Locus 6589

Sequence ID dm3.chr3L
Location 8,017,395 – 8,017,540
Length 145
Max. P 0.999714
window9070 window9071

overview

Window 0

Location 8,017,395 – 8,017,540
Length 145
Sequences 4
Columns 165
Reading direction forward
Mean pairwise identity 76.07
Shannon entropy 0.37346
G+C content 0.55967
Mean single sequence MFE -62.75
Consensus MFE -40.04
Energy contribution -40.98
Covariance contribution 0.94
Combinations/Pair 1.06
Mean z-score -4.39
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.24
SVM RNA-class probability 0.999714
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8017395 145 + 24543557
--GCGAGGGAGAGGGCUAUAAAAAGGG--------GGAAAUGAGAAGGGGAAUG----------UGGGAGUGUGAGGCGUGCGAAGUGUGCACAAAAUUAAAAUUAGGCACGAACGCUGUCUCAUUCCCGCGCGUGCACCCCUUCUCCCUCGCGCACUAGCGACC
--((((((((((...........((((--------(...(((.(...(((((((----------.((.(((((..((((((((.....)))))..(((....)))..)).)..))))).)).))))))).).)))...)))))))))))))))((....)).... ( -60.10, z-score =  -3.34, R)
>droSec1.super_0 304833 145 + 21120651
--GCGAGGGAGAGGGCCAUAAAAAGGG--------GGAAAUGAGCAGGGGAAUGG---------UGGGAGUGUGAGGCGUGCGAAGUGUGCAUAAAAUUAAAAUUAGGCACGAACGCUGUCUCAUUCCCGCGCGUGCACCCCU-CUCCCUUGCGCAUUAGCGACC
--(((((((((((((((((........--------....))).)).((...((((---------(((((..((((((((.(((...(((((.(((........))).)))))..))))))))))))))))).)))...)))))-)))))))))((....)).... ( -64.40, z-score =  -4.29, R)
>droYak2.chr3L 8603017 164 + 24197627
GCGAGAGGGAGGGGGCUAUAAAAGGCGAAAGGCAAGGGAAAGAGAAGGGGAAUGGGUAUGGGAAUGGGAGUGUGAGGCGUGCGAAGUGUGCAUAAAAUUAAAAUUAGGCACGAACGCUGUCUCUUUCCCGCUCGUGCACCCCG-CUCCCUCACGCAUUAGCGACC
(((.(((((((((((........(.(....).)......................(((((((...(((((...((((((.(((...(((((.(((........))).)))))..))))))))).))))).))))))).)))).-))))))).))).......... ( -66.60, z-score =  -3.72, R)
>droEre2.scaffold_4784 22414454 117 - 25762168
---------------------------------------GCGAGGGAGAGGGCGAU--------UGGGAGUGUGAGGCGUGCGAAGCGUGCAUAAAAUUAAAAUUAGGCACGAACGCUGUCUCAUUCCCGCUCGUGCACCCCU-CUCCCUCACGCAUUAGCGACC
---------------------------------------..((((((((((((((.--------(((((..((((((((.(((...(((((.(((........))).)))))..)))))))))))))))).))).....))))-))))))).(((....)))... ( -59.90, z-score =  -6.21, R)
>consensus
__GCGAGGGAGAGGGCUAUAAAAAGGG________GGAAAUGAGAAGGGGAAUGG_________UGGGAGUGUGAGGCGUGCGAAGUGUGCAUAAAAUUAAAAUUAGGCACGAACGCUGUCUCAUUCCCGCGCGUGCACCCCU_CUCCCUCACGCAUUAGCGACC
.........................................(((.(((((...............((((..((((((((.(((...(((((.(((........))).)))))..)))))))))))))))((....)).))))).))).....(((....)))... (-40.04 = -40.98 +   0.94)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 1

Location 8,017,395 – 8,017,540
Length 145
Sequences 4
Columns 165
Reading direction reverse
Mean pairwise identity 76.07
Shannon entropy 0.37346
G+C content 0.55967
Mean single sequence MFE -51.80
Consensus MFE -32.99
Energy contribution -33.17
Covariance contribution 0.19
Combinations/Pair 1.09
Mean z-score -3.62
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.62
SVM RNA-class probability 0.999049
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 8017395 145 - 24543557
GGUCGCUAGUGCGCGAGGGAGAAGGGGUGCACGCGCGGGAAUGAGACAGCGUUCGUGCCUAAUUUUAAUUUUGUGCACACUUCGCACGCCUCACACUCCCA----------CAUUCCCCUUCUCAUUUCC--------CCCUUUUUAUAGCCCUCUCCCUCGC--
....((....))((((((((((.((((((....)))((((((((((..(((...((((.(((........))).))))....)))..(.....).......----------.........))))))))))--------............)))))))))))))-- ( -51.10, z-score =  -3.22, R)
>droSec1.super_0 304833 145 - 21120651
GGUCGCUAAUGCGCAAGGGAG-AGGGGUGCACGCGCGGGAAUGAGACAGCGUUCGUGCCUAAUUUUAAUUUUAUGCACACUUCGCACGCCUCACACUCCCA---------CCAUUCCCCUGCUCAUUUCC--------CCCUUUUUAUGGCCCUCUCCCUCGC--
....((....))((.((((((-(((((((....)))(((((((((.(((((...((((.(((........))).))))....)))..(.....).......---------.........)))))))))))--------............)))))))))).))-- ( -48.80, z-score =  -2.67, R)
>droYak2.chr3L 8603017 164 - 24197627
GGUCGCUAAUGCGUGAGGGAG-CGGGGUGCACGAGCGGGAAAGAGACAGCGUUCGUGCCUAAUUUUAAUUUUAUGCACACUUCGCACGCCUCACACUCCCAUUCCCAUACCCAUUCCCCUUCUCUUUCCCUUGCCUUUCGCCUUUUAUAGCCCCCUCCCUCUCGC
..........(((.(((((((-.(((((((....))((((((((((..(((...((((.(((........))).))))....)))..(.....)..........................))))))))))...................)))))))))))).))) ( -54.90, z-score =  -4.13, R)
>droEre2.scaffold_4784 22414454 117 + 25762168
GGUCGCUAAUGCGUGAGGGAG-AGGGGUGCACGAGCGGGAAUGAGACAGCGUUCGUGCCUAAUUUUAAUUUUAUGCACGCUUCGCACGCCUCACACUCCCA--------AUCGCCCUCUCCCUCGC---------------------------------------
....((....))(((((((((-((((..((....))((((.((((.(.(((..(((((.(((........))).)))))...)))..).))))...)))).--------....)))))))))))))--------------------------------------- ( -52.40, z-score =  -4.45, R)
>consensus
GGUCGCUAAUGCGCGAGGGAG_AGGGGUGCACGAGCGGGAAUGAGACAGCGUUCGUGCCUAAUUUUAAUUUUAUGCACACUUCGCACGCCUCACACUCCCA_________CCAUUCCCCUUCUCAUUUCC________CCCUUUUUAUAGCCCUCUCCCUCGC__
...(((....))).....(((.(((((.((....))((((.((((.(.(((...((((.(((........))).))))....)))..).))))...))))...............))))).)))......................................... (-32.99 = -33.17 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:10:40 2011