Locus 2500

Sequence ID dm3.chr2L
Location 19,533,069 – 19,533,168
Length 99
Max. P 0.659038
window3440 window3441

overview

Window 0

Location 19,533,069 – 19,533,168
Length 99
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 71.12
Shannon entropy 0.54860
G+C content 0.35828
Mean single sequence MFE -23.38
Consensus MFE -12.34
Energy contribution -13.35
Covariance contribution 1.01
Combinations/Pair 1.44
Mean z-score -1.00
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.23
SVM RNA-class probability 0.604263
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 19533069 99 + 23011544
GCAUUCCUUAAUAAAUUUUUAAUUGCUUUGCAUAUAAGGAAUAUGCAACACAAUUGCACGAUUUACCAACCAUAAAUGGUUAUGUGUGGGCAA-UGCAGU----
(((((((............((((((..((((((((.....))))))))..))))))((((....((((........))))....)))))).))-)))...---- ( -26.80, z-score =  -2.38, R)
>droSim1.chr2L 19220324 100 + 22036055
GCAUUCCUUAAUAAAUUUUUAAUUGCUUUGCAUAUAAGGAAUAUGCAACACAAUUGCACGAUUGACCAACGGUAAAUGGUUAUGAGUGGGCAAAUGCAGC----
(((((((............((((((..((((((((.....))))))))..))))))(((...((((((........))))))...)))))..)))))...---- ( -26.80, z-score =  -2.38, R)
>droSec1.super_7 3147713 100 + 3727775
GCAUUCCUUAAUAAAUUUUUAAUUGCUUUGCAUAUAAGGAAUAUGCAACACAAUUGCACGAUUGACCAACGGUAAAUGGUUAUGAGUGGGCAAAUGCAGC----
(((((((............((((((..((((((((.....))))))))..))))))(((...((((((........))))))...)))))..)))))...---- ( -26.80, z-score =  -2.38, R)
>droYak2.chr2R 6029713 104 + 21139217
GCAUUCCUUAAUAAAUUAAUAAUUGCUUUGCAUAUAAGGCAUAUGCAACACAAUUGCAUGAUUGACCAUCUAAGUAUGGCUAUGUGUUGGCAAAUAUAAAUAGU
..............(((.(((.(((((..(((((((.(.(((((((((.....))))(((......)))....))))).)))))))).))))).))).)))... ( -20.70, z-score =   0.24, R)
>droEre2.scaffold_4845 17823032 99 - 22589142
GCAUUCCUUAAUAAAUUUUUAAUUGCUUGGCAUAUAAGGCACAUGCAGCACAAUUGCAUGAUUGACCAACGAUG-AUGGCUAUGUGUGGGCAAAUGCAGU----
((((...((((.......))))((((.(.(((((((.(.(((((((((.....)))))))((((.....)))).-.)).)))))))).)))))))))...---- ( -22.80, z-score =   0.79, R)
>droMoj3.scaffold_6500 16191916 76 + 32352404
--------------AUUUUGGUAAGAUCUUUAUU---AGAGUUGGCAGCACUUUUGC-UG--UAGCCAUGAAUACGUAUCUGAAAAGGGGCAGCUU--------
--------------(((((((((((...))))))---)))))..((((((....)))-))--).((((((....))).(((....)))))).....-------- ( -16.40, z-score =   0.10, R)
>consensus
GCAUUCCUUAAUAAAUUUUUAAUUGCUUUGCAUAUAAGGAAUAUGCAACACAAUUGCACGAUUGACCAACGAUAAAUGGCUAUGAGUGGGCAAAUGCAGC____
((.................((((((..((((((((.....))))))))..))))))(((...((((((........))))))...))).))............. (-12.34 = -13.35 +   1.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 19,533,069 – 19,533,168
Length 99
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 71.12
Shannon entropy 0.54860
G+C content 0.35828
Mean single sequence MFE -19.98
Consensus MFE -12.72
Energy contribution -14.41
Covariance contribution 1.69
Combinations/Pair 1.31
Mean z-score -0.66
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.36
SVM RNA-class probability 0.659038
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 19533069 99 - 23011544
----ACUGCA-UUGCCCACACAUAACCAUUUAUGGUUGGUAAAUCGUGCAAUUGUGUUGCAUAUUCCUUAUAUGCAAAGCAAUUAAAAAUUUAUUAAGGAAUGC
----...(((-((.((......((((((....))))))((((((..(..((((((.((((((((.....)))))))).)))))).)..))))))...))))))) ( -26.00, z-score =  -2.17, R)
>droSim1.chr2L 19220324 100 - 22036055
----GCUGCAUUUGCCCACUCAUAACCAUUUACCGUUGGUCAAUCGUGCAAUUGUGUUGCAUAUUCCUUAUAUGCAAAGCAAUUAAAAAUUUAUUAAGGAAUGC
----...((((((...(((.....((((........)))).....))).((((((.((((((((.....)))))))).))))))..............)))))) ( -23.20, z-score =  -1.76, R)
>droSec1.super_7 3147713 100 - 3727775
----GCUGCAUUUGCCCACUCAUAACCAUUUACCGUUGGUCAAUCGUGCAAUUGUGUUGCAUAUUCCUUAUAUGCAAAGCAAUUAAAAAUUUAUUAAGGAAUGC
----...((((((...(((.....((((........)))).....))).((((((.((((((((.....)))))))).))))))..............)))))) ( -23.20, z-score =  -1.76, R)
>droYak2.chr2R 6029713 104 - 21139217
ACUAUUUAUAUUUGCCAACACAUAGCCAUACUUAGAUGGUCAAUCAUGCAAUUGUGUUGCAUAUGCCUUAUAUGCAAAGCAAUUAUUAAUUUAUUAAGGAAUGC
..............((........(((((......))))).........((((((.(((((((((...))))))))).)))))).............))..... ( -19.10, z-score =   0.31, R)
>droEre2.scaffold_4845 17823032 99 + 22589142
----ACUGCAUUUGCCCACACAUAGCCAU-CAUCGUUGGUCAAUCAUGCAAUUGUGCUGCAUGUGCCUUAUAUGCCAAGCAAUUAAAAAUUUAUUAAGGAAUGC
----...((((((((.........((((.-......)))).......))((((((...(((((((...)))))))...))))))..............)))))) ( -18.49, z-score =   1.26, R)
>droMoj3.scaffold_6500 16191916 76 - 32352404
--------AAGCUGCCCCUUUUCAGAUACGUAUUCAUGGCUA--CA-GCAAAAGUGCUGCCAACUCU---AAUAAAGAUCUUACCAAAAU--------------
--------...............((((...((((..((((..--.(-(((....)))))))).....---))))...)))).........-------------- (  -9.90, z-score =   0.16, R)
>consensus
____ACUGCAUUUGCCCACACAUAACCAUUUAUCGUUGGUCAAUCAUGCAAUUGUGUUGCAUAUUCCUUAUAUGCAAAGCAAUUAAAAAUUUAUUAAGGAAUGC
.......((((((((.........((((........)))).......))((((((.((((((((.....)))))))).))))))..............)))))) (-12.72 = -14.41 +   1.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:25 2011