Locus 1841

Sequence ID dm3.chr2L
Location 14,369,723 – 14,369,846
Length 123
Max. P 0.959633
window2532 window2533 window2534

overview

Window 2

Location 14,369,723 – 14,369,824
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 86.09
Shannon entropy 0.23615
G+C content 0.53538
Mean single sequence MFE -31.76
Consensus MFE -29.42
Energy contribution -28.98
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -1.77
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14369723 101 - 23011544
UCCAACUCCAGCUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCGCAUGAUGGCUACAUUGGCGGCGGC
...(((..((((..((((.............))))..))))..)))..((((((.....))))))....((.((((((.(((((....))))))))))))) ( -37.62, z-score =  -2.60, R)
>droSim1.chr2L 14118310 101 - 22036055
UCCAACUCCAACUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCGCAUGAUGGCUACAUUGGCGGCGGC
..((((..((((..(((............)))..))))..))))....((((((.....))))))....((.((((((.(((((....))))))))))))) ( -32.80, z-score =  -1.61, R)
>droSec1.super_3 629341 101 - 7220098
UCCAACUCCAACUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCGCAUGAUGGCUACAUUGGCGGCGGC
..((((..((((..(((............)))..))))..))))....((((((.....))))))....((.((((((.(((((....))))))))))))) ( -32.80, z-score =  -1.61, R)
>droYak2.chr2L 14473766 90 - 22324452
------UCCAACUCCA-----ACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCGCAUGAUGGCUACAUUGGCGGCGGC
------..........-----........((((((((..((((((...((((((.....))))))....))).((((.....)))).)))..)))))))). ( -30.20, z-score =  -1.69, R)
>droEre2.scaffold_4929 6123401 84 - 26641161
------------UCCA-----ACUCCGACUUGCUGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCACAUGAUGGCUACAUUGGCGGCACC
------------..((-----((..((((.....))))..))))....((((((.....))))))...(((.(((((.(((.......))))))))))).. ( -25.40, z-score =  -1.32, R)
>consensus
UCCAACUCCAACUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGCAUGCCGCAUGAUGGCUACAUUGGCGGCGGC
.............................((((((((..((((((...((((((.....))))))....))).((((.....)))).)))..)))))))). (-29.42 = -28.98 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,369,753 – 14,369,846
Length 93
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 89.12
Shannon entropy 0.18287
G+C content 0.47463
Mean single sequence MFE -24.11
Consensus MFE -17.63
Energy contribution -18.55
Covariance contribution 0.92
Combinations/Pair 1.05
Mean z-score -2.62
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.35
SVM RNA-class probability 0.929744
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14369753 93 + 23011544
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACGGCGGAGUGAAGUGAAGCCGGAGCUGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....))))))..(((..((((..((((.............))))..))))..)))........))).....(....)... ( -28.82, z-score =  -3.33, R)
>droSim1.chr2L 14118340 93 + 22036055
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACGGCGGAGUGAAGUGAAGCCGGAGUUGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....))))))..(((..((((..((((.............))))..))))..)))........))).....(....)... ( -26.42, z-score =  -2.63, R)
>droSec1.super_3 629371 93 + 7220098
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACGGCGGAGUGAAGUGAAGCCGGAGUUGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....))))))..(((..((((..((((.............))))..))))..)))........))).....(....)... ( -26.42, z-score =  -2.63, R)
>droYak2.chr2L 14473796 82 + 22324452
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACGGCGGAGUGAAGU-----------UGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....))))))...((..((((..((((........))-----------))..))))..))...))).....(....)... ( -22.00, z-score =  -2.69, R)
>droEre2.scaffold_4929 6123431 76 + 26641161
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACAGC------AAGU-----------CGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....)))))).........((..((((------....-----------....))))..))...))).....(....)... ( -16.90, z-score =  -1.79, R)
>consensus
GCAAUAUGCUCGACUAACGAGCAAAAACAACAGCAACGGCGGAGUGAAGUGAAGCCGGAG_UGGAGUUGGAGUAACUGCAACAUGGAAACUAC
(((...((((((.....))))))...((..((((..((((...................))))..))))..))...))).....(....)... (-17.63 = -18.55 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 14,369,753 – 14,369,846
Length 93
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 89.12
Shannon entropy 0.18287
G+C content 0.47463
Mean single sequence MFE -20.42
Consensus MFE -14.40
Energy contribution -15.86
Covariance contribution 1.46
Combinations/Pair 1.09
Mean z-score -2.05
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.571519
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14369753 93 - 23011544
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCAGCUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((......(((..((((..((((.............))))..))))..)))..((((((.....)))))).))))) ( -25.42, z-score =  -3.16, R)
>droSim1.chr2L 14118340 93 - 22036055
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCAACUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((.....((((..((((..(((............)))..))))..))))....((((((.....)))))).))))) ( -20.60, z-score =  -1.84, R)
>droSec1.super_3 629371 93 - 7220098
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCAACUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((.....((((..((((..(((............)))..))))..))))....((((((.....)))))).))))) ( -20.60, z-score =  -1.84, R)
>droYak2.chr2L 14473796 82 - 22324452
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCA-----------ACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((.....((((..((-----------((...........))))..))))....((((((.....)))))).))))) ( -17.10, z-score =  -1.71, R)
>droEre2.scaffold_4929 6123431 76 - 26641161
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCG-----------ACUU------GCUGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((.....((((..((-----------((..------...))))..))))....((((((.....)))))).))))) ( -18.40, z-score =  -1.69, R)
>consensus
GUAGUUUCCAUGUUGCAGUUACUCCAACUCCA_CUCCGGCUUCACUUCACUCCGCCGUUGCUGUUGUUUUUGCUCGUUAGUCGAGCAUAUUGC
..............(((((.....((((..((((..(((............)))..))))..))))....((((((.....)))))).))))) (-14.40 = -15.86 +   1.46)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:39:52 2011