Locus 3111

Sequence ID	dm3.chr2R
Location	2,566,853 – 2,566,905
Length	52
Max. P	0.994442

overview

Window 2

Location	2,566,853 – 2,566,905
Length	52
Sequences	6
Columns	61
Reading direction	forward
Mean pairwise identity	72.48
Shannon entropy	0.48474
G+C content	0.56058
Mean single sequence MFE	-15.72
Consensus MFE	-9.77
Energy contribution	-11.22
Covariance contribution	1.45
Combinations/Pair	1.19
Mean z-score	-1.24
Structure conservation index	0.62
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.74
SVM RNA-class probability	0.804979
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2566853 52 + 21146708
----CCUACUCUCCAACCUGCCAACCUCUGAGGUGGACGGAGAUCGAAGAUCGGAG-----
----......((((...((((((.((.....))))).))).((((...))))))))----- ( -15.10, z-score =  -0.69, R)
>droSim1.chr2R 1388922 52 + 19596830
----CCUACUCUCCAACCUGCCAACCUCUGAGGUGGCCGGAGAUCGAAGAUCGGAG-----
----......((((..((.((((.((.....)))))).)).((((...))))))))----- ( -18.50, z-score =  -1.91, R)
>droSec1.super_1 231143 52 + 14215200
----CCUACUCUCCAACCUGCCAACCUCUGAGGUGGCCGGAGAUCGAAGAUCGGAG-----
----......((((..((.((((.((.....)))))).)).((((...))))))))----- ( -18.50, z-score =  -1.91, R)
>droYak2.chr2L 15309721 52 + 22324452
----CCUACUCUCCAACCUGCCAGCCUCAGAGGUGGCCGGAGAUCGAAGAUCGGAG-----
----......((((..((.((((.((.....)))))).)).((((...))))))))----- ( -18.50, z-score =  -1.28, R)
>droEre2.scaffold_4929 6661945 52 - 26641161
----CCUACUCUCCAACCUGCCAGCCUCGGAGGUGGCCGGAGAUCGAAGAUCGGAG-----
----......((((..((.((((.((.....)))))).)).((((...))))))))----- ( -18.50, z-score =  -0.82, R)
>droGri2.scaffold_15245 12249785 61 + 18325388
UCUUUUAGCUCAAAAACUUGAUGCCCCAAAUUGUGCCCACGCCAAAGAAAUAAAAAAAAAA
..(((((((((((....)))).))......(((.((....))))).....)))))...... (  -5.20, z-score =  -0.84, R)
>consensus
____CCUACUCUCCAACCUGCCAACCUCUGAGGUGGCCGGAGAUCGAAGAUCGGAG_____
..........((((..((.((((.((.....)))))).)).((((...))))))))..... ( -9.77 = -11.22 +   1.45)

alignment

secondary structure

dotplot

Window 3

Location	2,566,853 – 2,566,905
Length	52
Sequences	6
Columns	61
Reading direction	reverse
Mean pairwise identity	72.48
Shannon entropy	0.48474
G+C content	0.56058
Mean single sequence MFE	-21.15
Consensus MFE	-18.63
Energy contribution	-18.97
Covariance contribution	0.34
Combinations/Pair	1.39
Mean z-score	-2.00
Structure conservation index	0.88
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.70
SVM RNA-class probability	0.994442
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2566853 52 - 21146708
-----CUCCGAUCUUCGAUCUCCGUCCACCUCAGAGGUUGGCAGGUUGGAGAGUAGG----
-----(((((((((((((((((.(.......).)))))))).)))))))))......---- ( -20.90, z-score =  -2.01, R)
>droSim1.chr2R 1388922 52 - 19596830
-----CUCCGAUCUUCGAUCUCCGGCCACCUCAGAGGUUGGCAGGUUGGAGAGUAGG----
-----..((..((((((((((((((((........)))))).))))))))))...))---- ( -23.10, z-score =  -2.46, R)
>droSec1.super_1 231143 52 - 14215200
-----CUCCGAUCUUCGAUCUCCGGCCACCUCAGAGGUUGGCAGGUUGGAGAGUAGG----
-----..((..((((((((((((((((........)))))).))))))))))...))---- ( -23.10, z-score =  -2.46, R)
>droYak2.chr2L 15309721 52 - 22324452
-----CUCCGAUCUUCGAUCUCCGGCCACCUCUGAGGCUGGCAGGUUGGAGAGUAGG----
-----..((..((((((((((((((((........)))))).))))))))))...))---- ( -25.60, z-score =  -2.71, R)
>droEre2.scaffold_4929 6661945 52 + 26641161
-----CUCCGAUCUUCGAUCUCCGGCCACCUCCGAGGCUGGCAGGUUGGAGAGUAGG----
-----..((..((((((((((((((((........)))))).))))))))))...))---- ( -25.60, z-score =  -2.64, R)
>droGri2.scaffold_15245 12249785 61 - 18325388
UUUUUUUUUUAUUUCUUUGGCGUGGGCACAAUUUGGGGCAUCAAGUUUUUGAGCUAAAAGA
....(((((((.(((...(((.(((((.(.....)..)).))).)))...))).))))))) (  -8.60, z-score =   0.29, R)
>consensus
_____CUCCGAUCUUCGAUCUCCGGCCACCUCAGAGGUUGGCAGGUUGGAGAGUAGG____
.......((..((((((((((((((((........)))))).))))))))))...)).... (-18.63 = -18.97 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:54 2011