Locus 5223

Sequence ID dm3.chr2R
Location 18,690,708 – 18,690,897
Length 189
Max. P 0.972742
window7164 window7165 window7166 window7167 window7168

overview

Window 4

Location 18,690,708 – 18,690,800
Length 92
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 75.79
Shannon entropy 0.40182
G+C content 0.50102
Mean single sequence MFE -30.14
Consensus MFE -18.10
Energy contribution -18.06
Covariance contribution -0.04
Combinations/Pair 1.30
Mean z-score -1.41
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.541064
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18690708 92 + 21146708
AAGCGGAAGAGAAGUAACUGACCUGCGAUCGGGAAGGUGACCUUCCCCAGG------GGCGCCGACUAUACAUAUGU---UUGUAUGUAUGUACAUAG-GUG----------
...(....)............((((.....(((((((...)))))))))))------..((((.((.((((((((..---..)))))))))).....)-)))---------- ( -26.80, z-score =  -0.93, R)
>droSim1.chrX 16221022 92 + 17042790
AAGCGGAAGAGAAGUAACUGACCUGCGAUCGGGAAGGUGACCUUCCCCAGG------GGCGCCGACUAUACAUACAU---UUGUAUGUAUGUACAUAG-GUG----------
...(....)............((((.....(((((((...)))))))))))------..((((.....(((((((((---....)))))))))....)-)))---------- ( -29.30, z-score =  -1.86, R)
>droSec1.super_9 1992093 92 + 3197100
AAGCGGAAGAGAAGUAACUGACCUGCGAUCGAGAAGGUGACCUUCCCCAGG------GUCGCCGCCUAUACAUACGU---UUGUAUGUAUGUACAUAG-GUG----------
..((((.((........))...)))).........((((((((......))------))))))((((((((((((((---....)))))))))..)))-)).---------- ( -32.50, z-score =  -3.25, R)
>droYak2.chr2R 16157351 110 + 21139217
AAGCGGAAGAGGAGUAACUGACCUGCGAUCAGGAAGGUGACCUUCCCCAGAAGG--AGAGAGAGUCUAUAUAUGUACAUGUUGUAUGUAUGUACAUAGUGUGUACAUAGGUG
...(....).(((.(..((..(((.(.....((((((...))))))...).)))--..))..).)))...((((((((..((((((....)))))..)..)))))))).... ( -27.50, z-score =  -0.82, R)
>droEre2.scaffold_4845 20054172 109 + 22589142
AAGCGGAAGAGGAGCAACUGACCUGCGAUCGGGGAGGUGACCUUCCCAGGGGCGCCGACUAUCGUCUGUACGCACAU---ACAUACCUAUGUACAUAGUGCGCACAUAGGUG
..(((..(((.(((((.......)))..(((((((((...))))))).((....))))...)).)))...)))....---...(((((((((.(.......).))))))))) ( -34.60, z-score =  -0.22, R)
>consensus
AAGCGGAAGAGAAGUAACUGACCUGCGAUCGGGAAGGUGACCUUCCCCAGG______GGCGCCGACUAUACAUACAU___UUGUAUGUAUGUACAUAG_GUG__________
..((((...((......))...))))....(((((((...)))))))...................((((((((((.....))))))))))..................... (-18.10 = -18.06 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,690,708 – 18,690,800
Length 92
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 75.79
Shannon entropy 0.40182
G+C content 0.50102
Mean single sequence MFE -28.00
Consensus MFE -15.36
Energy contribution -15.52
Covariance contribution 0.16
Combinations/Pair 1.19
Mean z-score -1.71
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.32
SVM RNA-class probability 0.642782
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18690708 92 - 21146708
----------CAC-CUAUGUACAUACAUACAA---ACAUAUGUAUAGUCGGCGCC------CCUGGGGAAGGUCACCUUCCCGAUCGCAGGUCAGUUACUUCUCUUCCGCUU
----------.((-((.((.(((((((((...---...))))))).))))(((..------..(.(((((((...))))))).).))))))).................... ( -22.40, z-score =  -0.93, R)
>droSim1.chrX 16221022 92 - 17042790
----------CAC-CUAUGUACAUACAUACAA---AUGUAUGUAUAGUCGGCGCC------CCUGGGGAAGGUCACCUUCCCGAUCGCAGGUCAGUUACUUCUCUUCCGCUU
----------.((-((.(((((((((((....---)))))))))))....(((..------..(.(((((((...))))))).).))))))).................... ( -28.80, z-score =  -2.71, R)
>droSec1.super_9 1992093 92 - 3197100
----------CAC-CUAUGUACAUACAUACAA---ACGUAUGUAUAGGCGGCGAC------CCUGGGGAAGGUCACCUUCUCGAUCGCAGGUCAGUUACUUCUCUUCCGCUU
----------...-...(((((((((......---..)))))))))(((((.(((------(.(((((((((...))))))).....))))))((......))...))))). ( -27.10, z-score =  -1.95, R)
>droYak2.chr2R 16157351 110 - 21139217
CACCUAUGUACACACUAUGUACAUACAUACAACAUGUACAUAUAUAGACUCUCUCU--CCUUCUGGGGAAGGUCACCUUCCUGAUCGCAGGUCAGUUACUCCUCUUCCGCUU
....((((((((...(((((....))))).....))))))))....(((.((.(((--((....))))))))))......(((((.....)))))................. ( -25.30, z-score =  -1.96, R)
>droEre2.scaffold_4845 20054172 109 - 22589142
CACCUAUGUGCGCACUAUGUACAUAGGUAUGU---AUGUGCGUACAGACGAUAGUCGGCGCCCCUGGGAAGGUCACCUCCCCGAUCGCAGGUCAGUUGCUCCUCUUCCGCUU
.((((.((((((((((((((((....))))))---).)))))))))(((....))).(((....((((.(((...))).))))..))))))).................... ( -36.40, z-score =  -1.02, R)
>consensus
__________CAC_CUAUGUACAUACAUACAA___AUGUAUGUAUAGACGGCGCC______CCUGGGGAAGGUCACCUUCCCGAUCGCAGGUCAGUUACUUCUCUUCCGCUU
.................((((((((.............))))))))...................(((((((...)))))))....((.((..((......))...)))).. (-15.36 = -15.52 +   0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,690,738 – 18,690,836
Length 98
Sequences 5
Columns 123
Reading direction forward
Mean pairwise identity 69.69
Shannon entropy 0.49256
G+C content 0.46320
Mean single sequence MFE -37.44
Consensus MFE -16.24
Energy contribution -16.16
Covariance contribution -0.08
Combinations/Pair 1.44
Mean z-score -2.58
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972742
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18690738 98 + 21146708
GGGAAGGUGACCUUCCCCAGGGGCGCCGA-------CUAUACAUAUGU---UUGUAUGUAUGUACAUAG-----------GUGCAGGGUAUACAGAGGUA----UAUCACUGUACAUAUAUUG
(((((((...)))))))(((..(((((.(-------(.((((((((..---..)))))))))).....)-----------))))..(((((((....)))----)))).)))........... ( -34.90, z-score =  -2.13, R)
>droSim1.chrX 16221052 98 + 17042790
GGGAAGGUGACCUUCCCCAGGGGCGCCGA-------CUAUACAUACAU---UUGUAUGUAUGUACAUAG-----------GUGCAGCAUGUACAGAGGUA----UAUCACUGUACAAAUAUUG
(((((((...)))))))..(..(((((..-------...(((((((((---....)))))))))....)-----------))))..).(((((((.((..----..)).)))))))....... ( -37.40, z-score =  -3.55, R)
>droSec1.super_9 1992123 98 + 3197100
GAGAAGGUGACCUUCCCCAGGGUCGCCGC-------CUAUACAUACGU---UUGUAUGUAUGUACAUAG-----------GUGCAGCAUGUACAGAGGUA----UAUCACUGUACAAAUAUUG
.....((((((((......))))))))((-------((((((((((((---....)))))))))..)))-----------))......(((((((.((..----..)).)))))))....... ( -36.80, z-score =  -3.78, R)
>droYak2.chr2R 16157381 120 + 21139217
AGGAAGGUGACCUUCCCCAGAAGGAGAGAGA---GUCUAUAUAUGUACAUGUUGUAUGUAUGUACAUAGUGUGUACAUAGGUGCAGGGUAUUCAGAGGUACAUAUAUCACCGUACACAUCUUG
.(...((((((((((....))))).......---.....(((((((((((.((((((.(((((((((...))))))))).)))))).))........))))))))))))))...)........ ( -38.60, z-score =  -2.29, R)
>droEre2.scaffold_4845 20054202 105 + 22589142
GGGGAGGUGACCUUCCC-AGGGGCGCCGACUAUCGUCUGUACGCACAU---ACAUACCUAUGUACAUAGUGCGCACAUAGGUGUAGGGUAUGCAGAGGUG-----CACAUCGUG---------
(((((((...)))))))-.((.((((((.....).((((((..(...(---((..((((((((.(.......).)))))))))))..)..))))))))))-----)...))...--------- ( -39.50, z-score =  -1.15, R)
>consensus
GGGAAGGUGACCUUCCCCAGGGGCGCCGA_______CUAUACAUACAU___UUGUAUGUAUGUACAUAG___________GUGCAGGGUAUACAGAGGUA____UAUCACUGUACAAAUAUUG
(((((((...))))))).....................(((((((((.....)))))))))((((...............((((.....))))...(((.........)))))))........ (-16.24 = -16.16 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,690,738 – 18,690,836
Length 98
Sequences 5
Columns 123
Reading direction reverse
Mean pairwise identity 69.69
Shannon entropy 0.49256
G+C content 0.46320
Mean single sequence MFE -32.82
Consensus MFE -13.88
Energy contribution -14.84
Covariance contribution 0.96
Combinations/Pair 1.26
Mean z-score -2.29
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.915241
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18690738 98 - 21146708
CAAUAUAUGUACAGUGAUA----UACCUCUGUAUACCCUGCAC-----------CUAUGUACAUACAUACAA---ACAUAUGUAUAG-------UCGGCGCCCCUGGGGAAGGUCACCUUCCC
.......(((((((.(...----...).)))))))....((.(-----------(..((((((((.......---...)))))))).-------..)).)).....(((((((...))))))) ( -26.40, z-score =  -1.13, R)
>droSim1.chrX 16221052 98 - 17042790
CAAUAUUUGUACAGUGAUA----UACCUCUGUACAUGCUGCAC-----------CUAUGUACAUACAUACAA---AUGUAUGUAUAG-------UCGGCGCCCCUGGGGAAGGUCACCUUCCC
.......(((((((.(...----...).)))))))....((.(-----------(..(((((((((((....---))))))))))).-------..)).)).....(((((((...))))))) ( -35.00, z-score =  -3.53, R)
>droSec1.super_9 1992123 98 - 3197100
CAAUAUUUGUACAGUGAUA----UACCUCUGUACAUGCUGCAC-----------CUAUGUACAUACAUACAA---ACGUAUGUAUAG-------GCGGCGACCCUGGGGAAGGUCACCUUCUC
.......(((((((.(...----...).)))))))((((((..-----------...(((((((((......---..))))))))).-------))))))......(((((((...))))))) ( -33.60, z-score =  -3.23, R)
>droYak2.chr2R 16157381 120 - 21139217
CAAGAUGUGUACGGUGAUAUAUGUACCUCUGAAUACCCUGCACCUAUGUACACACUAUGUACAUACAUACAACAUGUACAUAUAUAGAC---UCUCUCUCCUUCUGGGGAAGGUCACCUUCCU
....((((((((((((......(((........)))....))))((((((((.....))))))))..........))))))))...(((---.((.(((((....))))))))))........ ( -31.50, z-score =  -1.71, R)
>droEre2.scaffold_4845 20054202 105 - 22589142
---------CACGAUGUG-----CACCUCUGCAUACCCUACACCUAUGUGCGCACUAUGUACAUAGGUAUGU---AUGUGCGUACAGACGAUAGUCGGCGCCCCU-GGGAAGGUCACCUCCCC
---------...((.(((-----.((((((((((((.....(((((((((((.....)))))))))))..))---))))((((...(((....))).))))....-.)).))))))).))... ( -37.60, z-score =  -1.86, R)
>consensus
CAAUAUUUGUACAGUGAUA____UACCUCUGUAUACCCUGCAC___________CUAUGUACAUACAUACAA___AUGUAUGUAUAG_______UCGGCGCCCCUGGGGAAGGUCACCUUCCC
.......(((((((.(..........).)))))))......................((((((((.............))))))))....................(((((((...))))))) (-13.88 = -14.84 +   0.96)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,690,800 – 18,690,897
Length 97
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 82.58
Shannon entropy 0.30523
G+C content 0.44907
Mean single sequence MFE -22.10
Consensus MFE -13.66
Energy contribution -15.10
Covariance contribution 1.44
Combinations/Pair 1.17
Mean z-score -1.79
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.514798
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18690800 97 - 21146708
GCAGACCC-UUUUCCAAGGACGGAGGUCCUUUUGUCCUGCAUUCUUAUCAAUCCUGAAUACACAAUAUAUGUACAGUGAUA----UACCUCUGUAUACCCUG
.(((..((-((....))))((((((((.....(((((((........(((....))).((((.......))))))).))))----.)))))))).....))) ( -19.90, z-score =  -1.31, R)
>droSim1.chrX 16221114 95 - 17042790
GCAGACCCUUUUUCCAAGGACGGAGGUCCUUUUGUCCU---UUCUUAUCAAUCCUGAAUACACAAUAUUUGUACAGUGAUA----UACCUCUGUACAUGCUG
(((............((((((((((....)))))))))---)...........................(((((((.(...----...).)))))))))).. ( -21.50, z-score =  -2.07, R)
>droSec1.super_9 1992185 98 - 3197100
GCAGACCCUUUUUCCAAGGACCAGGGUCCUUUUGUCCUUCAUUCUUAUCAAUCCUGAAUACACAAUAUUUGUACAGUGAUA----UACCUCUGUACAUGCUG
(((((((((...((....))..))))))...((((..((((.............))))...))))....(((((((.(...----...).)))))))))).. ( -22.02, z-score =  -2.33, R)
>droYak2.chr2R 16157461 101 - 21139217
GCAGACCC-UUUUCCAAGGACGGAGGUCCUUUUGUCCUGUUGUCCCAGCAAUCCUGAAUACACAAGAUGUGUACGGUGAUAUAUGUACCUCUGAAUACCCUG
.(((..((-((....)))).(((((((.(...(((((((......(((.....)))..(((((.....)))))))).))))...).)))))))......))) ( -25.40, z-score =  -1.23, R)
>droEre2.scaffold_4845 20054281 87 - 22589142
GCAGACCC-UUUUCCAAGGACGGAGGUCCUUUUGUCCUGCCUUCCCAGCAAUCCUGAAUACACACGAUGUG--------------CACCUCUGCAUACCCUA
(((((...-.......(((((((((....))))))))).........((((((.((......)).))).))--------------)...)))))........ ( -21.70, z-score =  -2.00, R)
>consensus
GCAGACCC_UUUUCCAAGGACGGAGGUCCUUUUGUCCUGCAUUCUUAUCAAUCCUGAAUACACAAUAUGUGUACAGUGAUA____UACCUCUGUAUACCCUG
(((((...........(((((((((....)))))))))............((((((..((((.......))))))).))).........)))))........ (-13.66 = -15.10 +   1.44)

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 22:44:13 2011