Locus 6917

Sequence ID dm3.chr3L
Location 10,744,852 – 10,745,033
Length 181
Max. P 0.980666
window9523 window9524 window9525 window9526

overview

Window 3

Location 10,744,852 – 10,744,958
Length 106
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 66.88
Shannon entropy 0.57650
G+C content 0.34163
Mean single sequence MFE -24.28
Consensus MFE -8.57
Energy contribution -9.92
Covariance contribution 1.35
Combinations/Pair 1.38
Mean z-score -2.69
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.01
SVM RNA-class probability 0.979085
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10744852 106 - 24543557
-----AUUUCCGAACUCAAGCUAUU--AAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUCAGCCUUCCUCAGGAGCUUUCAUUUGCCCAUUGGCAA
-----......((..((((((((..--.(((((((....)))))))....))))))))..))................(((.......((.((........))))...))).. ( -24.10, z-score =  -3.41, R)
>droSim1.chr3L 10138191 106 - 22553184
-----AUUGCCGAACUCAAGCUAUU--AAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUUGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCAA
-----.(((((((..((((((((..--.(((((((....)))))))....)))))))).........(((((.......((((...)))).......)))))....))))))) ( -30.54, z-score =  -3.99, R)
>droSec1.super_0 2965059 106 - 21120651
-----AUUGCCGAACUCAAGCUAUU--AAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUUGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCAA
-----.(((((((..((((((((..--.(((((((....)))))))....)))))))).........(((((.......((((...)))).......)))))....))))))) ( -30.54, z-score =  -3.99, R)
>droYak2.chr3L 10757261 92 - 24197627
-----------UAUUUCAAGUUAUU--AAAUUCCUUCUACGGUAUACACUUAGUUUGAAAUUCUUUACAAAUUAUGUAGCAUUCGCCAGGAGCUUUAA--UGGCCAA------
-----------........((((((--((((((((....(((..((((..(((((((.((....)).)))))))))))....)))..))))).)))))--))))...------ ( -18.00, z-score =  -2.06, R)
>droWil1.scaffold_180949 109932 111 + 6375548
GUGGAACAGAUGUUGUUAACUUUUUUGAAAAUUGUUCCAUUAUUAAAAUUUA-CUUGAGUUUUUGCACGUAUAGUUUUGUGUGUUGCUUCAAUUUGAAGUUUGAAAUUUUCA-
(((((((((.(....((((.....)))).).)))))))))............-..((((..((((((((........)))))...(((((.....)))))...)))..))))- ( -18.20, z-score =  -0.01, R)
>consensus
_____AUUGCCGAACUCAAGCUAUU__AAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUUGCCUGCCUCAGGAGCUUUCAUUUGGCCAUUGGCAA
........(((((..((((((((.....(((((((....)))))))....))))))))....................((((......)).)).............))))).. ( -8.57 =  -9.92 +   1.35)

alignment

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secondary structure

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Window 4

Location 10,744,887 – 10,744,998
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 82.43
Shannon entropy 0.28964
G+C content 0.29223
Mean single sequence MFE -23.38
Consensus MFE -14.59
Energy contribution -16.28
Covariance contribution 1.69
Combinations/Pair 1.00
Mean z-score -2.64
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946908
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10744887 111 + 24543557
UGAAUAAUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGAAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGCA
.........(((((((..((((........(((((((((....))))))))).........(((((.((((((.....)))))).)))))......))))..))..))))) ( -30.20, z-score =  -4.46, R)
>droSim1.chr3L 10138226 111 + 22553184
AAAAUAAUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAA
.............(((..((((........(((((((((....))))))))).........(((((.((((((.....))).))))))))......))))..)))...... ( -25.20, z-score =  -2.85, R)
>droSec1.super_0 2965094 111 + 21120651
AAAAUAAUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGCAAGAAAGACUUCUUGAA
....................((((.(((..(((((((((....))))))))).))).))))(((((.((((((.....))).))))))))...((((((....)))))).. ( -27.40, z-score =  -2.94, R)
>droYak2.chr3L 10757288 88 + 24197627
UACAUAAUUUGUAAAGAAUUUCAAACUAAGUGUAUACCGUAGAAGGAAUUUAAUAACUUGA------------AAUAAUCAUUUGCGAGCAUAGAAUUAA-----------
.......(((((((((((((((((((.....))...((......))...........))))------------)))..)).))))))))...........----------- ( -10.70, z-score =  -0.31, R)
>consensus
AAAAUAAUUUGUAAAGGAUUUCAAACUAAAUGAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAA
.......((((((((.((((((((.(((..(((((((((....))))))))).))).)))).((((....))))..)))).))))))))...................... (-14.59 = -16.28 +   1.69)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,744,887 – 10,744,998
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 82.43
Shannon entropy 0.28964
G+C content 0.29223
Mean single sequence MFE -19.76
Consensus MFE -12.11
Energy contribution -12.68
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -2.99
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.05
SVM RNA-class probability 0.980666
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10744887 111 - 24543557
UGCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUUCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUCA
.(((..(((.....)))...)))(((.((((((.....)))))).)))..((((((((...(((((((....)))))))....)))))))).................... ( -25.80, z-score =  -5.35, R)
>droSim1.chr3L 10138226 111 - 22553184
UUCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUU
...(((((...............(((..(((((.....)))))..)))..((((((((...(((((((....)))))))....)))))))).............))))).. ( -21.70, z-score =  -3.64, R)
>droSec1.super_0 2965094 111 - 21120651
UUCAAGAAGUCUUUCUUGCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUU
..((((((....)))))).....(((..(((((.....)))))..)))..((((((((...(((((((....)))))))....)))))))).................... ( -24.70, z-score =  -3.60, R)
>droYak2.chr3L 10757288 88 - 24197627
-----------UUAAUUCUAUGCUCGCAAAUGAUUAUU------------UCAAGUUAUUAAAUUCCUUCUACGGUAUACACUUAGUUUGAAAUUCUUUACAAAUUAUGUA
-----------.......(((((.((..(((((((...------------...)))))))............))))))).((.(((((((.((....)).))))))).)). (  -6.84, z-score =   0.61, R)
>consensus
UUCAAUAAGUCUUUCUUUCAUGCUCGCAAAUGAUUAUUUCAUUGCCGAACUCAAGCUAUUAAAUUCCGUCUACGGAAUUCAUUUAGUUUGAAAUCCUUUACAAAUUAUUUA
..................................................((((((((...(((((((....)))))))....)))))))).................... (-12.11 = -12.68 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,744,918 – 10,745,033
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 65.36
Shannon entropy 0.57217
G+C content 0.35949
Mean single sequence MFE -23.60
Consensus MFE -7.30
Energy contribution -10.05
Covariance contribution 2.75
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533106
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 10744918 115 + 24543557
GAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGAAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGCAAUUGUAAUGAGCACGGCAGCAAGGACCUGAAACCU
((((((((....))))))))....(((...(((((.((((((.....)))))).)))))..........(.((((((((....)))))))))..)))....(((........))) ( -32.70, z-score =  -3.77, R)
>droSim1.chr3L 10138257 115 + 22553184
GAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAAACUGGAAUGAGUAGGGAUGCAAGUACCCAAAACCU
((((((((....))))))))....(((((.(((((.((((((.....))).))))))))...........(((((((........))))))).......)))))........... ( -26.80, z-score =  -2.15, R)
>droSec1.super_0 2965125 115 + 21120651
GAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGCAAGAAAGACUUCUUGAAAUUGGAAUGAGUAGGGAUGCAAGUACCCAAAACCU
((((((((....))))))))....((((..(((((.((((((.....))).))))))))...((((((....))))))..........)))).(((.((....)))))....... ( -28.30, z-score =  -1.89, R)
>droWil1.scaffold_180949 110006 88 - 6375548
GAACAAUUUUCAAAAAAGUUAACAACAUCUGUUCCAC-----AUUAGCUAUUAGC-------AAAAAAUAUCUUUACGUAAAUAAGAUGU-CAAACCGAUA--------------
..........................(((.(((....-----....((.....))-------.....(((((((.........)))))))-..))).))).-------------- (  -6.60, z-score =  -0.00, R)
>consensus
GAAUUCCGUAGACGGAAUUUAAUAGCUUGAGUUCGGCAAUGAAAUAAUCAUUUGCGAGCAUGAAAGAAAGACUUAUUGAAAUUGGAAUGAGCAGGGAUGCAAGUACCCAAAACCU
((((((((....))))))))..........(((((..(((((.....)))))..)))))........................................................ ( -7.30 = -10.05 +   2.75)

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 23:17:02 2011