Locus 7203

Sequence ID	dm3.chr3L
Location	12,962,673 – 12,962,732
Length	59
Max. P	0.878814

overview

Window 1

Location	12,962,673 – 12,962,732
Length	59
Sequences	6
Columns	61
Reading direction	forward
Mean pairwise identity	97.21
Shannon entropy	0.05328
G+C content	0.29203
Mean single sequence MFE	-8.88
Consensus MFE	-9.38
Energy contribution	-9.10
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-0.86
Structure conservation index	1.06
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.04
SVM RNA-class probability	0.878814
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12962673 59 + 24543557
-AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG-AAUUUAUUUGUUUUGAUA
-..........(((((((((((((((....(((.....))).-..))))))))))))))). (  -8.80, z-score =  -0.90, R)
>droSim1.chr3L 12344957 59 + 22553184
-AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG-AAUUUAUUUGUUUUGAUA
-..........(((((((((((((((....(((.....))).-..))))))))))))))). (  -8.80, z-score =  -0.90, R)
>droSec1.super_0 5134329 59 + 21120651
-AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG-AAUUUAUUUGUUUUGAUA
-..........(((((((((((((((....(((.....))).-..))))))))))))))). (  -8.80, z-score =  -0.90, R)
>droYak2.chr3L 13040282 59 + 24197627
-AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG-AAUUUAUUUGUUUUGAUA
-..........(((((((((((((((....(((.....))).-..))))))))))))))). (  -8.80, z-score =  -0.90, R)
>droEre2.scaffold_4784 12969524 59 + 25762168
-AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG-AAUUUAUUUGUUUUGAUA
-..........(((((((((((((((....(((.....))).-..))))))))))))))). (  -8.80, z-score =  -0.90, R)
>droAna3.scaffold_13337 6497484 61 - 23293914
AAAGCUGCUAAAUUAAGAUAAAUGAACACAUUUAGCCGGGGGGAAUUUAUUUGUUUUGAUA
...........(((((((((((((((.........((....))..))))))))))))))). (  -9.30, z-score =  -0.64, R)
>consensus
_AAACUGCUAAAUUAAGAUAAAUGAGCACAUUUAGCCGGAGG_AAUUUAUUUGUUUUGAUA
...........(((((((((((((((....(((.....)))....))))))))))))))). ( -9.38 =  -9.10 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	12,962,673 – 12,962,732
Length	59
Sequences	6
Columns	61
Reading direction	reverse
Mean pairwise identity	97.21
Shannon entropy	0.05328
G+C content	0.29203
Mean single sequence MFE	-5.79
Consensus MFE	-5.79
Energy contribution	-5.79
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-0.86
Structure conservation index	1.00
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.26
SVM RNA-class probability	0.619449
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 12962673 59 - 24543557
UAUCAAAACAAAUAAAUU-CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU-
..................-......(((((((................))))))).....- (  -5.79, z-score =  -0.85, R)
>droSim1.chr3L 12344957 59 - 22553184
UAUCAAAACAAAUAAAUU-CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU-
..................-......(((((((................))))))).....- (  -5.79, z-score =  -0.85, R)
>droSec1.super_0 5134329 59 - 21120651
UAUCAAAACAAAUAAAUU-CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU-
..................-......(((((((................))))))).....- (  -5.79, z-score =  -0.85, R)
>droYak2.chr3L 13040282 59 - 24197627
UAUCAAAACAAAUAAAUU-CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU-
..................-......(((((((................))))))).....- (  -5.79, z-score =  -0.85, R)
>droEre2.scaffold_4784 12969524 59 - 25762168
UAUCAAAACAAAUAAAUU-CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU-
..................-......(((((((................))))))).....- (  -5.79, z-score =  -0.85, R)
>droAna3.scaffold_13337 6497484 61 + 23293914
UAUCAAAACAAAUAAAUUCCCCCCGGCUAAAUGUGUUCAUUUAUCUUAAUUUAGCAGCUUU
.........................(((((((................)))))))...... (  -5.79, z-score =  -0.87, R)
>consensus
UAUCAAAACAAAUAAAUU_CCUCCGGCUAAAUGUGCUCAUUUAUCUUAAUUUAGCAGUUU_
.........................(((((((................)))))))...... ( -5.79 =  -5.79 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:22:23 2011