Locus 13679

Sequence ID dm3.chrX
Location 8,315,810 – 8,315,929
Length 119
Max. P 0.898035
window18824 window18825

overview

Window 4

Location 8,315,810 – 8,315,929
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.74
Shannon entropy 0.44059
G+C content 0.37881
Mean single sequence MFE -21.26
Consensus MFE -12.64
Energy contribution -13.84
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -1.24
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.532842
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8315810 119 + 22422827
UCGUAAUCGUUUUUAGGGCAAACU-GUUUAUCCAUAAAAAAUGUGGGCUUUGUAAAUAGCAUCAAUUCGCUUUUUUGUGGGUCAUCCAAAAAGAAACCGAAACACCCACACACACCCACA
.........((((((((..((...-..))..)).)))))).((((((...((((((.(((........))).))).((((((..((............))...)))))))))..)))))) ( -22.40, z-score =  -0.20, R)
>droEre2.scaffold_4690 11956190 109 - 18748788
UAGCGAUCGUUUUAGGUGUAAACUGAUUAUCCAGAGAAAAGUGUGGGCUUUUUACAUAGCAUCAAUUCGCUUUUU-GUAGGUCAUCCAAACAGAAACCAAAACACCCACA----------
..............(((((...(((......)))......((.((((...((((((.(((........)))...)-)))))...)))).))..........)))))....---------- ( -20.60, z-score =  -0.42, R)
>droYak2.chrX 8770905 119 - 21770863
UAGUAAUUGUUUUUAGAGCAAACAUAUUAUCCAGGAAAAAGUGUGGGCCUUUUGAAUAGCAUCAAUUCGCUUUUU-GUGGGUCAUCCAAAAAGAAACCAAAACACCCACACACACCCACA
..((((((((((.......))))).)))))...((.....(((((((..(((((....((........))(((((-.(((.....))).)))))...)))))..)))))))....))... ( -23.60, z-score =  -0.85, R)
>droSec1.super_35 165291 110 + 471130
UCUUAAUCGUUUUAAGUUUAAACU-A---------AAAAAACGUGGGCCUUUUAAAUAGCAUCUAUUCGCUUUUUUGUGGGUCAUCCAAAAAGAAACCAAAACACCCACACACACCCACA
........(((((.(((....)))-.---------..)))))(((((......(((.(((........))).)))(((((((.....................)))))))....))))). ( -20.70, z-score =  -2.32, R)
>droSim1.chrX_random 2494456 95 + 5698898
---------------UCGUAAACU-A---------AAAAAACGUGGGCUUUUCAAAUAGCAUCAAUUCGCUUUUUUGUGGGUCAUCCAAAAAGAAACCAAAACACCCACACACACCCACA
---------------.........-.---------.......(((((......(((.(((........))).)))(((((((.....................)))))))....))))). ( -19.00, z-score =  -2.42, R)
>consensus
UAGUAAUCGUUUUAAGUGUAAACU_AUU___C___AAAAAAUGUGGGCUUUUUAAAUAGCAUCAAUUCGCUUUUUUGUGGGUCAUCCAAAAAGAAACCAAAACACCCACACACACCCACA
..........................................(((((..........(((........))).....((((((.....................)))))).....))))). (-12.64 = -13.84 +   1.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 8,315,810 – 8,315,929
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.74
Shannon entropy 0.44059
G+C content 0.37881
Mean single sequence MFE -28.28
Consensus MFE -18.62
Energy contribution -18.66
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -1.54
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.14
SVM RNA-class probability 0.898035
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8315810 119 - 22422827
UGUGGGUGUGUGUGGGUGUUUCGGUUUCUUUUUGGAUGACCCACAAAAAAGCGAAUUGAUGCUAUUUACAAAGCCCACAUUUUUUAUGGAUAAAC-AGUUUGCCCUAAAAACGAUUACGA
(((((((...(((((((((.(((((((((((((((.....)))...))))).))))))).)).)))))))..))))))).((((((.((.(((..-...))))).))))))......... ( -31.00, z-score =  -1.28, R)
>droEre2.scaffold_4690 11956190 109 + 18748788
----------UGUGGGUGUUUUGGUUUCUGUUUGGAUGACCUAC-AAAAAGCGAAUUGAUGCUAUGUAAAAAGCCCACACUUUUCUCUGGAUAAUCAGUUUACACCUAAAACGAUCGCUA
----------(((((((..((..(.......)..))..))))))-)...(((((..((((.(((.(..(((((......)))))..))))...))))((((.......))))..))))). ( -24.00, z-score =  -0.86, R)
>droYak2.chrX 8770905 119 + 21770863
UGUGGGUGUGUGUGGGUGUUUUGGUUUCUUUUUGGAUGACCCAC-AAAAAGCGAAUUGAUGCUAUUCAAAAGGCCCACACUUUUUCCUGGAUAAUAUGUUUGCUCUAAAAACAAUUACUA
...(((...((((((((.((((((....(((.(((.....))).-))).((((......))))..)))))).))))))))....)))(((.((((.(((((.......)))))))))))) ( -30.80, z-score =  -1.41, R)
>droSec1.super_35 165291 110 - 471130
UGUGGGUGUGUGUGGGUGUUUUGGUUUCUUUUUGGAUGACCCACAAAAAAGCGAAUAGAUGCUAUUUAAAAGGCCCACGUUUUUU---------U-AGUUUAAACUUAAAACGAUUAAGA
.((((((.(.(((((((..((..(.......)..))..)))))))(((.((((......)))).)))...).))))))(((((..---------.-(((....))).)))))........ ( -29.60, z-score =  -2.26, R)
>droSim1.chrX_random 2494456 95 - 5698898
UGUGGGUGUGUGUGGGUGUUUUGGUUUCUUUUUGGAUGACCCACAAAAAAGCGAAUUGAUGCUAUUUGAAAAGCCCACGUUUUUU---------U-AGUUUACGA---------------
.((((((...(((((((..((..(.......)..))..)))))))(((.((((......)))).))).....)))))).......---------.-.........--------------- ( -26.00, z-score =  -1.87, R)
>consensus
UGUGGGUGUGUGUGGGUGUUUUGGUUUCUUUUUGGAUGACCCACAAAAAAGCGAAUUGAUGCUAUUUAAAAAGCCCACAUUUUUU___G___AAU_AGUUUACACUAAAAACGAUUACGA
..........(((((((.(((((((((((....))).))))........((((......))))....)))).)))))))......................................... (-18.62 = -18.66 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:25:49 2011