Locus 13640

Sequence ID dm3.chrX
Location 8,057,778 – 8,057,873
Length 95
Max. P 0.636167
window18769 window18770

overview

Window 9

Location 8,057,778 – 8,057,873
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 66.15
Shannon entropy 0.65953
G+C content 0.57130
Mean single sequence MFE -29.97
Consensus MFE -13.40
Energy contribution -14.83
Covariance contribution 1.44
Combinations/Pair 1.38
Mean z-score -0.90
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.636167
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8057778 95 + 22422827
CGGGCCAACGGUAAAGCACAACAAAGUGUGGUCACCACUACGAAUUGGGCCAGAAAUCGGUGGCCAAGUGGAUCUGGCAUGGAGAUGGCGACGAA
((.((((.(......((((......)))).(((((((((........(((((........))))).)))))...)))).....).))))..)).. ( -26.60, z-score =   0.15, R)
>droEre2.scaffold_4690 10429285 93 + 18748788
-CGGCCAACGGUAAAGCAGCACCAACUGCG-CCACCACUUCGAAUUGGGCCAGAAAUCGGUGGCCAAGUGCAGCUGGAGUGGAGGUGGAGGCGAG
-..(((..(......((((......))))(-((.((((((((.(((.(((((........))))).))).....)))))))).))))..)))... ( -34.10, z-score =  -0.74, R)
>droYak2.chrX 8518261 74 - 21770863
CUGGCCAACGGUAAAG----------UGUGG-CACCACUACGAAUUGGGCCAGAAAUCGGUGACCAAGUGGCGCUGGCUACGAAA----------
((((((..((((...(----------((((.-...))).))..))))))))))...((((((.((....))))))))........---------- ( -24.30, z-score =  -0.96, R)
>droSec1.super_44 143956 95 + 251150
CAGGCCAACGGUAAAGCACAACAAAGUGCGGCCACCACUACGAAUUGGGCCAGAAAUCGGUGGCCAAGUGGAUCUGGCAUGAAGGUGGCGACGCA
((.((((..(((...((((......)))).))).(((((........(((((........))))).)))))...)))).))...(((....))). ( -34.00, z-score =  -1.60, R)
>droSim1.chrX_random 2415371 95 + 5698898
CAGGCCAACGGUAAAGCACAACAAAGUGCGGCCACCACUGCGAAUUGGGCCAGAAAUCGCUGGCCAAGUGGAUCUGGCAUGGAGGUGGCGACGCA
((.((((..(((...((((......)))).))).(((((........((((((......)))))).)))))...)))).))...(((....))). ( -38.70, z-score =  -2.16, R)
>dp4.chrXR_group6 6066568 72 + 13314419
----------GUAAAGUGCG-------GCAGCUCGUGCUCCAAAUGGUGCUCCAAAUGAUGAUCCAAGUGGGGCAGGAUACCGGCCUGU------
----------.........(-------((...((.(((((((..(((..(((.....)).)..)))..))))))).)).....)))...------ ( -22.10, z-score =  -0.09, R)
>consensus
CAGGCCAACGGUAAAGCACAACAAAGUGCGGCCACCACUACGAAUUGGGCCAGAAAUCGGUGGCCAAGUGGAGCUGGCAUGGAGGUGGCGACG_A
...((((..(((...((((......)))).))).(((((........(((((........))))).)))))...))))................. (-13.40 = -14.83 +   1.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 8,057,778 – 8,057,873
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 66.15
Shannon entropy 0.65953
G+C content 0.57130
Mean single sequence MFE -25.64
Consensus MFE -11.25
Energy contribution -11.28
Covariance contribution 0.03
Combinations/Pair 1.46
Mean z-score -0.84
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.529077
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8057778 95 - 22422827
UUCGUCGCCAUCUCCAUGCCAGAUCCACUUGGCCACCGAUUUCUGGCCCAAUUCGUAGUGGUGACCACACUUUGUUGUGCUUUACCGUUGGCCCG
......((((.(.....((((((.....((((...))))..))))))............(((((.((((......))))..)))))).))))... ( -23.50, z-score =  -0.65, R)
>droEre2.scaffold_4690 10429285 93 - 18748788
CUCGCCUCCACCUCCACUCCAGCUGCACUUGGCCACCGAUUUCUGGCCCAAUUCGAAGUGGUGG-CGCAGUUGGUGCUGCUUUACCGUUGGCCG-
...(((........(((.((((((((.....((((((.(((((.((......))))))))))))-))))))))).).))..........)))..- ( -30.07, z-score =  -0.70, R)
>droYak2.chrX 8518261 74 + 21770863
----------UUUCGUAGCCAGCGCCACUUGGUCACCGAUUUCUGGCCCAAUUCGUAGUGGUG-CCACA----------CUUUACCGUUGGCCAG
----------.......(((((((((....)))..........(((((((........))).)-)))..----------.......))))))... ( -20.70, z-score =  -1.14, R)
>droSec1.super_44 143956 95 - 251150
UGCGUCGCCACCUUCAUGCCAGAUCCACUUGGCCACCGAUUUCUGGCCCAAUUCGUAGUGGUGGCCGCACUUUGUUGUGCUUUACCGUUGGCCUG
......((((.(.....((((...(((((.(((((........)))))........))))))))).((((......))))......).))))... ( -28.40, z-score =  -0.81, R)
>droSim1.chrX_random 2415371 95 - 5698898
UGCGUCGCCACCUCCAUGCCAGAUCCACUUGGCCAGCGAUUUCUGGCCCAAUUCGCAGUGGUGGCCGCACUUUGUUGUGCUUUACCGUUGGCCUG
...(((((((((....(((..((.......((((((......))))))....)))))..)))))).((((......)))).........)))... ( -31.80, z-score =  -1.07, R)
>dp4.chrXR_group6 6066568 72 - 13314419
------ACAGGCCGGUAUCCUGCCCCACUUGGAUCAUCAUUUGGAGCACCAUUUGGAGCACGAGCUGC-------CGCACUUUAC----------
------...(((.(((.((.(((.(((..(((.((........))...)))..))).))).)))))))-------).........---------- ( -19.40, z-score =  -0.69, R)
>consensus
U_CGUCGCCACCUCCAUGCCAGAUCCACUUGGCCACCGAUUUCUGGCCCAAUUCGUAGUGGUGGCCGCACUUUGUUGUGCUUUACCGUUGGCCUG
.................(((((........(((((........))))).........(((.....)))...................)))))... (-11.25 = -11.28 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:25:04 2011