Locus 12653

Sequence ID dm3.chrX
Location 1,425,133 – 1,425,264
Length 131
Max. P 0.822777
window17394 window17395

overview

Window 4

Location 1,425,133 – 1,425,241
Length 108
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 63.49
Shannon entropy 0.56960
G+C content 0.61776
Mean single sequence MFE -38.23
Consensus MFE -15.25
Energy contribution -16.62
Covariance contribution 1.38
Combinations/Pair 1.17
Mean z-score -1.62
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.694446
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1425133 108 + 22422827
UUAAUGCUAAUUGCUGUCACCCCGC--CCACCUGCCGGAAUGGGCGGCUUGAAAGUUGGCCCUGGUGACCACCAUGCUCCCCUG-AUCACCACCUGCUGGGGAGCGCAUUC
..(((((........((((((..((--(((((....))..)))))((((........))))..))))))......(((((((..-.............)))))))))))). ( -42.96, z-score =  -2.68, R)
>droEre2.scaffold_4644 1409299 90 + 2521924
UUAAUGCUAAUUGCUGCCACCC-GC--CCAUCCGCCG-----GGCGGCUUGAAAGGUGGCCCAGGUGGCCCUGGUGGCCACCAGCGACUCUGACCACC-------------
..........((((((((((((-((--((.......)-----))))........))))))...(((((((.....))))))))))))...........------------- ( -37.50, z-score =  -1.19, R)
>droYak2.chrX 1316457 85 + 21770863
UUAAUGCUAAUUGCUGCCACCCCGCGUCCACCUGCCG-----CGCGGCUAGAAAGGUGGCCUCUG-AUCACUUGGGGCAGGGAGCGCAUUC--------------------
..(((((.....(((.((.(((((.(((((((((((.-----...))).....))))))......-...)).)))))..)).)))))))).-------------------- ( -29.70, z-score =   0.11, R)
>droSec1.super_10 1246702 108 + 3036183
UUAAUGCUAAUUGCUGUCACCCCGC--CCACCUGCCGGAAUUGGCGGCUUGAAAGGUGGCCCUUGUGGCCGCCAUGCUUCCCUG-ACCACCACCUGCUGGGAAGCGCAUUC
..(((((.....(((((((.((.((--......)).))...)))))))......(((((((.....)))))))..(((((((..-.............)))))))))))). ( -42.76, z-score =  -2.71, R)
>consensus
UUAAUGCUAAUUGCUGCCACCCCGC__CCACCUGCCG_____GGCGGCUUGAAAGGUGGCCCUGGUGGCCCCCAUGCCCCCCAG_ACCACCACCUGCU_____________
.....((.....)).((((((......((((((((((.......)))).....))))))....)))))).......................................... (-15.25 = -16.62 +   1.38)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,425,164 – 1,425,264
Length 100
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 61.23
Shannon entropy 0.60537
G+C content 0.63034
Mean single sequence MFE -39.41
Consensus MFE -16.85
Energy contribution -17.54
Covariance contribution 0.69
Combinations/Pair 1.32
Mean z-score -1.48
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.822777
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 1425164 100 + 22422827
GCCGGAAUGGGCGGCUUGAAAGUUGGCCCUGGUGACCACCAUGCUCCCCUGAUCACCACCUGCUGGGGAGCGCAUUCUGCGGCCGACUUUGGUGUCAUUU
(((......)))(((.(.((((((((((.((((....)))).(((((((...............)))))))((.....)))))))))))).).))).... ( -44.36, z-score =  -2.41, R)
>droEre2.scaffold_4644 1409329 83 + 2521924
-----GCCGGGCGGCUUGAAAGGUGGCCCAGGUGGCC--------CUGGUGGCCACCAGCGACUCUGA----CCACCAGCGGCUGGCUUUGGGGUCAUUU
-----((.((((.(((.....))).)))).(((((((--------.....))))))).))(((((..(----...((((...))))..)..))))).... ( -41.30, z-score =  -1.10, R)
>droYak2.chrX 1316490 75 + 21770863
-----GCCGCGCGGCUAGAAAGGUGGCCUCUG-AUCA--------CUUGGGGCAGGGAGCGCAUU-----------CUGCGGCUGACUUGGGGGUCAUUU
-----(((((((.(((.....))).))(((((-..(.--------....)..)))))........-----------..)))))(((((....)))))... ( -25.70, z-score =   0.50, R)
>droSec1.super_10 1246733 100 + 3036183
GCCGGAAUUGGCGGCUUGAAAGGUGGCCCUUGUGGCCGCCAUGCUUCCCUGACCACCACCUGCUGGGAAGCGCAUUCUGCGGCCGACUUUGGUGUCAUUU
((((((.(((((.((..(((.(((((((.....)))))))..(((((((...............)))))))...))).)).))))).))))))....... ( -46.26, z-score =  -2.91, R)
>consensus
_____AACGGGCGGCUUGAAAGGUGGCCCUGGUGGCC________CCCCUGACCACCACCGGCUGGGA____CAUUCUGCGGCCGACUUUGGGGUCAUUU
............(((((.((((.((((((....)........(((((((...............))))))).........))))).)))).))))).... (-16.85 = -17.54 +   0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:06:17 2011