Locus 933

Sequence ID dm3.chr2L
Location 6,851,951 – 6,852,115
Length 164
Max. P 0.988238
window1262 window1263 window1264 window1265

overview

Window 2

Location 6,851,951 – 6,852,071
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.20
Shannon entropy 0.45492
G+C content 0.39820
Mean single sequence MFE -31.74
Consensus MFE -19.54
Energy contribution -20.86
Covariance contribution 1.32
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.31
SVM RNA-class probability 0.988238
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6851951 120 + 23011544
AUUCUUUAUUUUACUUCUUUUUUCGAGAGCAUUAGUCGCAAGUGCGUCUUCGCUAGCUUUGGAAUGUGUACUCGCUAAUAUGGAAGUAUGUACACACUGCAUAGAAUGAAAAAACGCUAU
....(((((((((........(((.(((((...((.(((....))).))......))))).)))(((((((..(((........)))..))))))).....))))))))).......... ( -28.10, z-score =  -0.90, R)
>droEre2.scaffold_4929 15770796 115 + 26641161
---UAUUAUUUUGCCACUUUUUCAGAGCUCA--AGUCGCAAGUGCGUCUUUGCUAGCAUUGGAGUGUGUACUCGCUAACUCGAAAGUGUGUACACACUGCCUAGAAUGUAAAAUCUUGUA
---....(((((((...........(((..(--((.(((....))).))).)))......(((((((((((.((((........)))).))))))))).))......)))))))...... ( -33.30, z-score =  -2.13, R)
>droYak2.chr2L 16271950 118 - 22324452
UUAAUUUAUUUUGCUCCUUUUUGAGAGUUUG--AGUCUCGAAUGCGUCUUUGCUAACGUUGGAGUGUGUACUCGCUAACUGGGCAGUGUGUACACACCGCAUACAAUGUAAAAUCACUUA
.......(((((((......((((((.....--..))))))((((((((..((....)).)))((((((((.((((........)))).))))))))))))).....)))))))...... ( -32.80, z-score =  -2.04, R)
>droSec1.super_3 2392143 104 + 7220098
UUUCUUUAUUUUGCUUCUUUUUUCGAGAGCAUUAGUCGCAAGUGCGUCUUCGCUAACUUUGGAGUGUGUACUCGCUAACAUGAAAGUGUGUACACACUCGCUAU----------------
...........((((.(((.....)))))))......(((((((((....)))..))))..((((((((((.((((........)))).))))))))))))...---------------- ( -31.90, z-score =  -3.13, R)
>droSim1.chr2L 6651487 104 + 22036055
UUUCUUUAUUUUGUUUCUUUUUUCGAGCGCAUUAGUCGCAAGUGCGUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAAAAUGGAAGUGUGUACACACUCGCUAU----------------
.........................(((((...((.(((....))).))..))........((((((((((.((((........)))).)))))))))))))..---------------- ( -32.60, z-score =  -3.12, R)
>consensus
UUUCUUUAUUUUGCUUCUUUUUUCGAGAGCAUUAGUCGCAAGUGCGUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAACAUGGAAGUGUGUACACACUGCCUAGAAUG_AAAA_C_____
.....................(((((((.....((.(((....))).))......)).)))))((((((((.((((........)))).))))))))....................... (-19.54 = -20.86 +   1.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,851,951 – 6,852,071
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.20
Shannon entropy 0.45492
G+C content 0.39820
Mean single sequence MFE -26.66
Consensus MFE -15.28
Energy contribution -15.00
Covariance contribution -0.28
Combinations/Pair 1.20
Mean z-score -1.70
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870533
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6851951 120 - 23011544
AUAGCGUUUUUUCAUUCUAUGCAGUGUGUACAUACUUCCAUAUUAGCGAGUACACAUUCCAAAGCUAGCGAAGACGCACUUGCGACUAAUGCUCUCGAAAAAAGAAGUAAAAUAAAGAAU
...((((((((.(...((.((.(((((((((...((........))...))))))))).)).))...).))))))))............((((.((.......))))))........... ( -23.70, z-score =  -0.60, R)
>droEre2.scaffold_4929 15770796 115 - 26641161
UACAAGAUUUUACAUUCUAGGCAGUGUGUACACACUUUCGAGUUAGCGAGUACACACUCCAAUGCUAGCAAAGACGCACUUGCGACU--UGAGCUCUGAAAAAGUGGCAAAAUAAUA---
....(((........))).((.(((((((((.(.((........)).).)))))))))))..(((((((.(((.(((....))).))--)..)).((.....)))))))........--- ( -28.90, z-score =  -1.25, R)
>droYak2.chr2L 16271950 118 + 22324452
UAAGUGAUUUUACAUUGUAUGCGGUGUGUACACACUGCCCAGUUAGCGAGUACACACUCCAACGUUAGCAAAGACGCAUUCGAGACU--CAAACUCUCAAAAAGGAGCAAAAUAAAUUAA
....((((((....((((..(((((((....)))))))((.((((((((((....))))....))))))............((((..--.....)))).....)).))))...)))))). ( -25.90, z-score =  -1.23, R)
>droSec1.super_3 2392143 104 - 7220098
----------------AUAGCGAGUGUGUACACACUUUCAUGUUAGCGAGUACACACUCCAAAGUUAGCGAAGACGCACUUGCGACUAAUGCUCUCGAAAAAAGAAGCAAAAUAAAGAAA
----------------...((((((((((((.(.((........)).).))))))))))..((((..(((....)))))))))......((((.((.......))))))........... ( -27.30, z-score =  -2.32, R)
>droSim1.chr2L 6651487 104 - 22036055
----------------AUAGCGAGUGUGUACACACUUCCAUUUUAGCGAGUACACACUCCAAAGCUAGCGAAGACGCACUUGCGACUAAUGCGCUCGAAAAAAGAAACAAAAUAAAGAAA
----------------.((((((((((((((.(.((........)).).))))))))))....))))(((.((.(((....))).))....))).......................... ( -27.50, z-score =  -3.10, R)
>consensus
_____G_UUUU_CAUUAUAGGCAGUGUGUACACACUUCCAUGUUAGCGAGUACACACUCCAAAGCUAGCGAAGACGCACUUGCGACUAAUGCGCUCGAAAAAAGAAGCAAAAUAAAGAAA
......................(((((((((.(.((........)).).)))))))))................(((....))).................................... (-15.28 = -15.00 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,851,991 – 6,852,111
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 75.74
Shannon entropy 0.42224
G+C content 0.39761
Mean single sequence MFE -27.83
Consensus MFE -18.57
Energy contribution -19.21
Covariance contribution 0.64
Combinations/Pair 1.05
Mean z-score -1.43
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.82
SVM RNA-class probability 0.826103
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6851991 120 + 23011544
AGUGCGUCUUCGCUAGCUUUGGAAUGUGUACUCGCUAAUAUGGAAGUAUGUACACACUGCAUAGAAUGAAAAAACGCUAUCUUAUUCCAGAACCUCAAAUCUUGUACAGCUUGAACUCUU
.(((((...........((((((((((((((..(((........)))..)))))).....((((..(......)..))))...))))))))...........)))))............. ( -22.35, z-score =   0.34, R)
>droEre2.scaffold_4929 15770831 119 + 26641161
AGUGCGUCUUUGCUAGCAUUGGAGUGUGUACUCGCUAACUCGAAAGUGUGUACACACUGCCUAGAAUGUAAAAUCUUGUACAUCCUUCAGGAUUGAAAA-UCUGUACAGUUGGAACUUUU
.((((..........((((((((((((((((.((((........)))).))))))))).))...)))))..(((((((.........))))))).....-...))))............. ( -32.40, z-score =  -1.70, R)
>droYak2.chr2L 16271988 119 - 22324452
AAUGCGUCUUUGCUAACGUUGGAGUGUGUACUCGCUAACUGGGCAGUGUGUACACACCGCAUACAAUGUAAAAUCACUUACAUUUUCCAGAACUCCAAA-ACUGUACAGUUUGAAUUUUU
.((((((((..((....)).)))((((((((.((((........)))).)))))))))))))..(((((((......))))))).............((-(((....)))))........ ( -30.40, z-score =  -1.64, R)
>droSec1.super_3 2392183 104 + 7220098
AGUGCGUCUUCGCUAACUUUGGAGUGUGUACUCGCUAACAUGAAAGUGUGUACACACU----------------CGCUAUCAUUUUCCAGAACCCAAAAUCUUGUACAGUUUGAACUUUU
((((((....)))........((((((((((.((((........)))).)))))))))----------------)))).........((((...(((....))).....))))....... ( -25.70, z-score =  -1.80, R)
>droSim1.chr2L 6651527 104 + 22036055
AGUGCGUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAAAAUGGAAGUGUGUACACACU----------------CGCUAUCAUUUUCCUGAACCUAAAAUGUUGUACAGUUUGAAAUUUU
.(((((.......((((....((((((((((.((((........)))).)))))))))----------------))))).((((((.........)))))).)))))............. ( -28.30, z-score =  -2.35, R)
>consensus
AGUGCGUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAACAUGGAAGUGUGUACACACUGC_UA_AAUG_AAAA_CGCUAUCAUUUUCCAGAACCCAAAAUCUUGUACAGUUUGAACUUUU
.(((((............(((((((((((((.((((........)))).))))))))............................)))))............)))))............. (-18.57 = -19.21 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,851,996 – 6,852,115
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.41
Shannon entropy 0.46253
G+C content 0.39426
Mean single sequence MFE -26.16
Consensus MFE -15.22
Energy contribution -15.82
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.18
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.548077
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 6851996 119 + 23011544
GUCUUCGCUAGCUUUGGAAUGUGUACUCGCUAAUAUGGAAGUAUGUACACACUGCAUAGAAUGAAAAAACGCUAUCUUAUUCCAGAACCUCAAAUCUUGUACAGCUUGAACUCUUUUAG-
(..((((..(((((((((((((((((..(((........)))..)))))).....((((..(......)..))))...))))))))....((.....))....)))))))..)......- ( -18.90, z-score =   0.71, R)
>droEre2.scaffold_4929 15770836 119 + 26641161
GUCUUUGCUAGCAUUGGAGUGUGUACUCGCUAACUCGAAAGUGUGUACACACUGCCUAGAAUGUAAAAUCUUGUACAUCCUUCAGGAUUGAAAAU-CUGUACAGUUGGAACUUUUCGGAG
.......(((((...(((((((((((.((((........)))).))))))))).))((((......(((((((.........))))))).....)-)))....)))))............ ( -32.10, z-score =  -1.64, R)
>droYak2.chr2L 16271993 119 - 22324452
GUCUUUGCUAACGUUGGAGUGUGUACUCGCUAACUGGGCAGUGUGUACACACCGCAUACAAUGUAAAAUCACUUACAUUUUCCAGAACUCCAAA-ACUGUACAGUUUGAAUUUUUUAGAG
.......((((...(((((((((....)))...((((((.((((....)))).))....(((((((......)))))))..)))).))))))((-(((....))))).......)))).. ( -29.10, z-score =  -1.23, R)
>droSec1.super_3 2392188 103 + 7220098
GUCUUCGCUAACUUUGGAGUGUGUACUCGCUAACAUGAAAGUGUGUACACACU----------------CGCUAUCAUUUUCCAGAACCCAAAAUCUUGUACAGUUUGAACUUUUAGAG-
...........(((((((((((((((.((((........)))).)))))))))----------------)............((((...(((....))).....))))......)))))- ( -23.50, z-score =  -1.43, R)
>droSim1.chr2L 6651532 103 + 22036055
GUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAAAAUGGAAGUGUGUACACACU----------------CGCUAUCAUUUUCCUGAACCUAAAAUGUUGUACAGUUUGAAAUUUUAGAG-
......(.((((....((((((((((.((((........)))).)))))))))----------------))))).)............(((((((.(((.......))).)))))))..- ( -27.20, z-score =  -2.30, R)
>consensus
GUCUUCGCUAGCUUUGGAGUGUGUACUCGCUAACAUGGAAGUGUGUACACACUGC_UA_AAUG_AAAA_CGCUAUCAUUUUCCAGAACCCAAAAUCUUGUACAGUUUGAACUUUUAGAG_
.................(((((((((.((((........)))).)))))))))................................................................... (-15.22 = -15.82 +   0.60)

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 21:22:18 2011