mean single sequence MFE	-17.46
Consensus MFE	-8.94
Energy contribution	-7.94
Covariance contribution	-1.00
Combinations/Pair	1.58
Mean z-score	-0.83
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.56
SVM RNA-class probability	0.741375
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8725123 103 - 22422827
-GUGCUUAGUGCGCCCUUUGUUUUCGCCCACAUUUUUUCCAAGGGGCUACAGACAUACAUAAUUCCCCGGCCGCCACGUUGCAACCCAACAUUUUCGCACCUCG
-((((...(((.((((((((...................)))))))))))...........................((((.....))))......)))).... ( -20.61, z-score =  -0.57, R)
>droSec1.super_34 98179 89 - 457129
-GUGCUUAGUGCGCCCUUUGUUUUCGCCCAC----UUCCUAGGGGGC--------UUCAUAAUUCCCCGGC--CCGUUCCAAACCCGGACAUUUUCGCACCUCG
-.......(((((.....(((....((((.(----(....)).))))--------...........((((.--...........)))))))....))))).... ( -20.70, z-score =  -0.24, R)
>droMoj3.scaffold_6473 5936987 88 - 16943266
AAUGUUUAAUGCGC------UUUUCGCAUAU----CACACAAAAUGC----AACAACAAAACUUUUACAACACUUUUGUUGCA--UUGACAUUUUCGCACCUCU
((((((..(((((.------....)))))..----.......(((((----(((((...................))))))))--))))))))........... ( -16.01, z-score =  -2.63, R)
>droVir3.scaffold_12726 281500 83 + 2840439
AAUGUUUAAUGCGC------UUUUCGCAUAU----CACACAAAGUGC----AACAAGAACA-----ACAGCAUAUUUGUUACA--UUGACGUUUUCGCACCUCU
..(((...(((((.------....)))))..----.)))....((((----..(((.((((-----(........)))))...--)))..(....))))).... ( -12.50, z-score =   0.11, R)
>consensus
_AUGCUUAAUGCGC______UUUUCGCACAC____CACACAAAGGGC____AACAAAAAUAAUUCCACAGCA_CCUUGUUACA__CUGACAUUUUCGCACCUCG
........(((((............((((..............)))).....................(((......)))...............))))).... ( -8.94 =  -7.94 +  -1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:26:42 2011