Locus 8000

Sequence ID dm3.chr3L
Location 19,322,628 – 19,322,701
Length 73
Max. P 0.995274
window11010 window11011

overview

Window 0

Location 19,322,628 – 19,322,701
Length 73
Sequences 11
Columns 77
Reading direction forward
Mean pairwise identity 86.47
Shannon entropy 0.29199
G+C content 0.49654
Mean single sequence MFE -23.30
Consensus MFE -20.59
Energy contribution -20.69
Covariance contribution 0.10
Combinations/Pair 1.06
Mean z-score -2.69
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.78
SVM RNA-class probability 0.995274
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19322628 73 + 24543557
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACAAAGCAGGCGAAA----
......((((((....(((((((...((((....)))))))))))....))))))(((........)))....---- ( -25.90, z-score =  -3.27, R)
>droSim1.chr3L_random 856132 73 + 1049610
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACGGACCAGGCGAAA----
......((((((....(((((((...((((....)))))))))))....))))))(((........)))....---- ( -25.90, z-score =  -2.78, R)
>droSec1.super_29 23671 73 + 700605
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACGGACCAGGCGAAA----
......((((((....(((((((...((((....)))))))))))....))))))(((........)))....---- ( -25.90, z-score =  -2.78, R)
>droYak2.chr3L 2968012 73 - 24197627
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACAGACCGAGCAACA----
......((((((....(((((((...((((....)))))))))))....))))))(((.......).))....---- ( -21.80, z-score =  -2.15, R)
>droEre2.scaffold_4784 19135432 73 + 25762168
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACAGACCAGGCAAUA----
......((((((....(((((((...((((....)))))))))))....))))))(((........)))....---- ( -25.90, z-score =  -3.54, R)
>droAna3.scaffold_13337 5158064 69 - 23293914
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACAGCCGAGGC--------
......((((((....(((((((...((((....)))))))))))....))))))(((........)))-------- ( -24.20, z-score =  -2.62, R)
>droPer1.super_48 198774 69 + 581423
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACGACAGAAGC--------
......((((((....(((((((...((((....)))))))))))....))))))..............-------- ( -21.30, z-score =  -2.37, R)
>dp4.chrXR_group8 7408867 69 + 9212921
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACGACAGAAGC--------
......((((((....(((((((...((((....)))))))))))....))))))..............-------- ( -21.30, z-score =  -2.37, R)
>droVir3.scaffold_13049 12326835 77 - 25233164
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCAGCUUCGAAGCAAACGACA
......((((((....(((((((...((((....)))))))))))....))))))....(((....)))........ ( -23.40, z-score =  -2.21, R)
>droMoj3.scaffold_6680 14501254 59 + 24764193
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACGGGACGCCGAAGAAAGUGGCGCCA------------------
......((((((....((((((((..((.......))))))))))....))))))....------------------ ( -19.40, z-score =  -1.98, R)
>droGri2.scaffold_15110 987484 60 - 24565398
CAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGUCGCCAAAGAAAGUGGCGCCAC-----------------
......((((((....((((((...(((((....)))))))))))....)))))).....----------------- ( -21.30, z-score =  -3.46, R)
>consensus
AAACUUGCCAUUCAAAUUGGUGUCAACCAGUCAACUGGACGCCAAAGAAAGUGGCGCCACAGACCAGGC_A______
......((((((....(((((((...((((....)))))))))))....))))))...................... (-20.59 = -20.69 +   0.10)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 19,322,628 – 19,322,701
Length 73
Sequences 11
Columns 77
Reading direction reverse
Mean pairwise identity 86.47
Shannon entropy 0.29199
G+C content 0.49654
Mean single sequence MFE -22.07
Consensus MFE -17.85
Energy contribution -18.50
Covariance contribution 0.65
Combinations/Pair 1.05
Mean z-score -1.54
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.821418
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19322628 73 - 24543557
----UUUCGCCUGCUUUGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
----....(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... ( -22.50, z-score =  -1.65, R)
>droSim1.chr3L_random 856132 73 - 1049610
----UUUCGCCUGGUCCGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
----....(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... ( -22.50, z-score =  -1.22, R)
>droSec1.super_29 23671 73 - 700605
----UUUCGCCUGGUCCGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
----....(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... ( -22.50, z-score =  -1.22, R)
>droYak2.chr3L 2968012 73 + 24197627
----UGUUGCUCGGUCUGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
----(((((..(((((..((((((((.......))))).)))...)))))..)))))..((((((.....)))))). ( -23.00, z-score =  -1.33, R)
>droEre2.scaffold_4784 19135432 73 - 25762168
----UAUUGCCUGGUCUGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
----..(((((.((((..((((((((.......))))).)))...))))(((....))).........))))).... ( -23.90, z-score =  -1.91, R)
>droAna3.scaffold_13337 5158064 69 + 23293914
--------GCCUCGGCUGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
--------((((((((((.(((((((.......)))))))))))))).((((....))))........)))...... ( -27.60, z-score =  -3.06, R)
>droPer1.super_48 198774 69 - 581423
--------GCUUCUGUCGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
--------(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... ( -19.80, z-score =  -0.97, R)
>dp4.chrXR_group8 7408867 69 - 9212921
--------GCUUCUGUCGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
--------(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... ( -19.80, z-score =  -0.97, R)
>droVir3.scaffold_13049 12326835 77 + 25233164
UGUCGUUUGCUUCGAAGCUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
((((((((.......(((((((((((.......))))).))))))...((((....))))....))))))))..... ( -25.90, z-score =  -2.07, R)
>droMoj3.scaffold_6680 14501254 59 - 24764193
------------------UGGCGCCACUUUCUUCGGCGUCCCGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
------------------.((((((.........))))))(((((.(.((((....))))...).)))))....... ( -15.10, z-score =  -0.35, R)
>droGri2.scaffold_15110 987484 60 + 24565398
-----------------GUGGCGCCACUUUCUUUGGCGACCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUG
-----------------.....((((.((...(((((((((((....)))))))...))))...)).))))...... ( -20.20, z-score =  -2.24, R)
>consensus
______U_GCCUGGUCCGUGGCGCCACUUUCUUUGGCGUCCAGUUGACUGGUUGACACCAAUUUGAAUGGCAAGUUU
........(((........)))((((.((...((((.((((((....))))...)).))))...)).))))...... (-17.85 = -18.50 +   0.65)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:37:31 2011