Locus 6058

Sequence ID	dm3.chr3L
Location	3,380,350 – 3,380,442
Length	92
Max. P	0.998029

overview

Window 0

Location	3,380,350 – 3,380,442
Length	92
Sequences	8
Columns	98
Reading direction	forward
Mean pairwise identity	73.85
Shannon entropy	0.51118
G+C content	0.53972
Mean single sequence MFE	-38.86
Consensus MFE	-18.57
Energy contribution	-18.76
Covariance contribution	0.19
Combinations/Pair	1.42
Mean z-score	-3.08
Structure conservation index	0.48
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.24
SVM RNA-class probability	0.998029
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3380350 92 + 24543557
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUCGCUGCGUUGGCGUC------GGCAGCGCCGUCGACGCCCAAAUCG
..((((((((((((((.......)))))))))).((((((((((((..(((.((((.....))))..------))).))))))))))))..))))... ( -42.20, z-score =  -3.55, R)
>droSim1.chr3L 2915274 98 + 22553184
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUCGCUGCGUUGGCGUCGGCAGAGGCAGCGCCGUCGACGCCCAAAUCG
..((((((((((((((.......)))))))))).((((((((((((..(((((((((((....)).)))).))))).))))))))))))..))))... ( -49.50, z-score =  -4.75, R)
>droSec1.super_2 3372861 98 + 7591821
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUCGCUGCGUUGGCGUCGGCAGAGGCAGCGCCGUCGACGCCCAAAUCG
..((((((((((((((.......)))))))))).((((((((((((..(((((((((((....)).)))).))))).))))))))))))..))))... ( -49.50, z-score =  -4.75, R)
>droYak2.chr3L 3926962 92 + 24197627
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUUGCUGCGUUGGCGUC------GGCAGCGCCGUCGACGCCCAAAUCG
..((((((((((((((.......)))))))))).((((((((((((..(((.((((.....))))..------))).))))))))))))..))))... ( -40.40, z-score =  -3.15, R)
>droEre2.scaffold_4784 6070088 92 + 25762168
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUUGCUGCGUUGGCGUC------GGCAGCGCCGUCGCCGCCCAAAUCG
..((((((((((((((.......)))))))))).....(((((((((.((.((((((((....)).)------))))).)))).)))))))))))... ( -39.90, z-score =  -2.83, R)
>droAna3.scaffold_13337 13230375 89 - 23293914
------UUUUUG---UGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUCGCUGCGUUGGCGUCGACGGCGACAGCGGCGUCGAAGCCCCAAUCG
------......---(((((((....)))))))..(((((.(((...((...((((((((((.((....)).)))).)))))).))..)))))))).. ( -38.00, z-score =  -1.81, R)
>droGri2.scaffold_15110 5784364 76 + 24565398
------UUUUUG---UGAAUGAAAUUGUAUUCAACGUUGGCGUCAACGCGUCGCUGCUGUCGACGCU---------GUCUCCGUUGGCGUCCAA----
------......---((((((......))))))...((((((((((((((((((....).)))))).---------(....)))))))).))))---- ( -24.90, z-score =  -2.04, R)
>droVir3.scaffold_13049 18170450 84 - 25233164
------UAUUUG---UGAAUGAAAUUUCAUUGAACGUUAGCU-CUUGCCGCUGCCGCCGUUGACAGCG----AAACGUCGCCGUCAACGUCGCAGUCG
------.....(---(.(((((....)))))..))....((.-...)).(((((.(.(((((((.(((----(....)))).))))))).)))))).. ( -26.50, z-score =  -1.74, R)
>consensus
UUUUUGUGAAUGAAAUGAAUGAAAUUUCAUUCAACGUUGGCGGCGCGCGUCUCGCUGCGUUGGCGUC______GGCAGCGCCGUCGACGCCCAAAUCG
...............(((((((....))))))).((((((((.((((((...))).(((....)))...........))).))))))))......... (-18.57 = -18.76 +   0.19)

alignment

secondary structure

dotplot

Window 1

Location	3,380,350 – 3,380,442
Length	92
Sequences	8
Columns	98
Reading direction	reverse
Mean pairwise identity	73.85
Shannon entropy	0.51118
G+C content	0.53972
Mean single sequence MFE	-32.31
Consensus MFE	-13.85
Energy contribution	-14.27
Covariance contribution	0.42
Combinations/Pair	1.43
Mean z-score	-2.12
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.19
SVM RNA-class probability	0.906873
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 3380350 92 - 24543557
CGAUUUGGGCGUCGACGGCGCUGCC------GACGCCAACGCAGCGAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
...((((((((.((.((.((((((.------.........))))))...))))))))........((((((((((.......)))))))))))))).. ( -32.10, z-score =  -1.47, R)
>droSim1.chr3L 2915274 98 - 22553184
CGAUUUGGGCGUCGACGGCGCUGCCUCUGCCGACGCCAACGCAGCGAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
...(((((((((.(.((((((.((.(((((.(.((....))).)).))).)))))))).).)))))(((((((((.......))))))))).)))).. ( -35.20, z-score =  -1.88, R)
>droSec1.super_2 3372861 98 - 7591821
CGAUUUGGGCGUCGACGGCGCUGCCUCUGCCGACGCCAACGCAGCGAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
...(((((((((.(.((((((.((.(((((.(.((....))).)).))).)))))))).).)))))(((((((((.......))))))))).)))).. ( -35.20, z-score =  -1.88, R)
>droYak2.chr3L 3926962 92 - 24197627
CGAUUUGGGCGUCGACGGCGCUGCC------GACGCCAACGCAGCAAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
...(((((((((.(.((((((....------...((....)).((.....)))))))).).)))))(((((((((.......))))))))).)))).. ( -29.80, z-score =  -1.11, R)
>droEre2.scaffold_4784 6070088 92 - 25762168
CGAUUUGGGCGGCGACGGCGCUGCC------GACGCCAACGCAGCAAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
...(((((((((((..(((((....------).))))..(((........)))))))))).....((((((((((.......)))))))))))))).. ( -35.70, z-score =  -2.71, R)
>droAna3.scaffold_13337 13230375 89 + 23293914
CGAUUGGGGCUUCGACGCCGCUGUCGCCGUCGACGCCAACGCAGCGAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCA---CAAAAA------
((.(((((((.((((((.((....)).)))))).)))..(((.(((...))))))...)))))).(((((((....)))))))---......------ ( -31.90, z-score =  -1.01, R)
>droGri2.scaffold_15110 5784364 76 - 24565398
----UUGGACGCCAACGGAGAC---------AGCGUCGACAGCAGCGACGCGUUGACGCCAACGUUGAAUACAAUUUCAUUCA---CAAAAA------
----((((.((.(((((....)---------.((((((.(....))))))))))).)))))).((.((((........)))))---).....------ ( -24.10, z-score =  -2.85, R)
>droVir3.scaffold_13049 18170450 84 + 25233164
CGACUGCGACGUUGACGGCGACGUUU----CGCUGUCAACGGCGGCAGCGGCAAG-AGCUAACGUUCAAUGAAAUUUCAUUCA---CAAAUA------
((.((((..((((((((((((....)----)))))))))))...))))))....(-(((....))))(((((....)))))..---......------ ( -34.50, z-score =  -4.08, R)
>consensus
CGAUUUGGGCGUCGACGGCGCUGCC______GACGCCAACGCAGCGAGACGCGCGCCGCCAACGUUGAAUGAAAUUUCAUUCAUUUCAUUCACAAAAA
.......((((((...(((...)))......))))))..(((.((.....)))))..........(((((((....)))))))............... (-13.85 = -14.27 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:00:33 2011