Locus 316

Sequence ID dm3.chr2L
Location 2,262,880 – 2,262,978
Length 98
Max. P 0.998961
window429 window430

overview

Window 9

Location 2,262,880 – 2,262,978
Length 98
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 83.77
Shannon entropy 0.27241
G+C content 0.51130
Mean single sequence MFE -33.38
Consensus MFE -27.03
Energy contribution -28.15
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -3.25
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.09
SVM RNA-class probability 0.997386
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2262880 98 + 23011544
-----ACCCGCAGCGCAGACACACACUCACACAC----UUAAAUAAUUUAAUAUUCCGAGUGUUUCGACAUCGAAAUUUGCACUUCCAUGG-----GCGGCGCUGCGGGCGA
-----.((((((((((......((((((......----((((.....))))......))))))((((....))))...(((.((.....))-----)))))))))))))... ( -33.50, z-score =  -4.00, R)
>droYak2.chr2L 2244157 112 + 22324452
UCCCCCUCCCCUACACACACACACAAGCACAUACACGCUUAAAUAAUUUAAUAUUCAGAGUGUUUCGACAUCGAAAUUUGCACUUCGAUGGCCUGCGCUGCGUUGCGGGCGU
....................((((((((........)))).((((......))))....)))).....(((((((........)))))))(((((((......))))))).. ( -24.10, z-score =  -0.85, R)
>droEre2.scaffold_4929 2300109 103 + 26641161
----CCCCCGCAGCACACACACACACACACACUCACGCUUAAAUAAUUUAAUAUUCAGAGUGUUUCGACAUCGAAAUUUGCACUUCGAUGG-----CCUGCGCUGCGGGCGU
----..((((((((.((..(........((((((.......................)))))).....(((((((........))))))))-----..)).))))))))... ( -31.70, z-score =  -4.09, R)
>droSec1.super_5 437887 101 + 5866729
CCGCACCCCGCAGCGCAGACACACACUCACGC------UUAAAUAAUUUAAUAUUCCGAGUGUUUCGACAUCGAAAUUUGCACUUCGAUGG-----GCGGCGCUGCGGGCGU
....((((((((((((......((((((....------...................))))))..((.(((((((........))))))).-----.)))))))))))).)) ( -39.00, z-score =  -3.84, R)
>droSim1.chr2L 2221657 101 + 22036055
CCGCCCCCCGCAGCGCAGACACACACUCACGC------UUAAAUAAUUUAAUAUUCCGAGUGUUUCGACAUCGAAAUUUGCACUUCGAUGG-----GCGGCGCUGCGGGCGU
.(((((...(((((((......((((((....------...................))))))..((.(((((((........))))))).-----.)))))))))))))). ( -38.60, z-score =  -3.49, R)
>consensus
_C_CCCCCCGCAGCGCAGACACACACUCACAC_C____UUAAAUAAUUUAAUAUUCCGAGUGUUUCGACAUCGAAAUUUGCACUUCGAUGG_____GCGGCGCUGCGGGCGU
......((((((((((......((((((.............................)))))).....(((((((........))))))).........))))))))))... (-27.03 = -28.15 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 2,262,880 – 2,262,978
Length 98
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 83.77
Shannon entropy 0.27241
G+C content 0.51130
Mean single sequence MFE -43.28
Consensus MFE -31.88
Energy contribution -32.72
Covariance contribution 0.84
Combinations/Pair 1.07
Mean z-score -3.95
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.57
SVM RNA-class probability 0.998961
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 2262880 98 - 23011544
UCGCCCGCAGCGCCGC-----CCAUGGAAGUGCAAAUUUCGAUGUCGAAACACUCGGAAUAUUAAAUUAUUUAA----GUGUGUGAGUGUGUGUCUGCGCUGCGGGU-----
..(((((((((((...-----.(((.(((((....))))).)))..((.(((((((.(...((((.....))))----...).)))))))...)).)))))))))))----- ( -41.90, z-score =  -4.70, R)
>droYak2.chr2L 2244157 112 - 22324452
ACGCCCGCAACGCAGCGCAGGCCAUCGAAGUGCAAAUUUCGAUGUCGAAACACUCUGAAUAUUAAAUUAUUUAAGCGUGUAUGUGCUUGUGUGUGUGUGUAGGGGAGGGGGA
...(((...((((((((((((((((((((((....))))))))).....((((.(((((((......))))).)).))))....)))))))).)))))...)))........ ( -40.00, z-score =  -2.46, R)
>droEre2.scaffold_4929 2300109 103 - 26641161
ACGCCCGCAGCGCAGG-----CCAUCGAAGUGCAAAUUUCGAUGUCGAAACACUCUGAAUAUUAAAUUAUUUAAGCGUGAGUGUGUGUGUGUGUGUGUGCUGCGGGGG----
.(.(((((((((((.(-----((((((((((....))))))))).((..((((((((((((......)))))).....))))))...))...)).))))))))))).)---- ( -45.70, z-score =  -5.10, R)
>droSec1.super_5 437887 101 - 5866729
ACGCCCGCAGCGCCGC-----CCAUCGAAGUGCAAAUUUCGAUGUCGAAACACUCGGAAUAUUAAAUUAUUUAA------GCGUGAGUGUGUGUCUGCGCUGCGGGGUGCGG
((.((((((((((...-----.(((((((((....)))))))))..((.((((((((((((......)))))..------...)))))))...)).)))))))))))).... ( -43.60, z-score =  -3.69, R)
>droSim1.chr2L 2221657 101 - 22036055
ACGCCCGCAGCGCCGC-----CCAUCGAAGUGCAAAUUUCGAUGUCGAAACACUCGGAAUAUUAAAUUAUUUAA------GCGUGAGUGUGUGUCUGCGCUGCGGGGGGCGG
.(.((((((((((...-----.(((((((((....)))))))))..((.((((((((((((......)))))..------...)))))))...)).)))))))))).).... ( -45.20, z-score =  -3.81, R)
>consensus
ACGCCCGCAGCGCCGC_____CCAUCGAAGUGCAAAUUUCGAUGUCGAAACACUCGGAAUAUUAAAUUAUUUAA____G_GUGUGAGUGUGUGUCUGCGCUGCGGGGGG_G_
...((((((((((.........(((((((((....))))))))).....((((((.(((((......)))))............))))))......))))))))))...... (-31.88 = -32.72 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:10:38 2011