Locus 12914

Sequence ID dm3.chrX
Location 3,206,998 – 3,207,060
Length 62
Max. P 0.982184
window17757 window17758

overview

Window 7

Location 3,206,998 – 3,207,060
Length 62
Sequences 7
Columns 67
Reading direction forward
Mean pairwise identity 64.79
Shannon entropy 0.69477
G+C content 0.49829
Mean single sequence MFE -10.07
Consensus MFE -4.99
Energy contribution -4.10
Covariance contribution -0.89
Combinations/Pair 2.14
Mean z-score -1.42
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.10
SVM RNA-class probability 0.982184
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3206998 62 + 22422827
CACUCGCAGCCAGAUAGACAAGCGUGU----CCAUCCAGCAGUUUAUCCGCCAGUUUGUCAGUCAC-
............(((.(((((((.((.----.....))((.(.....).))..))))))).)))..- ( -10.70, z-score =  -1.37, R)
>droEre2.scaffold_4690 617842 66 + 18748788
CACUCGCAGCCAGAUAGACAGAUAGACCAGUCCAUCCAGCAGUUUAUCCACCAGUUUGUCAGUCAC-
............(((((((.(((((((..((.......)).))))))).....)))))))......- ( -10.40, z-score =  -2.29, R)
>droYak2.chrX 16594763 64 - 21770863
CAUUCGCAGCCAGAUAGACAGAUAGAC--GUCCAUCCAGCAGUUUAUCCACCAGUUUGUCAGUCAC-
............(((((((.(((((((--............))))))).....)))))))......- ( -11.20, z-score =  -3.17, R)
>droSec1.super_10 2913797 60 + 3036183
CACUCGCAGCCACAUAGACAAGCGU------CCAUCCAGCAGUUUAUCCGCCAGUUUGUCAGUCAC-
................((((((((.------.....).((.(.....).))..)))))))......- (  -7.40, z-score =  -1.05, R)
>droSim1.chrX 2294123 60 + 17042790
CACUCGCAGCCAGAUAGACAAGCGU------CCAUCCAGCAGUUUAUCCGCCAGUUUGUCAGUCAC-
............(((.((((((((.------.....).((.(.....).))..))))))).)))..- ( -10.10, z-score =  -1.99, R)
>droGri2.scaffold_14853 4390204 63 + 10151454
CACUCAAAAGCCACUCAAUCGUCAAUU----CAGUCAAUCUGUGAAUCAAUCAGACUGCCAAUCAAU
...........................----(((((....((.....))....)))))......... (  -4.30, z-score =   0.17, R)
>anoGam1.chr2R 42725602 63 - 62725911
AAAUCAACCUCGGACGGAUAUGCGUCGU--GCGGUUAGGC-GUGUGUGUGUGUGUGUAACAAUGAG-
........((((.(((.(((((((.((.--.((......)-)..))))))))).))).....))))- ( -16.40, z-score =  -0.26, R)
>consensus
CACUCGCAGCCAGAUAGACAAGCGU______CCAUCCAGCAGUUUAUCCGCCAGUUUGUCAGUCAC_
................(((((((..............................)))))))....... ( -4.99 =  -4.10 +  -0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 3,206,998 – 3,207,060
Length 62
Sequences 7
Columns 67
Reading direction reverse
Mean pairwise identity 64.79
Shannon entropy 0.69477
G+C content 0.49829
Mean single sequence MFE -16.00
Consensus MFE -4.44
Energy contribution -4.39
Covariance contribution -0.05
Combinations/Pair 1.77
Mean z-score -2.15
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.891910
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 3206998 62 - 22422827
-GUGACUGACAAACUGGCGGAUAAACUGCUGGAUGG----ACACGCUUGUCUAUCUGGCUGCGAGUG
-...........(((.(((......).((..(((((----(((....))))))))..)).)).))). ( -21.50, z-score =  -3.97, R)
>droEre2.scaffold_4690 617842 66 - 18748788
-GUGACUGACAAACUGGUGGAUAAACUGCUGGAUGGACUGGUCUAUCUGUCUAUCUGGCUGCGAGUG
-...........(((.(((......).((..(((((((.((....)).)))))))..)).)).))). ( -18.10, z-score =  -2.38, R)
>droYak2.chrX 16594763 64 + 21770863
-GUGACUGACAAACUGGUGGAUAAACUGCUGGAUGGAC--GUCUAUCUGUCUAUCUGGCUGCGAAUG
-..............(((......)))((..(((((((--(......))))))))..))........ ( -17.00, z-score =  -2.99, R)
>droSec1.super_10 2913797 60 - 3036183
-GUGACUGACAAACUGGCGGAUAAACUGCUGGAUGG------ACGCUUGUCUAUGUGGCUGCGAGUG
-((.((.......(..((((.....))))..)((((------((....)))))))).))........ ( -16.00, z-score =  -1.85, R)
>droSim1.chrX 2294123 60 - 17042790
-GUGACUGACAAACUGGCGGAUAAACUGCUGGAUGG------ACGCUUGUCUAUCUGGCUGCGAGUG
-...........(((.(((......).((..(((((------((....)))))))..)).)).))). ( -20.30, z-score =  -3.83, R)
>droGri2.scaffold_14853 4390204 63 - 10151454
AUUGAUUGGCAGUCUGAUUGAUUCACAGAUUGACUG----AAUUGACGAUUGAGUGGCUUUUGAGUG
(((.(..(((((((((.........)))))).(((.----((((...)))).))).)))..).))). ( -10.60, z-score =   0.23, R)
>anoGam1.chr2R 42725602 63 + 62725911
-CUCAUUGUUACACACACACACACAC-GCCUAACCGC--ACGACGCAUAUCCGUCCGAGGUUGAUUU
-.........................-...(((((..--..((((......))))...))))).... (  -8.50, z-score =  -0.28, R)
>consensus
_GUGACUGACAAACUGGCGGAUAAACUGCUGGAUGG______ACGCCUGUCUAUCUGGCUGCGAGUG
.............(((((((.....)))))))...........(((..(((.....))).))).... ( -4.44 =  -4.39 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:11:13 2011