Locus 7335

Sequence ID dm3.chr3L
Location 14,008,477 – 14,008,582
Length 105
Max. P 0.997714
window10099 window10100

overview

Window 9

Location 14,008,477 – 14,008,572
Length 95
Sequences 9
Columns 98
Reading direction reverse
Mean pairwise identity 56.76
Shannon entropy 0.88471
G+C content 0.57723
Mean single sequence MFE -41.73
Consensus MFE -10.83
Energy contribution -9.13
Covariance contribution -1.70
Combinations/Pair 2.00
Mean z-score -2.76
Structure conservation index 0.26
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.16
SVM RNA-class probability 0.997714
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14008477 95 - 24543557
---AGGUGGUCGAGUCUUGAAUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGAUUGUUGCCGCAGUAGGUGUUGCAGUUACAGUCGCUGUCG
---.(((..((((...))))..)))(((((((((.....)))))))))....(((((((((((.((.((((......)))).)).))))))))))).. ( -39.40, z-score =  -3.07, R)
>droSim1.chr3L_random 671121 95 - 1049610
---UGGUGGUCGAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGAUUGCUGCUGCAGUAGUUGUUGCAGUUGCAGUCGCUGUUG
---.((..(((((...)))))..))(((((((((.....)))))))))....(((((((((((.(((((((......))))))).))))))))))).. ( -51.50, z-score =  -5.52, R)
>droSec1.super_0 6154969 95 - 21120651
---UGGUGGUCGAGUCUUGACUGCCACUUUGCUCACGUCGAGCAGAGUUGUCGCAGCGAUUGCUGCUGCAGUAGUUGUUGCAGUUACAGUCGCUGUCG
---.((..(((((...)))))..))(((((((((.....)))))))))....((((((((((..(((((((......)))))))..)))))))))).. ( -48.20, z-score =  -4.64, R)
>droYak2.chr3L 14096252 95 - 24197627
---AGGUGGUUUAGUCUUCACUGCCGCUUUGCUAACAUCGAGCAGCGUGGCCGCAGCGACUGCUGCUGCAGUUGGUGUUGCAGUUACAGUUGCUGUCG
---.(((((........)))))(((((.(((((.......))))).))))).((((((((((..(((((((......)))))))..)))))))))).. ( -43.00, z-score =  -2.61, R)
>droEre2.scaffold_4784 14000475 95 - 25762168
---AGGGGGUUUAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGACUGCUGCUGCAGUUGUUGAUGCAGUUGCAGUUGCUGUAG
---.((.((((.......)))).))(((((((((.....)))))))))....(((((((((((.((((((........)))))).))))))))))).. ( -48.40, z-score =  -4.65, R)
>droAna3.scaffold_13337 11358499 82 + 23293914
UGGCGGCGUCCUGGUUUUCAACAUCACCUUGCCCACAUCGAGGAGCGUGGCCGCCGCAGCAGCGGUCGCCGUGGCAGUCGCC----------------
.((((((.....(((..........))).((((.((..((.....)).(((.(((((....))))).)))))))))))))))---------------- ( -31.50, z-score =   0.25, R)
>dp4.chrXR_group8 6783089 83 + 9212921
GGUUAGCGGACGGGAAUUGAUUGCACCUCCUGGUGCUGGUGCUACCGCUGUGGCUGUGGAUGUGGCUGCAGCUGUAGCUGUGC---------------
..((((((..(((((..((....))..))))).)))))).(((((.((((..((..(....)..))..)))).))))).....--------------- ( -35.20, z-score =  -1.98, R)
>droPer1.super_24 624713 83 - 1556852
GGUUAGCGGACGGGAAUUGAUUGCACCUCCUGGUGCUGGUGCUACCGCUGUGGCUGUGGAUGUGGCUGCAGCUGUAGCUGUGC---------------
..((((((..(((((..((....))..))))).)))))).(((((.((((..((..(....)..))..)))).))))).....--------------- ( -35.20, z-score =  -1.98, R)
>droMoj3.scaffold_6680 17721783 98 - 24764193
AGCUGCAGCGCGCGGUUUGGCAGUCGCCUUGGCCUCAACCACAGUCGCCGUUGCAAUGGCUGUUGUUGCUGUUGCUGGCAUUGCAGCCAUUGCUGCUG
(((.((((((.(((..((((..(..((....))..)..))).)..)))))))))(((((((((...((((......))))..)))))))))))).... ( -43.20, z-score =  -0.68, R)
>consensus
___UGGUGGUCGAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGCGUUGUCGCAGCGACUGCUGCUGCAGUUGUUGUUGCAGUU_CAGU_GCUGU_G
..............................................(((((.(((((....))))).))))).......................... (-10.83 =  -9.13 +  -1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,008,482 – 14,008,582
Length 100
Sequences 9
Columns 103
Reading direction reverse
Mean pairwise identity 58.04
Shannon entropy 0.86091
G+C content 0.56674
Mean single sequence MFE -38.88
Consensus MFE -10.83
Energy contribution -9.13
Covariance contribution -1.70
Combinations/Pair 2.00
Mean z-score -1.61
Structure conservation index 0.28
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.05
SVM RNA-class probability 0.881602
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14008482 100 - 24543557
CCAGUUUGAGAGGUGG---UCGAGUCUUGAAUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGAUUGUUGCCGCAGUAGGUGUUGCAGUUACAGUCGC
...(((..(((..(..---..)..)))..)))((.(((((((((.....))))))))).))....((((((((.((.((((......)))).)).)))))))) ( -34.50, z-score =  -1.52, R)
>droSim1.chr3L_random 671126 100 - 1049610
CCAGUUUGAGUGGUGG---UCGAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGAUUGCUGCUGCAGUAGUUGUUGCAGUUGCAGUCGC
.((..((((((((..(---((((...)))))..))))))(((((.....)))))))..)).....((((((((.(((((((......))))))).)))))))) ( -45.60, z-score =  -3.48, R)
>droSec1.super_0 6154974 100 - 21120651
CCAGCUUGAGUGGUGG---UCGAGUCUUGACUGCCACUUUGCUCACGUCGAGCAGAGUUGUCGCAGCGAUUGCUGCUGCAGUAGUUGUUGCAGUUACAGUCGC
.((((((((((((..(---((((...)))))..))))))(((((.....))))))))))).....(((((((..(((((((......)))))))..))))))) ( -47.40, z-score =  -3.75, R)
>droYak2.chr3L 14096257 100 - 24197627
CCAGUUUAACAGGUGG---UUUAGUCUUCACUGCCGCUUUGCUAACAUCGAGCAGCGUGGCCGCAGCGACUGCUGCUGCAGUUGGUGUUGCAGUUACAGUUGC
...........(((((---........)))))(((((.(((((.......))))).)))))....(((((((..(((((((......)))))))..))))))) ( -36.60, z-score =  -0.59, R)
>droEre2.scaffold_4784 14000480 100 - 25762168
CCAGCUUAAGAGGGGG---UUUAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGAGUUGUCGCAGCGACUGCUGCUGCAGUUGUUGAUGCAGUUGCAGUUGC
...((......((.((---((.......)))).))(((((((((.....)))))))))....)).((((((((.((((((........)))))).)))))))) ( -43.60, z-score =  -2.70, R)
>droAna3.scaffold_13337 11358500 91 + 23293914
CUGCCUUGAAUGGCGGCGUCCUGGUUUUCAACAUCACCUUGCCCACAUCGAGGAGCGUGGCCGCCGCAGCAGCGGUCGCCGUGGCAGUCGC------------
(((((.((...(((.(((((((.(.......((......)).......).)))).))).)))(((((....)))))...)).)))))....------------ ( -33.14, z-score =   0.67, R)
>dp4.chrXR_group8 6783094 88 + 9212921
UCAUCUUGAGGGUUAGCGGACGGGAAUUGAUUGCACCUCCUGGUGCUGGUGCUACCGCUGUGGCUGUGGAUGUGGCUGCAGCUGUAGC---------------
............((((((..(((((..((....))..))))).)))))).(((((.((((..((..(....)..))..)))).)))))--------------- ( -34.00, z-score =  -1.24, R)
>droPer1.super_24 624718 88 - 1556852
UCAUCUUGAGGGUUAGCGGACGGGAAUUGAUUGCACCUCCUGGUGCUGGUGCUACCGCUGUGGCUGUGGAUGUGGCUGCAGCUGUAGC---------------
............((((((..(((((..((....))..))))).)))))).(((((.((((..((..(....)..))..)))).)))))--------------- ( -34.00, z-score =  -1.24, R)
>droMoj3.scaffold_6680 17721788 103 - 24764193
CAUCCUUCACAGCUGCAGCGCGCGGUUUGGCAGUCGCCUUGGCCUCAACCACAGUCGCCGUUGCAAUGGCUGUUGUUGCUGUUGCUGGCAUUGCAGCCAUUGC
...........((.((((((.(((..((((..(..((....))..)..))).)..)))))))))(((((((((...((((......))))..))))))))))) ( -41.10, z-score =  -0.65, R)
>consensus
CCAGCUUGAGAGGUGG___UCGAGUCUUGACUGCCACUUUGCUCACAUCGAGCAGCGUUGUCGCAGCGACUGCUGCUGCAGUUGUUGUUGCAGUU_CAGU_GC
........................................................(((((.(((((....))))).)))))..................... (-10.83 =  -9.13 +  -1.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:24:58 2011