Locus 2150

Sequence ID dm3.chr2L
Location 16,626,920 – 16,627,056
Length 136
Max. P 0.889465
window2960 window2961 window2962 window2963

overview

Window 0

Location 16,626,920 – 16,627,019
Length 99
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 86.98
Shannon entropy 0.22602
G+C content 0.46000
Mean single sequence MFE -25.70
Consensus MFE -21.54
Energy contribution -22.14
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.889465
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16626920 99 + 23011544
GGGUCGUAAAAA-GAAAAGUGCAUAAAAUGUCUUGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUGUAUAUGUAUAUAUA
............-.....(((((((..((..((((((..((((((((........))))))))(((.....))))))).))..))...)))))))..... ( -29.10, z-score =  -2.67, R)
>droEre2.scaffold_4845 19697468 98 + 22589142
GGGUCGUAAAAAAGAAAAGUGCAUAAAAUGUCUUGCCAGUUCCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUAUGUACAUAUACU--
..................(((((((...(((((...(((((.......))))).)))))(((.(((.....)))))).......))))))).......-- ( -23.50, z-score =  -0.92, R)
>droYak2.chr2R 16662471 93 - 21139217
GGGUCGUAAAAA-GAAAAGUGCAUAAAAUGUCUUGUCAGUGGCUGUCAAACUGCAGGCAGUCAGCCAGCCAGGCGACACAGGUAUACCUACAUA------
..(((((.....-((.(((.((((...))))))).))..((((((.(..((((....))))..).)))))).)))))..(((....))).....------ ( -26.90, z-score =  -1.57, R)
>droSec1.super_7 274096 83 + 3727775
GGGUCGUAAAAA-GAAAAGUGCAUAAAAUGUCUUGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUA----------------
..(((((.....-((.(((.((((...))))))).))..((((((.(..((((....))))..).)))))).))))).......---------------- ( -24.50, z-score =  -2.00, R)
>droSim1.chr2L 16322541 83 + 22036055
GGGUCGUAAAAA-GAAAAGUGCAUAAAAUGUCUUGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUA----------------
..(((((.....-((.(((.((((...))))))).))..((((((.(..((((....))))..).)))))).))))).......---------------- ( -24.50, z-score =  -2.00, R)
>consensus
GGGUCGUAAAAA_GAAAAGUGCAUAAAAUGUCUUGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAU___UA__UA______
..(((((......((.(((.((((...))))))).))..((((((.(..((((....))))..).)))))).)))))....................... (-21.54 = -22.14 +   0.60)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,626,920 – 16,627,019
Length 99
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 86.98
Shannon entropy 0.22602
G+C content 0.46000
Mean single sequence MFE -21.40
Consensus MFE -18.14
Energy contribution -18.38
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.884264
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16626920 99 - 23011544
UAUAUAUACAUAUACAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACAAGACAUUUUAUGCACUUUUC-UUUUUACGACCC
..............((((...(((((.(.((((((...(((((....)))))...))))))..)....)))))..))))........-............ ( -21.70, z-score =  -2.61, R)
>droEre2.scaffold_4845 19697468 98 - 22589142
--AGUAUAUGUACAUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGGAACUGGCAAGACAUUUUAUGCACUUUUCUUUUUUACGACCC
--.((((((....))))))..((((((((.....)))....((((...(((((.....))))))))).)))))........................... ( -20.10, z-score =  -0.03, R)
>droYak2.chr2R 16662471 93 + 21139217
------UAUGUAGGUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUGCAGUUUGACAGCCACUGACAAGACAUUUUAUGCACUUUUC-UUUUUACGACCC
------.......(((((...(((((.(.((((((...(((((....)))))...))))))..)....)))))..))))).......-............ ( -25.20, z-score =  -1.78, R)
>droSec1.super_7 274096 83 - 3727775
----------------UACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACAAGACAUUUUAUGCACUUUUC-UUUUUACGACCC
----------------...((.(((((..((((((...(((((....)))))...)))))).)))))))..................-............ ( -20.00, z-score =  -2.21, R)
>droSim1.chr2L 16322541 83 - 22036055
----------------UACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACAAGACAUUUUAUGCACUUUUC-UUUUUACGACCC
----------------...((.(((((..((((((...(((((....)))))...)))))).)))))))..................-............ ( -20.00, z-score =  -2.21, R)
>consensus
______UA__UA___AUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACAAGACAUUUUAUGCACUUUUC_UUUUUACGACCC
...................((.(((((..((((((...(((((....)))))...)))))).)))))))............................... (-18.14 = -18.38 +   0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,626,952 – 16,627,056
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 78.51
Shannon entropy 0.37807
G+C content 0.46967
Mean single sequence MFE -28.96
Consensus MFE -16.56
Energy contribution -17.16
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.81
SVM RNA-class probability 0.824711
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16626952 104 + 23011544
UGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUGUAUAUGUAUAUAUAUGUACAUAGGUAGAAAACAGCUAAAAAGCAUAGAGCU
((((..((((((((........))))))))(((.....)))))))....(((((((((((....)))))))))))...........(((....)))........ ( -30.90, z-score =  -2.09, R)
>droEre2.scaffold_4845 19697501 103 + 22589142
UGCCAGUUCCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUAUGUACAUAUACUCGUAUAUAGUAGGUAGAAACGGCUAA-AAUCGUAGAGCU
.(((.(((.((..(..((((((.((.(((.(((.....))))))...(((((((....))))))).)).)))))).)..)).))))))...-............ ( -28.10, z-score =  -1.27, R)
>droYak2.chr2R 16662503 97 - 21139217
UGUCAGUGGCUGUCAAACUGCAGGCAGUCAGCCAGCCAGGCGACACAGGUAUACCUACAUACAUAUGU------AGGUAGAAAG-GGCUAAGAAGCGUAGAGCC
((((..((((((((........))))))))(((.....)))))))..(((.(((((((((....))))------))))).....-.(((....))).....))) ( -34.40, z-score =  -2.66, R)
>droSec1.super_7 274128 86 + 3727775
UGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUAUGUA------------------GGUAGAAAACGUCUAAAAAGCAUAGAGCU
((((..((((((((........))))))))(((.....)))))))..(((.(((((.------------------..((((.....))))....)))))..))) ( -25.70, z-score =  -1.98, R)
>droSim1.chr2L 16322573 86 + 22036055
UGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUAUGUA------------------GGUAGAAAACGUCUAAAAAGCAUAGAGCU
((((..((((((((........))))))))(((.....)))))))..(((.(((((.------------------..((((.....))))....)))))..))) ( -25.70, z-score =  -1.98, R)
>consensus
UGUCAGUGGCUGUCAAACUGUAGGCAGUCAGCCAGCCAGGCGACACAGGUAUAUGUA__UA_A____U_______GGUAGAAAACGGCUAAAAAGCAUAGAGCU
((((..((((((((........))))))))(((.....)))))))........................................................... (-16.56 = -17.16 +   0.60)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,626,952 – 16,627,056
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 78.51
Shannon entropy 0.37807
G+C content 0.46967
Mean single sequence MFE -25.96
Consensus MFE -17.36
Energy contribution -17.64
Covariance contribution 0.28
Combinations/Pair 1.11
Mean z-score -1.64
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.822074
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16626952 104 - 23011544
AGCUCUAUGCUUUUUAGCUGUUUUCUACCUAUGUACAUAUAUAUACAUAUACAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACA
........(((....)))...........((((((........))))))..........(((((..((((((...(((((....)))))...)))))).))))) ( -23.70, z-score =  -0.85, R)
>droEre2.scaffold_4845 19697501 103 - 22589142
AGCUCUACGAUU-UUAGCCGUUUCUACCUACUAUAUACGAGUAUAUGUACAUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGGAACUGGCA
............-...(((((((((...........(((.((((((....)))))).)))((((.(((...(((.....)))..)))..)))))))))).))). ( -28.10, z-score =  -1.24, R)
>droYak2.chr2R 16662503 97 + 21139217
GGCUCUACGCUUCUUAGCC-CUUUCUACCU------ACAUAUGUAUGUAGGUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUGCAGUUUGACAGCCACUGACA
(((..((((((....))).-.....(((((------((((....))))))))).....)))..)))((((((...(((((....)))))...))))))...... ( -35.60, z-score =  -3.37, R)
>droSec1.super_7 274128 86 - 3727775
AGCUCUAUGCUUUUUAGACGUUUUCUACC------------------UACAUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACA
(((.....)))...((((.....))))..------------------............(((((..((((((...(((((....)))))...)))))).))))) ( -21.20, z-score =  -1.38, R)
>droSim1.chr2L 16322573 86 - 22036055
AGCUCUAUGCUUUUUAGACGUUUUCUACC------------------UACAUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACA
(((.....)))...((((.....))))..------------------............(((((..((((((...(((((....)))))...)))))).))))) ( -21.20, z-score =  -1.38, R)
>consensus
AGCUCUAUGCUUUUUAGCCGUUUUCUACC_______A____U_UA__UACAUAUACCUGUGUCGCCUGGCUGGCUGACUGCCUACAGUUUGACAGCCACUGACA
(((.....)))................................................(((((..((((((...(((((....)))))...)))))).))))) (-17.36 = -17.64 +   0.28)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:45:46 2011