Locus 13259

Sequence ID	dm3.chrX
Location	5,371,231 – 5,371,360
Length	129
Max. P	0.748227

overview

Window 4

Location	5,371,231 – 5,371,330
Length	99
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	60.03
Shannon entropy	0.62689
G+C content	0.36940
Mean single sequence MFE	-20.55
Consensus MFE	-9.12
Energy contribution	-10.88
Covariance contribution	1.75
Combinations/Pair	1.39
Mean z-score	-1.22
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.748227
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5371231 99 + 22422827
AAUGAUUUAUUCUCUAACGGCCAUCGUAGUGCAGCAGUGCCAUUUUUUAAGGCAAUCUAAAUAAAUUAUCAUUGGCCUUAUUGGUAA-----GGUUAGUUAAAG
.((((((((((.....(((.....))).....((...((((.........))))..)).)))))))))).((((((((((....)))-----)))))))..... ( -18.60, z-score =  -0.37, R)
>droEre2.scaffold_4690 2727308 101 + 18748788
AUUGAUUUCUUCUCUAACGGCCAUCGAAGUGCAGCAGUGCUAUUU---CAGGCACUGUUAAUAAAUUAUCAUUGGCCUGUAUUAUGGCCCGUAACAAGCGAAAG
..................((((((...(((((((.((((((....---..))))))((((((........)))))))))))))))))))(((.....))).... ( -26.10, z-score =  -1.59, R)
>droYak2.chrX 18678878 90 - 21770863
CAUGAUUUAUUCUCUAUCGGCCAUCGAAGUGCAACAGUGCGAUUU---AAAGCACUGUAAAUAAAUUAUCAUUGGCCUAUAUGAUGG-----GAAAAG------
.........(((.((((((((((..(((((...(((((((.....---...)))))))......))).))..))))).....)))))-----)))...------ ( -24.80, z-score =  -3.10, R)
>droMoj3.scaffold_6473 10839982 91 + 16943266
CAAGAUUUAUGCCUUCACG-CAAUAGAAAUUCAAUCGUUAAAAAUU--CAUUCAAUGCUGACCUAAUUCGCCUGGGCAGCUAAAUAU----UGUUUAG------
(((.((((((((......)-))........................--........((((.((((.......))))))))))))).)----)).....------ ( -12.70, z-score =   0.18, R)
>consensus
AAUGAUUUAUUCUCUAACGGCCAUCGAAGUGCAACAGUGCAAUUU___AAGGCAAUGUAAAUAAAUUAUCAUUGGCCUGUAUGAUAG_____GAUAAG______
..................(((((..(((((...((((((((.........))))))))......)))))...)))))........................... ( -9.12 = -10.88 +   1.75)

alignment

secondary structure

dotplot

Window 5

Location	5,371,231 – 5,371,330
Length	99
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	60.03
Shannon entropy	0.62689
G+C content	0.36940
Mean single sequence MFE	-20.47
Consensus MFE	-7.50
Energy contribution	-10.25
Covariance contribution	2.75
Combinations/Pair	1.33
Mean z-score	-1.52
Structure conservation index	0.37
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.41
SVM RNA-class probability	0.682219
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5371231 99 - 22422827
CUUUAACUAACC-----UUACCAAUAAGGCCAAUGAUAAUUUAUUUAGAUUGCCUUAAAAAAUGGCACUGCUGCACUACGAUGGCCGUUAGAGAAUAAAUCAUU
(((((((.....-----(((....)))(((((((((....)))).(((..((((.........))))...)))........))))))))))))........... ( -18.10, z-score =  -1.50, R)
>droEre2.scaffold_4690 2727308 101 - 18748788
CUUUCGCUUGUUACGGGCCAUAAUACAGGCCAAUGAUAAUUUAUUAACAGUGCCUG---AAAUAGCACUGCUGCACUUCGAUGGCCGUUAGAGAAGAAAUCAAU
.((((((((((((..((((........))))..))))))........((((((...---.....))))))..)).(((..((....))..)))..))))..... ( -25.30, z-score =  -1.43, R)
>droYak2.chrX 18678878 90 + 21770863
------CUUUUC-----CCAUCAUAUAGGCCAAUGAUAAUUUAUUUACAGUGCUUU---AAAUCGCACUGUUGCACUUCGAUGGCCGAUAGAGAAUAAAUCAUG
------......-----...((.(((.(((((.(((..........(((((((...---.....)))))))......))).))))).)))))............ ( -21.69, z-score =  -2.86, R)
>droMoj3.scaffold_6473 10839982 91 - 16943266
------CUAAACA----AUAUUUAGCUGCCCAGGCGAAUUAGGUCAGCAUUGAAUG--AAUUUUUAACGAUUGAAUUUCUAUUG-CGUGAAGGCAUAAAUCUUG
------.....((----(.(((((..((((((.((((..(((((((((.(((((..--....))))).).))))...)))))))-).))..))))))))).))) ( -16.80, z-score =  -0.27, R)
>consensus
______CUAAUC_____CCAUCAAACAGGCCAAUGAUAAUUUAUUAACAGUGCCUG___AAAUAGCACUGCUGCACUUCGAUGGCCGUUAGAGAAUAAAUCAUG
...........................(((((.(((........((((((((((.........))))))))))....))).))))).................. ( -7.50 = -10.25 +   2.75)

alignment

secondary structure

dotplot

Window 6

Location	5,371,263 – 5,371,360
Length	97
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	56.88
Shannon entropy	0.68213
G+C content	0.32790
Mean single sequence MFE	-21.38
Consensus MFE	-5.49
Energy contribution	-4.30
Covariance contribution	-1.19
Combinations/Pair	1.83
Mean z-score	-1.89
Structure conservation index	0.26
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.21
SVM RNA-class probability	0.596566
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 5371263 97 + 22422827
-AGCAGUGCCAUUUUUUAAGGCAAUCUAAAUAAAUUAUCAUUGGCCUUAUUGGUAA-----GGUUAGUUAAAGUUGUUAAUCGGAUUUAAGAAUUUU-AUCUAU
-.((..(((((.....((((((.....................)))))).))))).-----.))(((.(((((((.((((......)))).))))))-).))). ( -20.50, z-score =  -1.90, R)
>droEre2.scaffold_4690 2727340 100 + 18748788
-AGCAGUGCUAUUU---CAGGCACUGUUAAUAAAUUAUCAUUGGCCUGUAUUAUGGCCCGUAACAAGCGAAAGUUGUUAAUCCAAUUUCCGAAUUUUUAUCUAC
-(((((((((....---..))))))))).(((((...((...((((........))))..((((((.(....)))))))...........))...))))).... ( -26.70, z-score =  -3.42, R)
>droYak2.chrX 18678910 88 - 21770863
-AACAGUGCGAUUU---AAAGCACUGUAAAUAAAUUAUCAUUGGCCUAUAUGAUG-----------GGAAAAGUUGUUAAUCCAAUUUUGGAAUUUU-AUCAAC
-.(((((((.....---...))))))).......(((((((........))))))-----------).....((((.(((((((....))))...))-).)))) ( -20.10, z-score =  -2.45, R)
>droMoj3.scaffold_6473 10840013 90 + 16943266
AAUCGUUAAAAAUU---CAUUCAAUGCUGACCUAAUUCGCCUGGGCAGCUAAAUAU----------UGUUUAGUGGCCAAUGCGGCGUAUGCGUUAU-AUUUAU
..............---.....(((((..........((((..(((.(((((((..----------.))))))).))).....))))...)))))..-...... ( -18.22, z-score =   0.22, R)
>consensus
_AGCAGUGCAAUUU___AAGGCAAUGUAAAUAAAUUAUCAUUGGCCUGUAUGAUA___________GGUAAAGUUGUUAAUCCAAUUUAAGAAUUUU_AUCUAC
..((((((((.........))))))))........................................................((((....))))......... ( -5.49 =  -4.30 +  -1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:17:52 2011