Locus 8611

Sequence ID dm3.chr3RHet
Location 1,825,970 – 1,826,155
Length 185
Max. P 0.899622
window11824 window11825

overview

Window 4

Location 1,825,970 – 1,826,155
Length 185
Sequences 4
Columns 193
Reading direction forward
Mean pairwise identity 54.76
Shannon entropy 0.75314
G+C content 0.56808
Mean single sequence MFE -73.03
Consensus MFE -21.33
Energy contribution -26.20
Covariance contribution 4.87
Combinations/Pair 1.54
Mean z-score -1.90
Structure conservation index 0.29
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.15
SVM RNA-class probability 0.899622
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1825970 185 + 2517507
UUACCGCAACCUGGUCAGCCUGGGGCCCGGGAUGACCCAAACCGUAAGGGGCUGAGCCGGGCCAGAACGAAGUGGUAUCUUCGUUACCUUCAGCAGGGUAAGUCACCUGCAGAAGCUUUGUCUCUGGCCAAGACACCGCUAGAGAAAAGGCCCAACUCUGCUUCCAAGCGUGCAAACUCCAGCUU--------
.....(((....(((((.(((((...))))).))))).....(((..(((((.(((..(((((..(((((((......)))))))..((((.(((((........))))).)))).....((((((((.........))))))))...)))))..))).)).)))..))))))............-------- ( -71.40, z-score =  -1.45, R)
>droGri2.scaffold_15200 144791 191 + 219039
AUGCCACCAAGGGGUCAACCCUGUGGGCUGGAUGACCUAAACCGGAGAAAUCUCUGCGGUUCUAGGGUCAAGUGGUACCAUCGGUACCUCCAGCAGAGACUCACCCCUGAUGAAGCCCUGAAAAAGGCCAAAGAGCCCAGGGAGGACGUUGCAG--CACCUACGCCAGCUCUAAAAAGGCGUAGCAACAAUCU
.(((..(((.((((....)))).)))((((((((((((.(((((.(((....))).)))))...))))))...((((((...)))))))))))).(..((((..(((((.....(((.(....).))).........)))))..)).))..).)--)).(((((((...........)))))))......... ( -73.74, z-score =  -2.37, R)
>droMoj3.scaffold_6496 25219154 185 - 26866924
UUGCCUCCACUCGGACAGCCCGGCGCUCGGGAUGAUCCGAAUCGGAGAGUCCUGAGCGGCUCACGUACCAAGUGGUAUAUGCGGUAUCUAGAGAAAGGCUUCCCGGCCGACGAGGCCUUUCGCAUGGCUAAAGAGCCAAAGCAGCCGGCAGCAAAUUACUUAAGCGGGCCCGAUUCGCUUGCCCC--------
((((.(((....)))..(((.((((((((((((..((((...))))..)))))))))(((((..(((((....)))))(((((....)....((((((((((.........)))))))))))))).......)))))......)))))).)))).........((((((.......))))))...-------- ( -76.60, z-score =  -1.86, R)
>droVir3.scaffold_12823 181990 182 - 2474545
-UAACGUCACCGGGACAACCCGGUGGCAAGGGUGAUCCAAACAGAAGAAACCUGAGCGGAUCGCGCACCAAAUGGUAUGUGCGCUACCUCAAAAAGGGAUUUCAUCCCGAUGAAGCCUUGCGCAUGGCCAGGGAGCCUGUGCAGCCAGCAGCCAAUUAUCUACGGGGUCCCGAUUUGCCUGCU----------
-......(((((((....)))))))((((((.((((((...(((.......)))...)))))((((((..........))))))....(((....(((((...)))))..)))).))))))(((.(((..((((.(((((((.....))((........))))))).)))).....)))))).---------- ( -70.40, z-score =  -1.91, R)
>consensus
UUACCGCCACCGGGACAACCCGGUGCCCGGGAUGACCCAAACCGGAGAAACCUGAGCGGAUCAAGAACCAAGUGGUAUCUGCGGUACCUCCAGAAGGGAUUCCCACCCGAUGAAGCCUUGCGCAUGGCCAAAGAGCCAAUGCAGCAAGCAGCAAAUUACCUACGCGAGCCCGAAAAGCCCGCC_C________
.((((((..(((((....)))))((((((((....(((.....)))....)))))))).............))))))(((((..........(((((((((((.......)))))))))))....(((......)))...)))))................................................ (-21.33 = -26.20 +   4.87)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,825,970 – 1,826,155
Length 185
Sequences 4
Columns 193
Reading direction reverse
Mean pairwise identity 54.76
Shannon entropy 0.75314
G+C content 0.56808
Mean single sequence MFE -76.65
Consensus MFE -20.91
Energy contribution -22.16
Covariance contribution 1.25
Combinations/Pair 1.75
Mean z-score -1.62
Structure conservation index 0.27
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.633514
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3RHet 1825970 185 - 2517507
--------AAGCUGGAGUUUGCACGCUUGGAAGCAGAGUUGGGCCUUUUCUCUAGCGGUGUCUUGGCCAGAGACAAAGCUUCUGCAGGUGACUUACCCUGCUGAAGGUAACGAAGAUACCACUUCGUUCUGGCCCGGCUCAGCCCCUUACGGUUUGGGUCAUCCCGGGCCCCAGGCUGACCAGGUUGCGGUAA
--------..((((.((..((((.((((((..((.((((((((((.........((..((((((.....))))))..))(((.(((((........))))).)))((.(((((((......))))))))))))))))))).)).......((((((((....))))))))))))))))..))..)).)))).. ( -78.40, z-score =  -1.79, R)
>droGri2.scaffold_15200 144791 191 - 219039
AGAUUGUUGCUACGCCUUUUUAGAGCUGGCGUAGGUG--CUGCAACGUCCUCCCUGGGCUCUUUGGCCUUUUUCAGGGCUUCAUCAGGGGUGAGUCUCUGCUGGAGGUACCGAUGGUACCACUUGACCCUAGAACCGCAGAGAUUUCUCCGGUUUAGGUCAUCCAGCCCACAGGGUUGACCCCUUGGUGGCAU
.........(((((((...........)))))))(((--(..(...(((((....(((((....))))).....)))))......((((((.((.((((((((((((((((...))))))...(((((...((((((..(((....))))))))).)))))))))))....)))))).))))))..)..)))) ( -80.90, z-score =  -2.55, R)
>droMoj3.scaffold_6496 25219154 185 + 26866924
--------GGGGCAAGCGAAUCGGGCCCGCUUAAGUAAUUUGCUGCCGGCUGCUUUGGCUCUUUAGCCAUGCGAAAGGCCUCGUCGGCCGGGAAGCCUUUCUCUAGAUACCGCAUAUACCACUUGGUACGUGAGCCGCUCAGGACUCUCCGAUUCGGAUCAUCCCGAGCGCCGGGCUGUCCGAGUGGAGGCAA
--------.((((..(.....)..))))((............(((.(((((((..(((((....))))).))(((((((((((.....))))..)))))))...........((..((((....))))..)))))))..)))....((((.(((((((.((.((((.....)))).))))))))))))))).. ( -71.70, z-score =   0.24, R)
>droVir3.scaffold_12823 181990 182 + 2474545
----------AGCAGGCAAAUCGGGACCCCGUAGAUAAUUGGCUGCUGGCUGCACAGGCUCCCUGGCCAUGCGCAAGGCUUCAUCGGGAUGAAAUCCCUUUUUGAGGUAGCGCACAUACCAUUUGGUGCGCGAUCCGCUCAGGUUUCUUCUGUUUGGAUCACCCUUGCCACCGGGUUGUCCCGGUGACGUUA-
----------(((((.(((..(((....))).......))).))))).((.((.((((...))))))...))(((((((((((..(((((...)))))....)))))..((((((..........))))))((((((..((((.....))))..))))))..))))))(((((((....)))))))......- ( -75.60, z-score =  -2.37, R)
>consensus
________G_GGCAGGCUAAUCGGGCCCGCGUAGAUAAUUGGCUGCUGGCUCCAUAGGCUCCUUGGCCAUGCGCAAGGCUUCAUCAGGAGGGAAUCCCUGCUGGAGGUACCGAAGAUACCACUUGGUACGAGAACCGCUCAGGUCUCUCCGGUUUGGAUCAUCCCGGCCACCGGGCUGACCCGGUGGCGGCAA
......................((((((((((((........))))))).......)))))....(((.........((((((..((((.....))))....))))))..(((.(((........))).)))..((((((.((((..((((((((((......))))..))))))..)))))))))).))).. (-20.91 = -22.16 +   1.25)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:48:49 2011