Locus 8075

Sequence ID dm3.chr3L
Location 20,060,303 – 20,060,440
Length 137
Max. P 0.830179
window11113 window11114 window11115

overview

Window 3

Location 20,060,303 – 20,060,401
Length 98
Sequences 7
Columns 111
Reading direction forward
Mean pairwise identity 69.26
Shannon entropy 0.59620
G+C content 0.57419
Mean single sequence MFE -26.22
Consensus MFE -13.43
Energy contribution -15.09
Covariance contribution 1.66
Combinations/Pair 1.25
Mean z-score -1.02
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.56
SVM RNA-class probability 0.744494
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20060303 98 + 24543557
GCCAAGCGAACUUUUCCUUGACGCCCUUUAAGUCCCUGGCAACGCCACCUGCUGACAGGUGGAGUCCUCC--GCCUAGACACUUCCACCAGCCGGGAUGG-----------
..((((.((.....))))))...........(((((.(((....(((((((....))))))).(((....--.....)))..........))))))))..----------- ( -29.60, z-score =  -0.90, R)
>droAna3.scaffold_13337 18222811 110 - 23293914
GCCGGGCCAACUUUUCCUUGACGCC-UUUAAGUCCUUGGCAACACCACCUGCUGACAGGAGGAGUUCUCCCAAAUAAUAAAAAAAAAAAAGCCAAGAACCACCCGACCUCC
..((((.............(((...-.....)))((((((.......((((....)))).(((....)))....................)))))).....))))...... ( -26.10, z-score =  -1.94, R)
>droEre2.scaffold_4784 19800023 95 + 25762168
ACCAAGCGAACU-UUCCUUGACGCCCUCUAAGUCCCUGGCAACGCCACCUGCUGACAGGUGGAGUCCUCC--GCCUAGACACUCCCACAAGCCGAGGG-------------
..((((.((...-.))))))...(((((...(((...(((.((.(((((((....))))))).)).....--)))..))).((......))..)))))------------- ( -28.90, z-score =  -1.25, R)
>droYak2.chr3L 3694052 98 - 24197627
GCCAAGCGAACUUUUCCUUGACGCCCUUUAAGUCCCUGGCAACGCCACCUGCUGACAGGUGGAGUCCUCC--GCCUAGACACUUCCACAAGCCGGAAAGG-----------
..........(((((((..(((.........)))...(((....(((((((....))))))).(((....--.....)))..........))))))))))----------- ( -27.50, z-score =  -0.76, R)
>droSec1.super_97 53141 98 + 93343
GCCAGGCGAACUGUUCCUUGACGCCCUUUAAGUCCCUGGCAACGCCACCUGCUGACAAGUGGAGUCCUCC--GCCUAGACACUUCUACCAGCCGGGUUGG-----------
((((((.((.......(((((......)))))))))))))....((((((((((....(((((....)))--)).((((....)))).))).)))).)))----------- ( -30.91, z-score =  -0.76, R)
>droSim1.chr3L 19353331 98 + 22553184
GCCGAGCGAACUUUUCCUUGACGCCCUUUAAGUCCCUGGCAACGCCACCUGCUGACAGGUGGAGUCCUCC--GCCUAGACACUUCUACCAGCCGGGUUGG-----------
((((((.((.....)))))(((.........)))...)))....((((((((((..(((((((....)))--))))(((....)))..))).)))).)))----------- ( -29.20, z-score =  -0.42, R)
>droWil1.scaffold_180698 1214438 83 + 11422946
----------------CAGCAAACUUUUUGAGGCCCUU-CGCCUUUACACGCCCUCAAAAAAAGACCUCCACCGCUCCA-ACGUCAAUCCGUCGCCCAUUG----------
----------------..((....(((((((((.....-.((........)))))))))))..(((......((.....-.)).......)))))......---------- ( -11.32, z-score =  -1.07, R)
>consensus
GCCAAGCGAACUUUUCCUUGACGCCCUUUAAGUCCCUGGCAACGCCACCUGCUGACAGGUGGAGUCCUCC__GCCUAGACACUUCCACCAGCCGGGAAGG___________
..................................((((((....(((((((....))))))).(((...........)))..........))))))............... (-13.43 = -15.09 +   1.66)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,060,303 – 20,060,401
Length 98
Sequences 7
Columns 111
Reading direction reverse
Mean pairwise identity 69.26
Shannon entropy 0.59620
G+C content 0.57419
Mean single sequence MFE -34.45
Consensus MFE -20.38
Energy contribution -20.25
Covariance contribution -0.13
Combinations/Pair 1.68
Mean z-score -0.66
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.48
SVM RNA-class probability 0.712553
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20060303 98 - 24543557
-----------CCAUCCCGGCUGGUGGAAGUGUCUAGGC--GGAGGACUCCACCUGUCAGCAGGUGGCGUUGCCAGGGACUUAAAGGGCGUCAAGGAAAAGUUCGCUUGGC
-----------(((((......)))))((((.(((.(((--....(((.(((((((....))))))).))))))))).)))).......((((((((.....)).)))))) ( -36.70, z-score =  -0.58, R)
>droAna3.scaffold_13337 18222811 110 + 23293914
GGAGGUCGGGUGGUUCUUGGCUUUUUUUUUUUUAUUAUUUGGGAGAACUCCUCCUGUCAGCAGGUGGUGUUGCCAAGGACUUAAA-GGCGUCAAGGAAAAGUUGGCCCGGC
....(((((((((((((((((.......((((((.....))))))(((.((.((((....)))).)).)))))))))))))....-(((...........))).))))))) ( -37.50, z-score =  -1.47, R)
>droEre2.scaffold_4784 19800023 95 - 25762168
-------------CCCUCGGCUUGUGGGAGUGUCUAGGC--GGAGGACUCCACCUGUCAGCAGGUGGCGUUGCCAGGGACUUAGAGGGCGUCAAGGAA-AGUUCGCUUGGU
-------------(((((.((((....))))((((.(((--....(((.(((((((....))))))).))))))..))))...)))))..(((((((.-...)).))))). ( -36.80, z-score =  -0.47, R)
>droYak2.chr3L 3694052 98 + 24197627
-----------CCUUUCCGGCUUGUGGAAGUGUCUAGGC--GGAGGACUCCACCUGUCAGCAGGUGGCGUUGCCAGGGACUUAAAGGGCGUCAAGGAAAAGUUCGCUUGGC
-----------........((((....((((.(((.(((--....(((.(((((((....))))))).))))))))).))))...))))((((((((.....)).)))))) ( -37.10, z-score =  -0.95, R)
>droSec1.super_97 53141 98 - 93343
-----------CCAACCCGGCUGGUAGAAGUGUCUAGGC--GGAGGACUCCACUUGUCAGCAGGUGGCGUUGCCAGGGACUUAAAGGGCGUCAAGGAACAGUUCGCCUGGC
-----------.....(((.((((.........)))).)--))..(((.(((((((....))))))).)))(((((((((.........)))..(((....))).)))))) ( -34.40, z-score =   0.04, R)
>droSim1.chr3L 19353331 98 - 22553184
-----------CCAACCCGGCUGGUAGAAGUGUCUAGGC--GGAGGACUCCACCUGUCAGCAGGUGGCGUUGCCAGGGACUUAAAGGGCGUCAAGGAAAAGUUCGCUCGGC
-----------((..((((.((((.........)))).)--((..(((.(((((((....))))))).))).)).))).......(((((.............))))))). ( -35.92, z-score =  -0.57, R)
>droWil1.scaffold_180698 1214438 83 - 11422946
----------CAAUGGGCGACGGAUUGACGU-UGGAGCGGUGGAGGUCUUUUUUUGAGGGCGUGUAAAGGCG-AAGGGCCUCAAAAAGUUUGCUG----------------
----------.....(((((((......)))-).((((....((((((((((.......((.(....).)))-))))))))).....))))))).---------------- ( -22.71, z-score =  -0.58, R)
>consensus
___________CCAUCCCGGCUGGUGGAAGUGUCUAGGC__GGAGGACUCCACCUGUCAGCAGGUGGCGUUGCCAGGGACUUAAAGGGCGUCAAGGAAAAGUUCGCUUGGC
...............((((((...((((....)))).........(((.(((((((....))))))).)))))).))).......(((((.............)))))... (-20.38 = -20.25 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,060,343 – 20,060,440
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 75.58
Shannon entropy 0.43831
G+C content 0.60443
Mean single sequence MFE -35.17
Consensus MFE -25.47
Energy contribution -24.90
Covariance contribution -0.57
Combinations/Pair 1.46
Mean z-score -1.21
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.83
SVM RNA-class probability 0.830179
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 20060343 97 - 24543557
AGCCCGUCGAGCCGCCCGAGAAGUACCUUGGAAC-ACCAGCCAU-CCCGGCUGGUGGAAG-UGUCUAGGCGGAGGACUCCACCUGUCAGCAGGUGGCGUU
...(((((.((.((((((((......)))))..(-(((((((..-...))))))))...)-)).)).)))))..(((.(((((((....))))))).))) ( -48.90, z-score =  -3.70, R)
>droEre2.scaffold_4784 19800062 84 - 25762168
---------AGCAGCCCGAGAAGU--CCUGGAGC-ACCAGCC---CUCGGCUUGUGGGAG-UGUCUAGGCGGAGGACUCCACCUGUCAGCAGGUGGCGUU
---------.((.((((.(.((((--(..((.((-....)))---)..))))).).)).)-)......))....(((.(((((((....))))))).))) ( -32.40, z-score =   0.25, R)
>droYak2.chr3L 3694092 88 + 24197627
---------AGCAGCCCGAGAAGUACCUUGGAAC-ACCAGCCUU-UCCGGCUUGUGGAAG-UGUCUAGGCGGAGGACUCCACCUGUCAGCAGGUGGCGUU
---------.((...(((((......)))))..(-((.((((..-...)))).)))....-.......))....(((.(((((((....))))))).))) ( -32.70, z-score =  -0.67, R)
>droSec1.super_97 53181 88 - 93343
---------AGCAGCCCGAGAAGUACCUUGGAAC-ACCAGCCAA-CCCGGCUGGUAGAAG-UGUCUAGGCGGAGGACUCCACUUGUCAGCAGGUGGCGUU
---------.((...(((((......)))))...-(((((((..-...))))))).....-.......))....(((.(((((((....))))))).))) ( -33.20, z-score =  -1.22, R)
>droSim1.chr3L 19353371 88 - 22553184
---------AGCAGCCCGAGAAGUACCUUGGAAC-ACCAGCCAA-CCCGGCUGGUAGAAG-UGUCUAGGCGGAGGACUCCACCUGUCAGCAGGUGGCGUU
---------.((...(((((......)))))...-(((((((..-...))))))).....-.......))....(((.(((((((....))))))).))) ( -35.90, z-score =  -1.87, R)
>droWil1.scaffold_180698 1214461 91 - 11422946
---------AGGACCUCAGCAAGUGCCCAGCAACUGUCAGCAAUGGGCGACGGAUUGACGUUGGAGCGGUGGAGGUCUUUUUUUGAGGGCGUGUAAAGGC
---------((((((((....(.((((((((..(((((.((.....)))))))......))))).))).).)))))))).........((.(....).)) ( -27.90, z-score =  -0.06, R)
>consensus
_________AGCAGCCCGAGAAGUACCUUGGAAC_ACCAGCCAU_CCCGGCUGGUGGAAG_UGUCUAGGCGGAGGACUCCACCUGUCAGCAGGUGGCGUU
...............(((........((((((...(((((((......)))))))........)))))))))..(((.(((((((....))))))).))) (-25.47 = -24.90 +  -0.57)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:38:59 2011