Locus 10251

Sequence ID dm3.chr3R
Location 12,490,787 – 12,490,889
Length 102
Max. P 0.995553
window14091 window14092

overview

Window 1

Location 12,490,787 – 12,490,889
Length 102
Sequences 12
Columns 116
Reading direction forward
Mean pairwise identity 71.67
Shannon entropy 0.59015
G+C content 0.43749
Mean single sequence MFE -27.77
Consensus MFE -9.93
Energy contribution -9.94
Covariance contribution 0.01
Combinations/Pair 1.12
Mean z-score -2.38
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959893
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12490787 102 + 27905053
GUUAUGG-CGCUGCU--------UGUGGAACGGAAAUGUGCAACAUUUCCGCUACUCACCCGAAAAACG---GG--CCAAUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGA
....(((-(((((.(--------(.(((..((((((((.....)))))))).......((((.....))---))--))).....)).))))))))..................... ( -33.80, z-score =  -3.94, R)
>droSim1.chr3R 18536794 102 - 27517382
GUUAUGG-CGCUGCU--------UCUGGAACGGAAAUGUGCAACAUUUCCGCUACUCACCCGAAAAACG---GG--CCAAUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGA
....(((-(((((..--------..(((..((((((((.....)))))))).......((((.....))---))--)))........))))))))..................... ( -31.80, z-score =  -3.67, R)
>droSec1.super_12 466757 102 - 2123299
GUUAUGG-CGCUGCU--------UCUGGAACGGAAAUGUGCAACAUUUCCGCUACUCACCCGAAAAACG---GG--CCAAUAAAAAUCGGCGCCAAGUGUCAAAUCUAAAUAAUGA
....(((-(((((..--------..(((..((((((((.....)))))))).......((((.....))---))--)))........))))))))..................... ( -31.10, z-score =  -3.07, R)
>droYak2.chr3R 16932321 102 - 28832112
GUUAUGG-CGCUGCU--------UCUGGAACGGAAAUGUGCAACAUUUCCGCUACUCACCCGAAAAACG---GG--CCAAUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGA
....(((-(((((..--------..(((..((((((((.....)))))))).......((((.....))---))--)))........))))))))..................... ( -31.80, z-score =  -3.67, R)
>droEre2.scaffold_4770 8605950 102 - 17746568
GUUAUGG-CGCUGCU--------UCUGGAACGGAAAUGUGCAACAUUUCCGCUGCUCACCCGAAAAACG---GG--CCAAUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAAUGA
....(((-(((((..--------..(((..((((((((.....)))))))).......((((.....))---))--)))........))))))))..................... ( -31.80, z-score =  -3.13, R)
>droAna3.scaffold_13340 16306227 100 - 23697760
GUUAUGGCCGAUUCG-----------GGAACGGAAAUGUGCAACAUUUCCGCUCUUCACCCGAAAAACG---GC--CCAAUAAAAAUCAACGCCAAGUGUCAAAUCUAAAUAGCGA
((((((((((.((((-----------((..((((((((.....)))))))).......))))))...))---))--)............((((...)))).........))))).. ( -30.00, z-score =  -3.24, R)
>dp4.chr2 17474257 104 + 30794189
GUUAUGGCAGCU------------CGGGAACGGAAAUGUGCAACAUUUCCGCACUUUACCCAAAAACGGGCCACAACUCGUAAAAAUCAGCGCCAAAUGUCAAAUCUAACUACCGA
....((((.(((------------.(((((((((((((.....))))))))....)).)))....(((((......))))).......)))))))..................... ( -26.60, z-score =  -2.07, R)
>droPer1.super_0 11322128 103 + 11822988
GUUAUGGCAGCU------------CGGGAACGGAAAUGUGCAACAUUUCCGCACUUUACCCAAAACGGGCC-ACAACUCGUAAAAAUCAGCGCCAAAUGUCAAAUCUAACUACCGA
....((((.(((------------.(((((((((((((.....))))))))....)).)))...(((((..-....))))).......)))))))..................... ( -26.60, z-score =  -2.04, R)
>droWil1.scaffold_181130 11525689 80 - 16660200
GUUAUGGCCUUUUCG-----------UGGACGGAAGUUUGAAACAUUUCCGCACUUUUACAGAUCGCCGAGUGU--CAAAUGGUAAAUUACGA-----------------------
....((((..(((.(-----------(((((((((((.......)))))))....))))))))..)))).....--.................----------------------- ( -13.90, z-score =   1.09, R)
>droVir3.scaffold_13047 13446516 111 - 19223366
AUUAUGG-AGCUGCGAGUCGAAACUAGAAACGGAAAUGUGCAACAUUUCCGCAGGCUCUUCAAAUGUUGUU-GC--CCAAUAAAAAUCAACGC-AAGUGUCAAACAUAAAUUACAC
.((((((-(((((((..((.......))..)(((((((.....)))))))))).))))......(((((..-..--.))))).......((..-..))......)))))....... ( -25.60, z-score =  -1.51, R)
>droMoj3.scaffold_6259 5991 102 + 16918
GUUAUGGGAGCUGC----------UAGAAGCGGAAAUGUGCAACAUUUCCGCAGGCUCUUCAAAUGUUGUU-GC--CCAAUAAAAAUCAACGC-AAGUGUCAAGCAUAAAUUACAC
.(((((((((((..----------.....(((((((((.....))))))))).)))))).....(((((..-..--.))))).......((..-..))......)))))....... ( -26.10, z-score =  -1.26, R)
>droGri2.scaffold_14906 3031967 104 - 14172833
GUUAUGG-AGCAGC-------AACUAGAAACGGAAAUGUGCAACAUUUCCGCAGGCUCUUCAAAUCGUGUU-GC--CCAAUAAAAAUCAACGC-AAGUGUCAAACAUAAAUUACAC
(((.(((-.(((((-------(....((..((((((((.....))))))))..((....))...)).))))-))--)))..........((..-..))....)))........... ( -24.10, z-score =  -2.05, R)
>consensus
GUUAUGG_CGCUGCU_________CUGGAACGGAAAUGUGCAACAUUUCCGCAACUCACCCGAAAAACG___GC__CCAAUAAAAAUCAGCGCCAAGUGUCAAAUCUAAAUAACGA
..............................((((((((.....))))))))................................................................. ( -9.93 =  -9.94 +   0.01)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,490,787 – 12,490,889
Length 102
Sequences 12
Columns 116
Reading direction reverse
Mean pairwise identity 71.67
Shannon entropy 0.59015
G+C content 0.43749
Mean single sequence MFE -31.94
Consensus MFE -12.10
Energy contribution -11.57
Covariance contribution -0.52
Combinations/Pair 1.33
Mean z-score -2.92
Structure conservation index 0.38
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.82
SVM RNA-class probability 0.995553
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 12490787 102 - 27905053
UCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAUUGG--CC---CGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCACA--------AGCAGCG-CCAUAAC
.....................((((((((.....((((.(--((---((.....))))).))))(((((((((.....)))))))))......--------..)))))-))).... ( -39.20, z-score =  -5.37, R)
>droSim1.chr3R 18536794 102 + 27517382
UCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAUUGG--CC---CGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCAGA--------AGCAGCG-CCAUAAC
.....................((((((((.((((((((.(--((---((.....))))).)))((((((((((.....))))))))))..)))--------)))))))-))).... ( -39.60, z-score =  -5.34, R)
>droSec1.super_12 466757 102 + 2123299
UCAUUAUUUAGAUUUGACACUUGGCGCCGAUUUUUAUUGG--CC---CGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCAGA--------AGCAGCG-CCAUAAC
.....................((((((.(.((((((((.(--((---((.....))))).)))((((((((((.....))))))))))..)))--------))).)))-))).... ( -35.00, z-score =  -3.86, R)
>droYak2.chr3R 16932321 102 + 28832112
UCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAUUGG--CC---CGUUUUUCGGGUGAGUAGCGGAAAUGUUGCACAUUUCCGUUCCAGA--------AGCAGCG-CCAUAAC
.....................((((((((.((((((((.(--((---((.....))))).)))((((((((((.....))))))))))..)))--------)))))))-))).... ( -39.60, z-score =  -5.34, R)
>droEre2.scaffold_4770 8605950 102 + 17746568
UCAUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAUUGG--CC---CGUUUUUCGGGUGAGCAGCGGAAAUGUUGCACAUUUCCGUUCCAGA--------AGCAGCG-CCAUAAC
.....................((((((((.(((((..(.(--((---((.....))))).)(.((((((((((.....)))))))))).))))--------)))))))-))).... ( -38.70, z-score =  -4.82, R)
>droAna3.scaffold_13340 16306227 100 + 23697760
UCGCUAUUUAGAUUUGACACUUGGCGUUGAUUUUUAUUGG--GC---CGUUUUUCGGGUGAAGAGCGGAAAUGUUGCACAUUUCCGUUCC-----------CGAAUCGGCCAUAAC
.(((((...............))))).............(--((---((...((((((.....((((((((((.....))))))))))))-----------)))).)))))..... ( -36.16, z-score =  -3.66, R)
>dp4.chr2 17474257 104 - 30794189
UCGGUAGUUAGAUUUGACAUUUGGCGCUGAUUUUUACGAGUUGUGGCCCGUUUUUGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUCCCG------------AGCUGCCAUAAC
(((((.(((((((.....)))))))))))).........((((((((..((..(((((......(((((((((.....))))))))).))))------------))).)))))))) ( -35.80, z-score =  -3.09, R)
>droPer1.super_0 11322128 103 - 11822988
UCGGUAGUUAGAUUUGACAUUUGGCGCUGAUUUUUACGAGUUGU-GGCCCGUUUUGGGUAAAGUGCGGAAAUGUUGCACAUUUCCGUUCCCG------------AGCUGCCAUAAC
(((((.(((((((.....)))))))))))).........(((((-(((..((((.(((......(((((((((.....))))))))).))))------------))).)))))))) ( -36.40, z-score =  -3.24, R)
>droWil1.scaffold_181130 11525689 80 + 16660200
-----------------------UCGUAAUUUACCAUUUG--ACACUCGGCGAUCUGUAAAAGUGCGGAAAUGUUUCAAACUUCCGUCCA-----------CGAAAAGGCCAUAAC
-----------------------((((..(((((...(((--........)))...))))).(..(((((...........)))))..))-----------)))............ ( -12.20, z-score =   0.65, R)
>droVir3.scaffold_13047 13446516 111 + 19223366
GUGUAAUUUAUGUUUGACACUU-GCGUUGAUUUUUAUUGG--GC-AACAACAUUUGAAGAGCCUGCGGAAAUGUUGCACAUUUCCGUUUCUAGUUUCGACUCGCAGCU-CCAUAAU
.......(((((........((-((.(..((....))..)--))-))...........((((.((((((((((.....)))))))(..((.......))..)))))))-)))))). ( -24.20, z-score =  -0.18, R)
>droMoj3.scaffold_6259 5991 102 - 16918
GUGUAAUUUAUGCUUGACACUU-GCGUUGAUUUUUAUUGG--GC-AACAACAUUUGAAGAGCCUGCGGAAAUGUUGCACAUUUCCGCUUCUA----------GCAGCUCCCAUAAC
((((............))))((-((...((........((--((-...............))))(((((((((.....))))))))).))..----------)))).......... ( -23.16, z-score =  -0.39, R)
>droGri2.scaffold_14906 3031967 104 + 14172833
GUGUAAUUUAUGUUUGACACUU-GCGUUGAUUUUUAUUGG--GC-AACACGAUUUGAAGAGCCUGCGGAAAUGUUGCACAUUUCCGUUUCUAGUU-------GCUGCU-CCAUAAC
.......(((((.(..((....-..))..)........((--((-(...(((((.(((......(((((((((.....)))))))))))).))))-------).))))-)))))). ( -23.30, z-score =  -0.41, R)
>consensus
UCGUUAUUUAGAUUUGACACUUGGCGCUGAUUUUUAUUGG__GC___CGUUUUUCGGGUAAGCAGCGGAAAUGUUGCACAUUUCCGUUCCAG_________AGCAGCG_CCAUAAC
.......................................................(((......(((((((((.....)))))))))))).......................... (-12.10 = -11.57 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:20:19 2011