Locus 3767

Sequence ID	dm3.chr2R
Location	7,724,586 – 7,724,729
Length	143
Max. P	0.812913

overview

Window 1

Location	7,724,586 – 7,724,692
Length	106
Sequences	4
Columns	106
Reading direction	reverse
Mean pairwise identity	84.30
Shannon entropy	0.23282
G+C content	0.51469
Mean single sequence MFE	-34.43
Consensus MFE	-27.19
Energy contribution	-27.50
Covariance contribution	0.31
Combinations/Pair	1.07
Mean z-score	-1.67
Structure conservation index	0.79
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.48
SVM RNA-class probability	0.710615
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7724586 106 - 21146708
UUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUAGCGGUCGCUGCAGCUGAGGAGACUCGGAUUCAGAUUCAGAUUCGGAUUCGG
....(((((....)))))(((((((((.(((..(((((((((.....((((((.(((....)))))))))(((....)))...))))))))).))).))))))))) ( -43.70, z-score =  -3.58, R)
>droSim1.chr2R 6257682 88 - 19596830
UUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCGCUGCAGCUGAGGAGACUCGGAUUCGG------------------
....(((((....)))))((((((((.....................((((((.(((....)))))))))(((....)))))))))))------------------ ( -29.20, z-score =  -0.76, R)
>droSec1.super_1 5276430 88 - 14215200
UUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCGCUGCAGCUGAGGAGACUCGGAUUCGG------------------
....(((((....)))))((((((((.....................((((((.(((....)))))))))(((....)))))))))))------------------ ( -29.20, z-score =  -0.76, R)
>droEre2.scaffold_4845 4518924 106 + 22589142
UUCCAUGCAACUUUGUUUCUGAAUCCGGGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCACUGCAGCUGAAUAGACUCGGACUCAGAUUCAGAUUCGGAUUCGG
..................(((((((((((((..((((((((.....(((((((((.(((...)))))))......)))))....)))))))).))))))))))))) ( -35.60, z-score =  -1.59, R)
>consensus
UUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCGCUGCAGCUGAGGAGACUCGGAUUCAG__________________
....(((((....)))))(((((((((.(((.....(((....))).((((((.(((....))))))))).....))).))))))))).................. (-27.19 = -27.50 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	7,724,626 – 7,724,729
Length	103
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	87.68
Shannon entropy	0.19451
G+C content	0.53695
Mean single sequence MFE	-33.65
Consensus MFE	-25.50
Energy contribution	-26.12
Covariance contribution	0.62
Combinations/Pair	1.09
Mean z-score	-1.72
Structure conservation index	0.76
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.03
SVM RNA-class probability	0.511536
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7724626 103 + 21146708
GCAGCGACCGCUAGCAACUCCUCUUUCAAAUUCCGGACGCGGAUUCAGAUACAAAGUUGCAUGGAAUUUAAUGUAGCACUUUUGAGCGGGGGCGGUAGCGGGG--
.......((((((.(...(((((.((((((.((((....))))............(((((((........)))))))...)))))).))))).).))))))..-- ( -33.50, z-score =  -1.64, R)
>droSim1.chr2R 6257704 105 + 19596830
GCAGCGACCGCCAGCAACUCCUCUUUCAAAUUCCGGACGCGGAUUCAGAUACAAAGUUGCAUGGAAUUUAAUGCAGCACUUUUCAGCGGGGCGGGGGCGGGGGCG
...((..(((((..(..((((.((.((....((((....))))....))......(((((((........))))))).......)).))))..).)))))..)). ( -36.60, z-score =  -1.65, R)
>droYak2.chr2R 11912108 96 - 21139217
GCAGCGACCGCCAGCAACUUCUCUUUCAAAUUCCGGGCCCGGAUUCAGAAACAAAGUUGCAUGGAAUUUAAUGCAGCACUUUUCUGCGGGGGCGGG---------
.......(((((.(((((((...((((....((((....))))....))))..)))))))...........(((((.......)))))..))))).--------- ( -32.60, z-score =  -1.74, R)
>droEre2.scaffold_4845 4518964 96 - 22589142
GCAGUGACCGCCAGCAACUCCUCUUUCAAAUUCCGGACCCGGAUUCAGAAACAAAGUUGCAUGGAAUUUAAUGCAGCACUUUUCUGCGGGGGCGGG---------
.......(((((.(((.......((((....((((....))))....))))....(((((((........))))))).......)))...))))).--------- ( -31.90, z-score =  -1.84, R)
>consensus
GCAGCGACCGCCAGCAACUCCUCUUUCAAAUUCCGGACCCGGAUUCAGAAACAAAGUUGCAUGGAAUUUAAUGCAGCACUUUUCAGCGGGGGCGGG_________
.......(((((.((........((((....((((....))))....))))....(((((((........)))))))........))...))))).......... (-25.50 = -26.12 +   0.62)

alignment

secondary structure

dotplot

Window 3

Location	7,724,626 – 7,724,729
Length	103
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	87.68
Shannon entropy	0.19451
G+C content	0.53695
Mean single sequence MFE	-32.88
Consensus MFE	-23.86
Energy contribution	-24.92
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.73
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.77
SVM RNA-class probability	0.812913
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 7724626 103 - 21146708
--CCCCGCUACCGCCCCCGCUCAAAAGUGCUACAUUAAAUUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUAGCGGUCGCUGC
--....((.(((((...((((....))))................((((((((...((.((.((((....)))).)).))....))))))))..))))).))... ( -27.60, z-score =  -1.41, R)
>droSim1.chr2R 6257704 105 - 19596830
CGCCCCCGCCCCCGCCCCGCUGAAAAGUGCUGCAUUAAAUUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCGCUGC
.((..(((((...((..((((....))))..))............((((((((...((.((.((((....)))).)).))....)))))))).)))))..))... ( -35.50, z-score =  -2.53, R)
>droYak2.chr2R 11912108 96 + 21139217
---------CCCGCCCCCGCAGAAAAGUGCUGCAUUAAAUUCCAUGCAACUUUGUUUCUGAAUCCGGGCCCGGAAUUUGAAAGAGAAGUUGCUGGCGGUCGCUGC
---------.(((((...((((.......))))............((((((((.((((.((.((((....)))).)).))))..)))))))).)))))....... ( -34.40, z-score =  -2.59, R)
>droEre2.scaffold_4845 4518964 96 + 22589142
---------CCCGCCCCCGCAGAAAAGUGCUGCAUUAAAUUCCAUGCAACUUUGUUUCUGAAUCCGGGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCACUGC
---------.(((((...((((.......))))............((((((((.((((.((.((((....)))).)).))))..)))))))).)))))....... ( -34.00, z-score =  -2.42, R)
>consensus
_________CCCGCCCCCGCAGAAAAGUGCUGCAUUAAAUUCCAUGCAACUUUGUAUCUGAAUCCGCGUCCGGAAUUUGAAAGAGGAGUUGCUGGCGGUCGCUGC
..........(((((...((........))...............((((((((.((((.((.((((....)))).)).))))..)))))))).)))))....... (-23.86 = -24.92 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:16:20 2011