Locus 11836

Sequence ID dm3.chr3R
Location 24,160,831 – 24,160,958
Length 127
Max. P 0.999642
window16267 window16268 window16269 window16270

overview

Window 7

Location 24,160,831 – 24,160,944
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.58
Shannon entropy 0.48929
G+C content 0.38837
Mean single sequence MFE -31.89
Consensus MFE -18.74
Energy contribution -20.97
Covariance contribution 2.23
Combinations/Pair 1.24
Mean z-score -3.52
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.12
SVM RNA-class probability 0.999642
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24160831 113 + 27905053
------CUAGGAUUUUCCAACAAGAUUGCGAGUUGGGCGAACGCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UUCUGCAAUAAUAUUUACAUCUUUACUUAA
------...((.....))......(((((.((..((((((((..(((((....((((((.......))))))..)))))..))))))))-..)))))))..................... ( -35.50, z-score =  -3.76, R)
>droSim1.chr3R 23843214 113 + 27517382
------CUAGGAUUUUCAAAAAAGAUUGCGAGUUUGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UCCUGCAAUAAUAUUUACAUCUUUACUUAA
------..(((((...........((((((.(...((((((((.(((((....((((((.......))))))..))))).)))))))).-.).)))))).........)))))....... ( -31.85, z-score =  -3.23, R)
>droSec1.super_22 764625 109 + 1066717
------CUAGGAUUUUCAAAU----UUGCGAGUUUGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGUUUAAUCUCAAGUUCGCCC-UCCUGCAAUAAUAUUUACAUCUUUACUUAA
------..(((((........----(((((.(...((((((((.(((((...(((((........)))))....))))).)))))))).-.).)))))..........)))))....... ( -28.27, z-score =  -2.71, R)
>droYak2.chr3R 6490021 110 - 28832112
------CUAGGAUUUUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGUGAUUAAUCUCAAGUUCGCCCCUCCUGCAUAAAUAUUUA----UUUACUUAA
------((((..........))))..((((.((.(((((((((.(((((....((..((.......))..))..))))).))))))))).)).))))..........----......... ( -35.20, z-score =  -4.38, R)
>droEre2.scaffold_4820 6583843 110 - 10470090
------CCAGGAUUUUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCCCAAUUACUGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUACUAUUUA----UUUACUUAA
------...((.....))...(((((((((.((.(((((((((.(((((....(((((.........)))))..))))).))))))))).)).)))))).)))....----......... ( -38.60, z-score =  -5.52, R)
>droMoj3.scaffold_6498 2595538 115 - 3408170
CUAUUAUAUGAAUGUACAUGCAAUAGCAUAGCCUUAGAGAUGGCAUGUUGCCCAAAGCUUAACCACGCUUACCUAUCU--AAUUCGAAC---UUGCAUUCACAAAUACAUAUAUAAUUUA
....((((((..(((..((((((((((((.(((........)))))))))....((((........))))........--.........---))))))..)))....))))))....... ( -21.90, z-score =  -1.49, R)
>consensus
______CUAGGAUUUUCAAACAAGAUUGCGAGUUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC_UCCUGCAAUAAUAUUUACAUCUUUACUUAA
........................((((((.....((((((((.(((((....((((((.......))))))..))))).)))))))).....))))))..................... (-18.74 = -20.97 +   2.23)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,160,831 – 24,160,944
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.58
Shannon entropy 0.48929
G+C content 0.38837
Mean single sequence MFE -31.18
Consensus MFE -14.80
Energy contribution -16.86
Covariance contribution 2.06
Combinations/Pair 1.11
Mean z-score -3.15
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.10
SVM RNA-class probability 0.997405
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24160831 113 - 27905053
UUAAGUAAAGAUGUAAAUAUUAUUGCAGAA-GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGCGUUCGCCCAACUCGCAAUCUUGUUGGAAAAUCCUAG------
.........(((...((((..(((((((..-((((((((.((((.......((((....)).)).........)))).))))))))..)).)))))..)))).....)))....------ ( -29.79, z-score =  -2.72, R)
>droSim1.chr3R 23843214 113 - 27517382
UUAAGUAAAGAUGUAAAUAUUAUUGCAGGA-GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAAUCUUUUUUGAAAAUCCUAG------
.........(((.((((.(..(((((((..-.((((((((((((.......((((....)).)).........))))))))))))...)).)))))..).))))...)))....------ ( -30.29, z-score =  -3.24, R)
>droSec1.super_22 764625 109 - 1066717
UUAAGUAAAGAUGUAAAUAUUAUUGCAGGA-GGGCGAACUUGAGAUUAAACGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAA----AUUUGAAAAUCCUAG------
.........(((.(((((....((((((..-.((((((((((((.......((((....)).)).........))))))))))))...)).))))----)))))...)))....------ ( -28.59, z-score =  -3.40, R)
>droYak2.chr3R 6490021 110 + 28832112
UUAAGUAAA----UAAAUAUUUAUGCAGGAGGGGCGAACUUGAGAUUAAUCACUGUAAUUGAGCAACAAACACCUCGAGUUCGCCCAUCUCGCAAUCUAGUUGGAAAAUCCUAG------
.((((((..----....))))))(((..((.(((((((((((((.........(((......)))........))))))))))))).))..)))........((.....))...------ ( -32.83, z-score =  -4.06, R)
>droEre2.scaffold_4820 6583843 110 + 10470090
UUAAGUAAA----UAAAUAGUAUUGCAGGAGGGGCGAACUUGAGAUUAAUCGCAGUAAUUGGGCAACAAACACCUCGAGUUCGCCCAUCUCGCAAUCUAGUUGGAAAAUCCUGG------
.........----....(((.(((((..((.(((((((((((((........(((...)))(....)......))))))))))))).))..))))))))...((.....))...------ ( -36.50, z-score =  -4.08, R)
>droMoj3.scaffold_6498 2595538 115 + 3408170
UAAAUUAUAUAUGUAUUUGUGAAUGCAA---GUUCGAAUU--AGAUAGGUAAGCGUGGUUAAGCUUUGGGCAACAUGCCAUCUCUAAGGCUAUGCUAUUGCAUGUACAUUCAUAUAAUAG
.......((((((....((((.((((((---..((.....--.))......(((((((((........(((.....)))........))))))))).)))))).))))..)))))).... ( -29.09, z-score =  -1.38, R)
>consensus
UUAAGUAAAGAUGUAAAUAUUAUUGCAGGA_GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAAUCUUGUUGGAAAAUCCUAG______
.......................(((.((...((((((((((((..........((......)).........))))))))))))...)).))).......................... (-14.80 = -16.86 +   2.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 24,160,839 – 24,160,958
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.42
Shannon entropy 0.47040
G+C content 0.38707
Mean single sequence MFE -29.82
Consensus MFE -18.74
Energy contribution -20.97
Covariance contribution 2.23
Combinations/Pair 1.24
Mean z-score -3.17
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.73
SVM RNA-class probability 0.999238
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24160839 119 + 27905053
UUCCAACAAGAUUGCGAGUUGGGCGAACGCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UUCUGCAAUAAUAUUUACAUCUUUACUUAAUGCAACUAUUACAG
..........(((((.((..((((((((..(((((....((((((.......))))))..)))))..))))))))-..)))))))................................... ( -33.80, z-score =  -3.30, R)
>droSim1.chr3R 23843222 119 + 27517382
UUCAAAAAAGAUUGCGAGUUUGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC-UCCUGCAAUAAUAUUUACAUCUUUACUUAAUGCAACUAUUACAC
..........((((((.(...((((((((.(((((....((((((.......))))))..))))).)))))))).-.).))))))................................... ( -31.00, z-score =  -3.37, R)
>droSec1.super_22 764633 115 + 1066717
UUCAAAU----UUGCGAGUUUGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGUUUAAUCUCAAGUUCGCCC-UCCUGCAAUAAUAUUUACAUCUUUACUUAAUGCAACUAUUACAC
.......----(((((.(...((((((((.(((((...(((((........)))))....))))).)))))))).-.).))))).................................... ( -27.40, z-score =  -2.67, R)
>droYak2.chr3R 6490029 116 - 28832112
UUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACAGUGAUUAAUCUCAAGUUCGCCCCUCCUGCAUAAAUAUUUA----UUUACUUAAUGCAACUAUUACAA
.......(((.(((((((..(((((((((.(((((....((..((.......))..))..))))).)))))))))))).....(((((....)----))))......)))))))...... ( -33.00, z-score =  -3.99, R)
>droEre2.scaffold_4820 6583851 116 - 10470090
UUCCAACUAGAUUGCGAGAUGGGCGAACUCGAGGUGUUUGUUGCCCAAUUACUGCGAUUAAUCUCAAGUUCGCCCCUCCUGCAAUACUAUUUA----UUUACUUAAUGCAACUGUUACAA
.......(((((((((.((.(((((((((.(((((....(((((.........)))))..))))).))))))))).)).)))))).)))....----....................... ( -36.90, z-score =  -5.07, R)
>droMoj3.scaffold_6498 2595552 115 - 3408170
UACAUGCAAUAGCAUAGCCUUAGAGAUGGCAUGUUGCCCAAAGCUUAACCACGCUUACCUAUCU--AAUUCGAAC---UUGCAUUCACAAAUACAUAUAUAAUUUACACAGCCAUUAAAG
...((((((((((((.(((........)))))))))....((((........))))........--.........---)))))).................................... ( -16.80, z-score =  -0.61, R)
>consensus
UUCAAACAAGAUUGCGAGUUGGGCGAACUCGAGGUGUUUGUUGCUCAAUUACGGCGAUUAAUCUCAAGUUCGCCC_UCCUGCAAUAAUAUUUACAUCUUUACUUAAUGCAACUAUUACAA
..........((((((.....((((((((.(((((....((((((.......))))))..))))).)))))))).....))))))................................... (-18.74 = -20.97 +   2.23)

alignment

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secondary structure

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dotplot

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Window 0

Location 24,160,839 – 24,160,958
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.42
Shannon entropy 0.47040
G+C content 0.38707
Mean single sequence MFE -33.41
Consensus MFE -16.02
Energy contribution -18.08
Covariance contribution 2.06
Combinations/Pair 1.17
Mean z-score -2.89
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993402
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24160839 119 - 27905053
CUGUAAUAGUUGCAUUAAGUAAAGAUGUAAAUAUUAUUGCAGAA-GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGCGUUCGCCCAACUCGCAAUCUUGUUGGAA
((((((((((((((((.......))))))...))))))))))..-((((((((.((((.......((((....)).)).........)))).))))))))..((.(((....))).)).. ( -34.19, z-score =  -2.92, R)
>droSim1.chr3R 23843222 119 - 27517382
GUGUAAUAGUUGCAUUAAGUAAAGAUGUAAAUAUUAUUGCAGGA-GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAAUCUUUUUUGAA
..((((((.(((((((.......))))))).))))))(((((..-.((((((((((((.......((((....)).)).........))))))))))))...)).)))............ ( -33.89, z-score =  -3.26, R)
>droSec1.super_22 764633 115 - 1066717
GUGUAAUAGUUGCAUUAAGUAAAGAUGUAAAUAUUAUUGCAGGA-GGGCGAACUUGAGAUUAAACGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAA----AUUUGAA
...(((((.(((((((.......))))))).)))))((((((..-.((((((((((((.......((((....)).)).........))))))))))))...)).))))----....... ( -33.99, z-score =  -3.89, R)
>droYak2.chr3R 6490029 116 + 28832112
UUGUAAUAGUUGCAUUAAGUAAA----UAAAUAUUUAUGCAGGAGGGGCGAACUUGAGAUUAAUCACUGUAAUUGAGCAACAAACACCUCGAGUUCGCCCAUCUCGCAAUCUAGUUGGAA
((((.....((((((.(((((..----....)))))))))))((((((((((((((((.........(((......)))........)))))))))))))..)))))))........... ( -33.93, z-score =  -3.47, R)
>droEre2.scaffold_4820 6583851 116 + 10470090
UUGUAACAGUUGCAUUAAGUAAA----UAAAUAGUAUUGCAGGAGGGGCGAACUUGAGAUUAAUCGCAGUAAUUGGGCAACAAACACCUCGAGUUCGCCCAUCUCGCAAUCUAGUUGGAA
.(.((((..((((.....)))).----....(((.(((((..((.(((((((((((((........(((...)))(....)......))))))))))))).))..)))))))))))).). ( -38.60, z-score =  -4.26, R)
>droMoj3.scaffold_6498 2595552 115 + 3408170
CUUUAAUGGCUGUGUAAAUUAUAUAUGUAUUUGUGAAUGCAA---GUUCGAAUU--AGAUAGGUAAGCGUGGUUAAGCUUUGGGCAACAUGCCAUCUCUAAGGCUAUGCUAUUGCAUGUA
........((.((((((......(((.(((((((((((....---)))))...)--))))).)))(((((((((........(((.....)))........))))))))).)))))))). ( -25.89, z-score =   0.49, R)
>consensus
CUGUAAUAGUUGCAUUAAGUAAAGAUGUAAAUAUUAUUGCAGGA_GGGCGAACUUGAGAUUAAUCGCCGUAAUUGAGCAACAAACACCUCGAGUUCGCCAAACUCGCAAUCUUGUUGGAA
........(((((............(((((......))))).....((((((((((((..........((......)).........))))))))))))......))))).......... (-16.02 = -18.08 +   2.06)

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 Wed Apr 20 00:50:37 2011