Locus 9228

Sequence ID dm3.chr3R
Location 5,022,562 – 5,022,704
Length 142
Max. P 0.986440
window12647 window12648 window12649

overview

Window 7

Location 5,022,562 – 5,022,670
Length 108
Sequences 7
Columns 120
Reading direction forward
Mean pairwise identity 65.08
Shannon entropy 0.67306
G+C content 0.40541
Mean single sequence MFE -24.70
Consensus MFE -8.14
Energy contribution -9.70
Covariance contribution 1.56
Combinations/Pair 1.57
Mean z-score -1.53
Structure conservation index 0.33
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.642164
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5022562 108 + 27905053
CCUCAACAAAAGCC--CCAACAAAAUCCAAUU-GCAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGG--GAGAAUAAUUGAAGCAUUG-------CAACCGGAAGGAAAAUUGGUUGAGG
(((((((.......--..............((-((......))))((.((((((((((.........--........)))))))))))-------)..((....)).......))))))) ( -28.83, z-score =  -2.96, R)
>droSim1.chr3R 11228120 107 - 27517382
CCUCAG-AAAAGCC--CCAACAAAAUCCAAUU-GCAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGG--GAGAAUAAUUGAAGCAUUG-------CAACCGGAAGGAAAAUUGGUUGAGG
((((((-....(..--....).....((((((-............((.((((((((((.........--........)))))))))))-------)..((....))..)))))))))))) ( -26.93, z-score =  -2.28, R)
>droSec1.super_0 4261151 107 - 21120651
CCUCAG-AAAAGCC--CCAACAAAAUCCAAUU-GCAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGG--GAGAAUAAUUGAAGCAUUG-------CAACCGGAAGGAAAAUUAGUUGAGG
((((((-.......--..............((-((......))))((.((((((((((.........--........)))))))))))-------)..((....))........)))))) ( -25.13, z-score =  -2.42, R)
>droYak2.chr3R 9071828 107 + 28832112
CCCCAG-AAAAGCC--CCAACAAAAUCCAAUU-GCAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGG--GGGAAUAAUUGAAGCAUUG-------CAACCGGAAGGAAAAUUGGUUGAGG
......-.....((--.((((.........((-((......))))((.((((((((((.........--........)))))))))))-------)..((....)).......)))).)) ( -24.23, z-score =  -0.57, R)
>droEre2.scaffold_4770 1167699 107 - 17746568
CACCAG-CAAAGCC--CCAACAAAAUCCAAUU-GCAUUUAAGUAAGCCAAUGCUUGAAGUAAAUAGG--GAGAAUAAUUGAAGCAUUG-------CAACCGGAAGGAAAAUUGGUUGAGG
.(((((-(((.((.--.(((.....(((..((-((.((((((((......))))))))))))....)--))......)))..)).)))-------)..((....)).....))))..... ( -27.50, z-score =  -2.39, R)
>droPer1.super_3 310934 85 - 7375914
-----------------------------CCUCACCCCAGGGGAAACCUUUUGAUUGAAUAAAGAUGUGGCAAAAAGGUAAGCCGCCG------CCACUUGAACGAAGAAUCGGCGGAAU
-----------------------------.....((((((((....))))..((((..........(((((.....((....))...)------))))..........)))))).))... ( -22.35, z-score =  -0.80, R)
>droMoj3.scaffold_6540 23920147 112 + 34148556
---CAUAAAAAGCUAAUUGCUAUGCUAUAGUUUGCCUUUUGGAGAAUCGA---AUCAAAGCAAGACG--GAAAUUGCUUUUCGCUCUUAAUUCAUCGACCUGUCGAAACAUCACUUGAAA
---..(((((.((.....(((((...)))))..)).)))))((((..(((---(...((((((....--....)))))))))).))))......((((....)))).............. ( -17.90, z-score =   0.70, R)
>consensus
CCUCAG_AAAAGCC__CCAACAAAAUCCAAUU_GCAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGG__GAGAAUAAUUGAAGCAUUG_______CAACCGGAAGGAAAAUUGGUUGAGG
....................................(((((.(((..(((((((((((...................)))))))))))..........((....))....))).))))). ( -8.14 =  -9.70 +   1.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,022,593 – 5,022,704
Length 111
Sequences 7
Columns 118
Reading direction forward
Mean pairwise identity 67.35
Shannon entropy 0.64178
G+C content 0.37175
Mean single sequence MFE -26.82
Consensus MFE -8.54
Energy contribution -10.30
Covariance contribution 1.76
Combinations/Pair 1.57
Mean z-score -2.71
Structure conservation index 0.32
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.24
SVM RNA-class probability 0.986440
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5022593 111 + 27905053
CAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGGGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAA-AAUUGGUUGAG-GCGAAGCUAAAAUGGCAUUUUAAAC-----GAUAGUUUUC
(((((.(((..(((((((((((((.................)))))))))).(((((((......-..))))))).)-))...))).))))).......((((-----....)))).. ( -28.03, z-score =  -3.04, R)
>droSim1.chr3R 11228150 111 - 27517382
CAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGGGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAA-AAUUGGUUGAG-GCGAAGCUAAAAUGGCAUUUUAAAC-----GAAAGUUUUC
(((((.(((..(((((((((((((.................)))))))))).(((((((......-..))))))).)-))...))).))))).......((((-----....)))).. ( -31.03, z-score =  -4.10, R)
>droSec1.super_0 4261181 111 - 21120651
CAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGGGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAA-AAUUAGUUGAG-GCGAAGCUAAAAUGGCAUUUUAAAC-----GAAAGUUUUC
(((((.(((..(((((((((((((.................))))))))))....((....))..-..........)-))...))).))))).......((((-----....)))).. ( -29.63, z-score =  -3.90, R)
>droYak2.chr3R 9071858 111 + 28832112
CAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGGGGGAAUAAUUGAAGCAUUGCAACCGGAAGGAA-AAUUGGUUGAG-GCGAGGCUAAAAUGGCAUUUUAAAC-----GAAAGUUUUC
(((((.(((..(((((((((((((.................)))))))))).(((((((......-..))))))).)-))...))).))))).......((((-----....)))).. ( -32.13, z-score =  -4.21, R)
>droEre2.scaffold_4770 1167729 111 - 17746568
CAUUUAAGUAAGCCAAUGCUUGAAGUAAAUAGGGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAA-AAUUGGUUGAG-GCGAGGCUAAAAUGGCAUUUUAAAC-----GAAAGUUUUC
(((((.(((..((((((((((.((.................)).))))))).(((((((......-..))))))).)-))...))).))))).......((((-----....)))).. ( -28.03, z-score =  -3.11, R)
>droPer1.super_3 310958 96 - 7375914
-----------------AUUGAAUAAAGAUGUGGCAAAAAGGUAAGCCGCCGCCACUUGAACGAAGAAUCGGCGGAAUACAAUCGGGAAAUGCCAUUUAAAAC-----GAAACUUUUU
-----------------.............((((((.....(((..((((((...(((.....)))...))))))..)))..........)))))).......-----.......... ( -20.76, z-score =  -0.81, R)
>droMoj3.scaffold_6540 23920178 109 + 34148556
------CCUUUUGGAGAAUCGAAUCAAAGCAAGACGGAAA--UUGCUUUUCGCU-CUUAAUUCAUCGACCUGUCGAAACAUCACUUGAAAUGUUACCAAAAAUCAGUUGACACAUUUC
------..(((((((((..((((...((((((........--)))))))))).)-)).......((((....))))(((((........))))).))))))................. ( -18.10, z-score =   0.24, R)
>consensus
CAUUUAAGUAAGCCAAUGCUUCAAGUAAAUAGGGAGAAUAAUUGAAGCAUUGCAACCGGAAGGAA_AAUUGGUUGAG_GCGAAGCUAAAAUGGCAUUUUAAAC_____GAAAGUUUUC
...........(((((((((((((.................))))))))).....((....)).....((((((........))))))..))))........................ ( -8.54 = -10.30 +   1.76)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,022,593 – 5,022,704
Length 111
Sequences 7
Columns 118
Reading direction reverse
Mean pairwise identity 67.35
Shannon entropy 0.64178
G+C content 0.37175
Mean single sequence MFE -21.00
Consensus MFE -6.41
Energy contribution -8.09
Covariance contribution 1.68
Combinations/Pair 1.50
Mean z-score -2.51
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.76
SVM RNA-class probability 0.966159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 5022593 111 - 27905053
GAAAACUAUC-----GUUUAAAAUGCCAUUUUAGCUUCGC-CUCAACCAAUU-UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCCCUAUUUACUUGAAGCAUUGGCUUACUUAAAUG
.........(-----((((((...(((.............-..(((((....-........))))).((((((((((.((...........)).)))))))))))))....))))))) ( -22.30, z-score =  -3.80, R)
>droSim1.chr3R 11228150 111 + 27517382
GAAAACUUUC-----GUUUAAAAUGCCAUUUUAGCUUCGC-CUCAACCAAUU-UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCCCUAUUUACUUGAAGCAUUGGCUUACUUAAAUG
.........(-----((((((...(((.............-..(((((....-........))))).((((((((((.((...........)).)))))))))))))....))))))) ( -22.30, z-score =  -3.75, R)
>droSec1.super_0 4261181 111 + 21120651
GAAAACUUUC-----GUUUAAAAUGCCAUUUUAGCUUCGC-CUCAACUAAUU-UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCCCUAUUUACUUGAAGCAUUGGCUUACUUAAAUG
.........(-----((((((...(((......((...((-(..........-........))).))((((((((((.((...........)).)))))))))))))....))))))) ( -21.17, z-score =  -3.32, R)
>droYak2.chr3R 9071858 111 - 28832112
GAAAACUUUC-----GUUUAAAAUGCCAUUUUAGCCUCGC-CUCAACCAAUU-UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCCCCCUAUUUACUUGAAGCAUUGGCUUACUUAAAUG
.........(-----((((((...(((.............-..(((((....-........))))).((((((((((.((...........)).)))))))))))))....))))))) ( -22.30, z-score =  -3.82, R)
>droEre2.scaffold_4770 1167729 111 + 17746568
GAAAACUUUC-----GUUUAAAAUGCCAUUUUAGCCUCGC-CUCAACCAAUU-UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCCCUAUUUACUUCAAGCAUUGGCUUACUUAAAUG
.........(-----((((((...(((.............-..(((((....-........))))).(((((((.((.((...........)).)).))))))))))....))))))) ( -16.10, z-score =  -1.94, R)
>droPer1.super_3 310958 96 + 7375914
AAAAAGUUUC-----GUUUUAAAUGGCAUUUCCCGAUUGUAUUCCGCCGAUUCUUCGUUCAAGUGGCGGCGGCUUACCUUUUUGCCACAUCUUUAUUCAAU-----------------
..........-----........(((((......((..(((..((((((...(((.....)))...))))))..)))..)).)))))..............----------------- ( -20.90, z-score =  -1.37, R)
>droMoj3.scaffold_6540 23920178 109 - 34148556
GAAAUGUGUCAACUGAUUUUUGGUAACAUUUCAAGUGAUGUUUCGACAGGUCGAUGAAUUAAG-AGCGAAAAGCAA--UUUCCGUCUUGCUUUGAUUCGAUUCUCCAAAAGG------
(((((((....((..(...)..)).)))))))...((((...((((....))))...))))((-((((((((((((--........))))))...)))).))))........------ ( -21.90, z-score =   0.44, R)
>consensus
GAAAACUUUC_____GUUUAAAAUGCCAUUUUAGCUUCGC_CUCAACCAAUU_UUCCUUCCGGUUGCAAUGCUUCAAUUAUUCUCCCUAUUUACUUGAAGCAUUGGCUUACUUAAAUG
...........................................(((((.............)))))(((((((((((.................)))))))))))............. ( -6.41 =  -8.09 +   1.68)

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 00:00:19 2011