Locus 2720

Sequence ID dm3.chr2L
Location 21,507,964 – 21,508,019
Length 55
Max. P 0.999927
window3734 window3735

overview

Window 4

Location 21,507,964 – 21,508,019
Length 55
Sequences 11
Columns 66
Reading direction forward
Mean pairwise identity 57.48
Shannon entropy 0.91578
G+C content 0.48139
Mean single sequence MFE -20.11
Consensus MFE -12.49
Energy contribution -13.75
Covariance contribution 1.25
Combinations/Pair 1.33
Mean z-score -2.26
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.95
SVM RNA-class probability 0.999927
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21507964 55 + 23011544
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUAUUGUCCGCA---UUCGCAGGAGAAAA--------
.((((((((((....)))))).....((((....))))...---...)))).......-------- ( -20.10, z-score =  -2.58, R)
>droSim1.chrU 6172939 55 - 15797150
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUGUUGUCCGCA---UUCGCAGGAGCCAA--------
.....((((((....))))))(((((((((....))))((.---...)).)))))...-------- ( -21.60, z-score =  -2.34, R)
>droSec1.super_91 93440 55 + 125313
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUGUUGUCCGCA---CUCGCAGGAGCCAA--------
.....((((((....))))))(((((((((....))))((.---...)).)))))...-------- ( -21.60, z-score =  -2.10, R)
>droYak2.chr2R_random 60460 58 - 67238
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUAAUGUCCGCAGCAUUCGUAGGAACAAA--------
.((((((((((....))))))(((.(((((....))))).)))..........)))).-------- ( -23.20, z-score =  -3.62, R)
>droEre2.scaffold_4845 19579875 55 - 22589142
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUUUUGUCCGCA---CUCGCAGGAGGAAA--------
..(((((((((....)))))).....((((....)))))))---(((....)))....-------- ( -21.40, z-score =  -2.38, R)
>droAna3.scaffold_13030 44769 54 - 47400
GUUGUGGCCCUGAAAAGGGCCUUUUUGGAUCAUUCUGCCCA----GCAAGCGAGCAAU--------
((((.((((((....)))))).....(((....)))...))----))...........-------- ( -17.50, z-score =  -0.99, R)
>droWil1.scaffold_181036 1021 60 + 110856
AUUGUGGCCCUGAAAAGGGCUUUUUUUUUAAAAGGAAGCGUGUGUUUAAGCUAGGGACAU------
.((.(((((((....)))((((((((.....))))))))..........)))).))....------ ( -14.80, z-score =  -0.85, R)
>droVir3.scaffold_13047 1623768 66 + 19223366
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUUUGUUUGCUUCCCGUACAAUGCACAUCUAGCUGAAUU
.....((((((....))))))(((.(((...((.(((............))).))..))).))).. ( -18.20, z-score =  -1.84, R)
>droMoj3.scaffold_6540 26886383 65 - 34148556
UUUGUGGCCCUGAAAAGGGCCUUUUGCUUCU-UCUUUUGGAUGUUCUGCAUACACCGAGGUAAGAU
.....((((((....)))))).......(((-(.((((((.(((.......))))))))).)))). ( -22.60, z-score =  -2.92, R)
>droGri2.scaffold_14978 525905 60 + 1124632
UUUGUGGCCCUGAAAAGGGCCUUUUGCUGCUAGCUGCUCGCUG------GUAUUUCUGCCUGCAAU
.((((((((((....))))))......(((((((.....))))------))).........)))). ( -23.60, z-score =  -2.79, R)
>anoGam1.chr2R 47876183 55 + 62725911
UUUGUGGUCCUGAAAAGGACCGAUUUGAGAGAACGAAGCCAAUCAUUUCAGUGGC-----------
(((((((((((....))))))...((....)))))))((((..........))))----------- ( -16.60, z-score =  -2.43, R)
>consensus
AUUGUGGCCCUGAAAAGGGCCGUUUUGGAUUAUUGUCCGCA___UUCGCAGGAGCCAA________
.....((((((....))))))............................................. (-12.49 = -13.75 +   1.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 21,507,964 – 21,508,019
Length 55
Sequences 11
Columns 66
Reading direction reverse
Mean pairwise identity 57.48
Shannon entropy 0.91578
G+C content 0.48139
Mean single sequence MFE -15.95
Consensus MFE -11.22
Energy contribution -11.15
Covariance contribution -0.07
Combinations/Pair 1.17
Mean z-score -1.80
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.40
SVM RNA-class probability 0.999792
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 21507964 55 - 23011544
--------UUUUCUCCUGCGAA---UGCGGACAAUAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------.......((((...---.))))...............((((((....))))))..... ( -15.70, z-score =  -2.52, R)
>droSim1.chrU 6172939 55 + 15797150
--------UUGGCUCCUGCGAA---UGCGGACAACAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------(((..(((.((...---.)))))...)))........((((((....))))))..... ( -16.30, z-score =  -1.62, R)
>droSec1.super_91 93440 55 - 125313
--------UUGGCUCCUGCGAG---UGCGGACAACAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------...((((....)))---)..(((......))).....((((((....))))))..... ( -17.20, z-score =  -1.44, R)
>droYak2.chr2R_random 60460 58 + 67238
--------UUUGUUCCUACGAAUGCUGCGGACAUUAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------(((((....)))))......(((......))).....((((((....))))))..... ( -15.40, z-score =  -2.01, R)
>droEre2.scaffold_4845 19579875 55 + 22589142
--------UUUCCUCCUGCGAG---UGCGGACAAAAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
--------.......((((...---.))))...............((((((....))))))..... ( -15.70, z-score =  -1.81, R)
>droAna3.scaffold_13030 44769 54 + 47400
--------AUUGCUCGCUUGC----UGGGCAGAAUGAUCCAAAAAGGCCCUUUUCAGGGCCACAAC
--------.(((((((.....----))))))).............((((((....))))))..... ( -18.10, z-score =  -1.59, R)
>droWil1.scaffold_181036 1021 60 - 110856
------AUGUCCCUAGCUUAAACACACGCUUCCUUUUAAAAAAAAAGCCCUUUUCAGGGCCACAAU
------.(((....(((..........)))................(((((....))))).))).. (  -8.00, z-score =  -0.71, R)
>droVir3.scaffold_13047 1623768 66 - 19223366
AAUUCAGCUAGAUGUGCAUUGUACGGGAAGCAAACAAAAGCAAAAGGCCCUUUUCAGGGCCACAAA
......(((...(((((...)))))...)))..............((((((....))))))..... ( -18.30, z-score =  -1.74, R)
>droMoj3.scaffold_6540 26886383 65 + 34148556
AUCUUACCUCGGUGUAUGCAGAACAUCCAAAAGA-AGAAGCAAAAGGCCCUUUUCAGGGCCACAAA
.((((.....(((((.......)))))......)-))).......((((((....))))))..... ( -16.90, z-score =  -1.95, R)
>droGri2.scaffold_14978 525905 60 - 1124632
AUUGCAGGCAGAAAUAC------CAGCGAGCAGCUAGCAGCAAAAGGCCCUUUUCAGGGCCACAAA
.((((.((.(....).)------)(((.....)))....))))..((((((....))))))..... ( -20.30, z-score =  -2.35, R)
>anoGam1.chr2R 47876183 55 - 62725911
-----------GCCACUGAAAUGAUUGGCUUCGUUCUCUCAAAUCGGUCCUUUUCAGGACCACAAA
-----------((((..........))))................((((((....))))))..... ( -13.50, z-score =  -2.00, R)
>consensus
________UUGGCUCCUGCGAA___UGCGGACAAUAAUCCAAAACGGCCCUUUUCAGGGCCACAAU
.............................................((((((....))))))..... (-11.22 = -11.15 +  -0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:56:34 2011