Locus 11857

Sequence ID dm3.chr3R
Location 24,238,990 – 24,239,158
Length 168
Max. P 0.967181
window16297 window16298

overview

Window 7

Location 24,238,990 – 24,239,080
Length 90
Sequences 7
Columns 100
Reading direction reverse
Mean pairwise identity 70.76
Shannon entropy 0.56010
G+C content 0.44839
Mean single sequence MFE -21.16
Consensus MFE -9.27
Energy contribution -12.01
Covariance contribution 2.74
Combinations/Pair 1.35
Mean z-score -2.14
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967181
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24238990 90 - 27905053
----------UUCUUUUUUUUUCCACCCAUUUCGGCCCUUUUAUCCUCCGCCAGCGCUCCUUGCAGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
----------....................((((((..((((((..((((((.(((((......))))))))))).))))))..)))))).......... ( -23.60, z-score =  -3.36, R)
>droSim1.chr3R 23926389 93 - 27517382
-------UUCUUUUUUUUUUUUCUACCGACUUCGGCCCUUUUAUCCUCCGCCAGCACUCCUUGCAGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
-------....................(((((((((..((((((..((((((.(((((......))))))))))).))))))..))))))..)))..... ( -27.00, z-score =  -4.55, R)
>droSec1.super_22 842374 90 - 1066717
----------UUCUUUUUUUUUCUACCGACUUCGGCCCUUUUAUCCUCCGCCAGCACUCCUUGCGGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
----------.................(((((((((..((((((..((((((.(((((......))))))))))).))))))..))))))..)))..... ( -27.00, z-score =  -4.08, R)
>droYak2.chr3R 6571600 100 + 28832112
UUCCUUUUUUUCCACCCCCCCACCUCCCAUUUUGGCCCUUUUAUCCUCCGCGAACGCUCCUUGCAGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
..............................((..((..((((((((.(((((...((.....))..))))).)))..)))))..))..)).......... ( -19.30, z-score =  -1.95, R)
>droEre2.scaffold_4820 6667121 87 + 10470090
-----------UUCUUUCCCCCCCACC-AUUUCGGCACUUUUAUCCUCCGCCAG-GCUCUUUGCAGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
-----------................-..(((((((.((((((((.((((...-((.....))...)))).)))..))))).))))))).......... ( -22.60, z-score =  -2.63, R)
>droAna3.scaffold_13340 17039329 93 - 23697760
-------CUCCUACUCUUGCCUGAGGAUCCUUCCGCUUCCCCCGGCCACCCCGGUUCGCCUUGCAGUGUGGUUGAAAUAAAAAUGUUGAAUCGUCAUAAA
-------(..((((.((.((..(.(((....)))((.....((((.....))))...)))..)))).))))..).......................... ( -15.10, z-score =   1.01, R)
>droWil1.scaffold_181089 8904479 91 - 12369635
---------UCCCCAUCCACCAGCAACAUUCUGGAUUCUCUUACACUAAGCGCAGAUGCCUUGCAUUGCGGUUGAAAUAAAAAUGUUGAAUCGUCAUAAA
---------..............(((((((..((.....)).....(((.(((((.(((...)))))))).))).......)))))))............ ( -13.50, z-score =   0.60, R)
>consensus
__________UUCCUUUUUCCUCCACCCAUUUCGGCCCUUUUAUCCUCCGCCAGCACUCCUUGCAGUGCGGUGGAAAUAAAAAUGUUGAAUCGUCAUAAA
..............................((((((..((((((..((((((.(((((......))))))))))).))))))..)))))).......... ( -9.27 = -12.01 +   2.74)

alignment

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secondary structure

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dotplot

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Window 8

Location 24,239,058 – 24,239,158
Length 100
Sequences 9
Columns 115
Reading direction reverse
Mean pairwise identity 69.59
Shannon entropy 0.59982
G+C content 0.45059
Mean single sequence MFE -20.05
Consensus MFE -9.38
Energy contribution -9.90
Covariance contribution 0.52
Combinations/Pair 1.12
Mean z-score -1.17
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.53
SVM RNA-class probability 0.731440
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24239058 100 - 27905053
UUUAUUUACC--CACACCGGGGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGUUGCUGCUGCUCCUAGCUACUUCCUGUUUUCU---UUUUUUUUCCACCCAUUU----------
..........--.......(((.(((..(((......((((((((.......))))))))......)))..)))))).......---..................---------- ( -20.90, z-score =  -1.45, R)
>droSim1.chr3R 23926457 103 - 27517382
UUUAUUUACC--CACACCGGGGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGUUGCUGCUGCUCCUUGCUACUUCCUGUUUUCUUUUUUUUUUUUCUACCGACUU----------
........((--(.....)))(((((.(((.......((((((((.......))))))))))).)))))....................................---------- ( -21.81, z-score =  -1.69, R)
>droSec1.super_22 842442 100 - 1066717
UUUAUUUACC--CACACCGGGGCAAACGGCUUUUACAAGCAGUAAAUUUAAGUUGCUGCUGCUCCUUGCUACUUCCUGUUUUCU---UUUUUUUUCUACCGACUU----------
........((--(.....)))((((..(((.......((((((((.......)))))))))))..))))...............---..................---------- ( -18.21, z-score =  -0.89, R)
>droYak2.chr3R 6571668 110 + 28832112
UUUAUUUACC--CACACCGGGGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGUUGCUGCUGCUCCUUGCUACUUCCUGUUUUCCUUUUUUUCCACCCCCCCACCUCCCAUUU---
........((--(.....)))(((((.(((.......((((((((.......))))))))))).)))))...........................................--- ( -21.81, z-score =  -1.72, R)
>droEre2.scaffold_4820 6667188 98 + 10470090
UUUAUUUACC--CACACCGGGGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGUUGAUGCUGCUCCUUGCUACUUCCUGUUUUCUUUCCCCCCCACCAUUU---------------
........((--(.....)))(((((.(((.(((((.....)))))....(((....)))))).)))))...............................--------------- ( -16.80, z-score =   0.02, R)
>droAna3.scaffold_13340 17039387 112 - 23697760
UUUAUUUACC--CACACCGGAGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGAUGAUUCUGCUUC-GGCUCCUGCUUUUGCUCCUACUCUUGCCUGAGGAUCCUUCCGCUUCCCC
..........--......(((((((((((.......((((((..((((......)))))))))).-.....)))))..)))))).......((..(((....)))..))...... ( -25.42, z-score =  -0.81, R)
>dp4.chr2 20499326 80 + 30794189
UUUAUUUACCCACACACCGGAGCAAGCGGCUUUUACCAGCAGUAAAUUUAAGUUGAUGCUUGCUC-GAAU-CUCCCCCUGCC---------------------------------
...................(((((((((((((((((.....))))....))))...)))))))))-....-...........--------------------------------- ( -16.00, z-score =  -1.12, R)
>droPer1.super_0 10186814 80 - 11822988
UUUAUUUACCCACACACCGGAGCAAGCGGCUUUUACCAGCAGUAAAUUUAAGUUGAUGCUUGCUC-GAAU-CUCCCCCCGCC---------------------------------
...................(((((((((((((((((.....))))....))))...)))))))))-....-...........--------------------------------- ( -16.00, z-score =  -1.35, R)
>droWil1.scaffold_181089 8904548 100 - 12369635
UUUAUUUGCC--CACACCGGAGCUGGCGGCUUUUACAAGCAGUAAAUUUAAGUUGAUGCUGCUUCCGCACAGUUUCCGCUUCCCCA-UCCACCAGCAACAUUC------------
..........--.....((((((((((((.......((((((((............)))))))))))).))).)))))........-................------------ ( -23.51, z-score =  -1.50, R)
>consensus
UUUAUUUACC__CACACCGGGGCAAGCGGCUUUUACAAGCAGUAAAUUUAAGUUGAUGCUGCUCCUGGCUACUUCCUGUUUUCU___UUUUCCAUCAACC_AC_U__________
..................((((((..((((((((((.....))))....))))))....)))))).................................................. ( -9.38 =  -9.90 +   0.52)

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 00:51:00 2011