Locus 6976

Sequence ID	dm3.chr3L
Location	11,242,062 – 11,242,162
Length	100
Max. P	0.990345

overview

Window 2

Location	11,242,062 – 11,242,162
Length	100
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	63.57
Shannon entropy	0.55743
G+C content	0.37051
Mean single sequence MFE	-19.82
Consensus MFE	-6.96
Energy contribution	-10.03
Covariance contribution	3.06
Combinations/Pair	1.05
Mean z-score	-2.36
Structure conservation index	0.35
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.24
SVM RNA-class probability	0.914909
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11242062 100 + 24543557
UUUCCAUUUCCAUUUGGCUGUCUGUCAUAAAUUACUUGCCAAAUUCCUUGGCAUUAACUUUGGCCGACAGCCCGGAAACAUAACUGUGUACAUACUUACA
.......((((....(((((((.((((....(((..((((((.....)))))).)))...)))).))))))).))))((((....))))........... ( -28.80, z-score =  -4.51, R)
>droSim1.chr3L 10636345 84 + 22553184
UUUCCAUUUCCAUUUGGCUGU----CAUAAAUUACUUGCCAAAUUCCUUGGCAUUAACUUUGGCCGACAGCCCGGAAACAUAUCUGUG------------
......(((((....((((((----(.((((.....((((((.....)))))).....))))...))))))).)))))..........------------ ( -24.00, z-score =  -3.77, R)
>droEre2.scaffold_4784 11252928 80 + 25762168
UUCCCAUUUCCAUUUGGCUGU----CAUAAAUUACUUGGCAAAUUCCUUGGCAUUAACUUUGGCCGACAGCCCGGAAACAUAUA----------------
......(((((....((((((----(...........((......))..(((..........)))))))))).)))))......---------------- ( -20.30, z-score =  -2.15, R)
>droWil1.scaffold_181017 627559 87 - 939937
UUGACAUUUCUUUAUGAGUUC-----UUAAACCACUUAACAAAAAUUUAAAGACCUAUAUUUAUAUACAAACUGAAAUUUGCUAUGUGUGUG--------
...((((.((((((....((.-----((((.....)))).)).....)))))).........(((((((((......)))).))))))))).-------- (  -6.20, z-score =   1.02, R)
>consensus
UUUCCAUUUCCAUUUGGCUGU____CAUAAAUUACUUGCCAAAUUCCUUGGCAUUAACUUUGGCCGACAGCCCGGAAACAUAUAUGUG____________
......(((((....((((((......((((.....((((((.....)))))).....))))....)))))).)))))...................... ( -6.96 = -10.03 +   3.06)

alignment

secondary structure

dotplot

Window 3

Location	11,242,062 – 11,242,162
Length	100
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	63.57
Shannon entropy	0.55743
G+C content	0.37051
Mean single sequence MFE	-23.17
Consensus MFE	-12.30
Energy contribution	-13.54
Covariance contribution	1.25
Combinations/Pair	1.32
Mean z-score	-2.10
Structure conservation index	0.53
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.41
SVM RNA-class probability	0.990345
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11242062 100 - 24543557
UGUAAGUAUGUACACAGUUAUGUUUCCGGGCUGUCGGCCAAAGUUAAUGCCAAGGAAUUUGGCAAGUAAUUUAUGACAGACAGCCAAAUGGAAAUGGAAA
((((......)))).......((((((.(((((((.(.((((((((.(((((((...)))))))..)))))).)).).)))))))....))))))..... ( -29.70, z-score =  -2.70, R)
>droSim1.chr3L 10636345 84 - 22553184
------------CACAGAUAUGUUUCCGGGCUGUCGGCCAAAGUUAAUGCCAAGGAAUUUGGCAAGUAAUUUAUG----ACAGCCAAAUGGAAAUGGAAA
------------.........((((((.((((((((....((((((.(((((((...)))))))..)))))).))----))))))....))))))..... ( -28.60, z-score =  -3.68, R)
>droEre2.scaffold_4784 11252928 80 - 25762168
----------------UAUAUGUUUCCGGGCUGUCGGCCAAAGUUAAUGCCAAGGAAUUUGCCAAGUAAUUUAUG----ACAGCCAAAUGGAAAUGGGAA
----------------.....((((((.((((((((((..........)))..((......))...........)----))))))....))))))..... ( -23.80, z-score =  -1.96, R)
>droWil1.scaffold_181017 627559 87 + 939937
--------CACACACAUAGCAAAUUUCAGUUUGUAUAUAAAUAUAGGUCUUUAAAUUUUUGUUAAGUGGUUUAA-----GAACUCAUAAAGAAAUGUCAA
--------.....((((.((((((....)))))).......(((..((..((((((..((....))..))))))-----..))..))).....))))... ( -10.60, z-score =  -0.04, R)
>consensus
____________CACAGAUAUGUUUCCGGGCUGUCGGCCAAAGUUAAUGCCAAGGAAUUUGGCAAGUAAUUUAUG____ACAGCCAAAUGGAAAUGGAAA
.....................((((((.((((((......((((((.(((((((...)))))))..)))))).......))))))....))))))..... (-12.30 = -13.54 +   1.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:18:05 2011