Locus 9671

Sequence ID dm3.chr3R
Location 8,114,360 – 8,114,483
Length 123
Max. P 0.771870
window13264 window13265 window13266

overview

Window 4

Location 8,114,360 – 8,114,458
Length 98
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 89.60
Shannon entropy 0.17020
G+C content 0.49834
Mean single sequence MFE -31.10
Consensus MFE -21.80
Energy contribution -21.80
Covariance contribution 0.00
Combinations/Pair 1.08
Mean z-score -2.36
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.746510
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8114360 98 + 27905053
UGCUCAUCCCGAAAAGUUAAGAUACCCAGAGAUACUCGGGAUACUGGGAUGGGAUGGGUUGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCA
.((((((((((...(((....((.(((.(((...)))))))))))....))))))))))(((((((((....)))))))))....((.(....).)). ( -34.90, z-score =  -2.50, R)
>droSim1.chr3R 14243629 93 - 27517382
UGUUCAUCCCGAAAAGUUAAGAUACCCAGAGAUACUCGGGAUACUGGGAUGGGAUG-----CAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCA
..(((((((((....((....)).(((.(((...))))))....))))))))).((-----(((((((....)))))))))....((.(....).)). ( -29.40, z-score =  -1.86, R)
>droSec1.super_0 7288099 93 - 21120651
UGUUCAUCCCGAAAAGUUAAGAUACCCAGAGAUACUCGGGAUACUGGGAUGGGAUG-----CAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCA
..(((((((((....((....)).(((.(((...))))))....))))))))).((-----(((((((....)))))))))....((.(....).)). ( -29.40, z-score =  -1.86, R)
>droYak2.chr3R 12431765 83 + 28832112
CGCUCAUCCCGAAAAGUUAAGAUACCCAGA--UACUCGGGAU--------GGGAUG-----CAGCUCUAGAUAGAGCUGCGAUAGGCGCAUAUGGGCA
..((((((((((..................--...)))))))--------))).((-----(((((((....)))))))))....((.(....).)). ( -32.60, z-score =  -3.11, R)
>droEre2.scaffold_4770 4244962 85 - 17746568
UGUUCAUCCCGAGAAGUUAAGAUACCCAGAGAUACUCGGGAU--------GGGAUG-----CAGCUCCAGAUAGAGUUGCGAUAGGCGCAUAUGGGCA
..(((((((((((...((..(.....)..))...))))))))--------))).((-----((((((......))))))))....((.(....).)). ( -29.20, z-score =  -2.45, R)
>consensus
UGUUCAUCCCGAAAAGUUAAGAUACCCAGAGAUACUCGGGAUACUGGGAUGGGAUG_____CAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCA
.(((((((((.....((....)).(((.(((...))))))..........))))).......((((((....))))))(((.....)))....)))). (-21.80 = -21.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,114,392 – 8,114,483
Length 91
Sequences 8
Columns 100
Reading direction forward
Mean pairwise identity 80.76
Shannon entropy 0.35818
G+C content 0.51740
Mean single sequence MFE -29.19
Consensus MFE -21.40
Energy contribution -22.04
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -1.23
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.22
SVM RNA-class probability 0.599034
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8114392 91 + 27905053
-------UACUCGGGAUACU-GGGAUGGGAUGGGUUGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCA-AGUUCUUUU
-------..(((((....))-)))..(((((..(((((((((((....)))))))))))..(((.(((.((((.....)))).)))))).-.)))))... ( -32.00, z-score =  -2.17, R)
>droSim1.chr3R 14243661 86 - 27517382
-------UACUCGGGAUACU-GGGAUGGGA-----UGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCA-AGUUCUUUU
-------..(((((....))-)))..((((-----(((((((((....)))))))).....(((.(((.((((.....)))).)))))).-.)))))... ( -29.00, z-score =  -1.69, R)
>droSec1.super_0 7288131 86 - 21120651
-------UACUCGGGAUACU-GGGAUGGGA-----UGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCA-AGUUCUUUU
-------..(((((....))-)))..((((-----(((((((((....)))))))).....(((.(((.((((.....)))).)))))).-.)))))... ( -29.00, z-score =  -1.69, R)
>droYak2.chr3R 12431795 78 + 28832112
----------------UACUCGGGAUGGGA-----UGCAGCUCUAGAUAGAGCUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCA-AGUUCUUUU
----------------.....(((((....-----(((((((((....)))))))))....(((.(((.((((.....)))).)))))).-.)))))... ( -26.30, z-score =  -1.07, R)
>droEre2.scaffold_4770 4244994 78 - 17746568
----------------UACUCGGGAUGGGA-----UGCAGCUCCAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCG-AGUUCUUUU
----------------.(((((.(((((..-----((((((((......))))))))............((((.....))))))))).))-)))...... ( -26.70, z-score =  -1.29, R)
>droAna3.scaffold_13340 19406484 97 - 23697760
UACUCGGAUACUUGGAUGCU-CGCCUGCUCGAAGCUGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGU-UGCCUCUGUUGCA-AGUUCUUUU
.....(((.(((((.((((.-.((((((.....))(((((((((....)))))))))..))))))))..((((...-.))))......))-))))))... ( -32.10, z-score =  -0.38, R)
>dp4.chr2 22900791 80 + 30794189
-------------------UGGGGAUGGGGCGG-CUGCAGCUCUAGAUAGAGUCGCGAUAGGCGCAUAUGGGCAGUGUGCCUCUGUUGCACAGUUCUUUC
-------------------.((((((...((((-((((.(((((....))))).)))..((((((((.......))))))))..)))))...)))))).. ( -29.20, z-score =  -0.79, R)
>droPer1.super_3 5676417 80 + 7375914
-------------------UGGGGAUGGGGCGG-CUGCAGCUCUAGAUAGAGUCGCGAUAGGCGCAUAUGGGCAGUGUGCCUCUGUUGCACAGUUCUUUC
-------------------.((((((...((((-((((.(((((....))))).)))..((((((((.......))))))))..)))))...)))))).. ( -29.20, z-score =  -0.79, R)
>consensus
________________UACU_GGGAUGGGA_____UGCAGCUCUAGAUAGAGUUGCGAUAGGCGCAUAUGGGCAGUUUGCCUCUGUUGCA_AGUUCUUUU
.....................(((((.........(((((((((....)))))))))....(((.(((.((((.....)))).))))))...)))))... (-21.40 = -22.04 +   0.64)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,114,392 – 8,114,483
Length 91
Sequences 8
Columns 100
Reading direction reverse
Mean pairwise identity 80.76
Shannon entropy 0.35818
G+C content 0.51740
Mean single sequence MFE -19.41
Consensus MFE -15.98
Energy contribution -15.58
Covariance contribution -0.40
Combinations/Pair 1.18
Mean z-score -1.16
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.64
SVM RNA-class probability 0.771870
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8114392 91 - 27905053
AAAAGAACU-UGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUAGAGCUGCAACCCAUCCCAUCCC-AGUAUCCCGAGUA-------
......(((-((((...(.(((.....))))...))).......(((.((((....)))).)))...............-........)))).------- ( -16.80, z-score =  -1.28, R)
>droSim1.chr3R 14243661 86 + 27517382
AAAAGAACU-UGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUAGAGCUGCA-----UCCCAUCCC-AGUAUCCCGAGUA-------
......(((-((((...(.(((.....))))...))).......(((.((((....)))).))).-----.........-........)))).------- ( -16.80, z-score =  -0.99, R)
>droSec1.super_0 7288131 86 + 21120651
AAAAGAACU-UGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUAGAGCUGCA-----UCCCAUCCC-AGUAUCCCGAGUA-------
......(((-((((...(.(((.....))))...))).......(((.((((....)))).))).-----.........-........)))).------- ( -16.80, z-score =  -0.99, R)
>droYak2.chr3R 12431795 78 - 28832112
AAAAGAACU-UGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAGCUCUAUCUAGAGCUGCA-----UCCCAUCCCGAGUA----------------
......(((-((((...(.(((.....))))...))).......((((((((....)))))))).-----.........)))).---------------- ( -23.40, z-score =  -2.99, R)
>droEre2.scaffold_4770 4244994 78 + 17746568
AAAAGAACU-CGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUGGAGCUGCA-----UCCCAUCCCGAGUA----------------
......(((-((((...(.(((.....))))...))).......(((.((((....)))).))).-----.........)))).---------------- ( -19.70, z-score =  -1.75, R)
>droAna3.scaffold_13340 19406484 97 + 23697760
AAAAGAACU-UGCAACAGAGGCA-ACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUAGAGCUGCAGCUUCGAGCAGGCG-AGCAUCCAAGUAUCCGAGUA
......(((-((..((.(.(((.-...)))).....(((((...(((.((((....)))).))).((.....)))))))-.........))...))))). ( -26.00, z-score =  -0.38, R)
>dp4.chr2 22900791 80 - 30794189
GAAAGAACUGUGCAACAGAGGCACACUGCCCAUAUGCGCCUAUCGCGACUCUAUCUAGAGCUGCAG-CCGCCCCAUCCCCA-------------------
....((...(((((...(.(((.....))))...)))))...))(((.((((....)))).)))..-..............------------------- ( -17.90, z-score =  -0.45, R)
>droPer1.super_3 5676417 80 - 7375914
GAAAGAACUGUGCAACAGAGGCACACUGCCCAUAUGCGCCUAUCGCGACUCUAUCUAGAGCUGCAG-CCGCCCCAUCCCCA-------------------
....((...(((((...(.(((.....))))...)))))...))(((.((((....)))).)))..-..............------------------- ( -17.90, z-score =  -0.45, R)
>consensus
AAAAGAACU_UGCAACAGAGGCAAACUGCCCAUAUGCGCCUAUCGCAACUCUAUCUAGAGCUGCA_____UCCCAUCCC_AGUA________________
....((....((((...(.(((.....))))...))))....))(((.((((....)))).))).................................... (-15.98 = -15.58 +  -0.40)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:08:51 2011