Locus 5277

Sequence ID dm3.chr2R
Location 19,127,173 – 19,127,275
Length 102
Max. P 0.837281
window7232 window7233

overview

Window 2

Location 19,127,173 – 19,127,275
Length 102
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 74.06
Shannon entropy 0.48383
G+C content 0.45783
Mean single sequence MFE -27.76
Consensus MFE -13.28
Energy contribution -15.17
Covariance contribution 1.89
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.534129
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19127173 102 + 21146708
AUUUGAACUUUUGGCACUCCGCAUGGUAAUUAAAGCGCAUA------AACAAGUCAAUAUCUGCGACAAUU-CAGCUGUCGCCCGAAUAGAAAGAGUGCCAGAAAGGGC
........((((((((((((((............)))....------...............((((((...-....))))))...........)))))))))))..... ( -26.40, z-score =  -1.28, R)
>droAna3.scaffold_13266 8220329 91 - 19884421
AAAUGUGUUUAUUACUCUCGCCAUGCUAAUUAAAGCACAUA------AAUAAGCCAAUAUCGAUGGGACAGCUGGAAGUCCCUCGGAGGGCGAGGGC------------
..............((((((((.((((......))))....------............((((.(((((........)))))))))..)))))))).------------ ( -30.50, z-score =  -2.91, R)
>droEre2.scaffold_4845 20495986 90 + 22589142
ACUCCAACUUUUGGCACUCCGCAGGGUAAUUGA------------------AGCCAGUAUCUGCGAGUUUU-CAGCUGUCGCCCGAAUAGCAAGAGUGCCAGAAAGGGC
...((...(((((((((((((((((...((((.------------------...)))).))))))......-..((((((....).)))))..)))))))))))..)). ( -33.40, z-score =  -2.76, R)
>droYak2.chr2R 19092267 108 + 21139217
AUUUGAACUUUUGGCACUCCGCAUGGUAAUUGAGGCGCAUAAUAAUAAACAAGCCAAUAUCUGCGAGUUCU-CAGCUGUCGCCCGAAUAGAAAGAGUGCCAGAAAGGGC
........(((((((((((((((.((((.....(((................)))..)))))))).((((.-..((....))..)))).....)))))))))))..... ( -28.59, z-score =  -0.82, R)
>droSec1.super_9 2420832 103 + 3197100
AUUUUAACUUUUGGCACUCCGCAUGGUAAUUAAAGCGCAUA------AACAAGUCAAUAUCUGCGACUUUUUCAGCUGUCGCCCGAAUAGAAAGAGUGCCAGAAAGGGC
........(((((((((((.(((((((....((((((((..------..............)))).))))....))))).)).(.....)...)))))))))))..... ( -25.39, z-score =  -0.97, R)
>droSim1.chr2R 17709241 102 + 19596830
AUUUGAACUUUUGGCACUCCGCAUGGUAAUUAAAGCGCAUA------AACAAGUCAAUAUCUGCGACUUUU-CAGCUGUCCCCCGAAUAGAAAGAGUGCCAGAAAGGGC
........(((((((((((((((.((((.............------..........)))))))).((.((-(...........))).))...)))))))))))..... ( -22.30, z-score =  -0.09, R)
>consensus
AUUUGAACUUUUGGCACUCCGCAUGGUAAUUAAAGCGCAUA______AACAAGCCAAUAUCUGCGACUUUU_CAGCUGUCGCCCGAAUAGAAAGAGUGCCAGAAAGGGC
........(((((((((((((((.((((.............................)))))))).............((....)).......)))))))))))..... (-13.28 = -15.17 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 19,127,173 – 19,127,275
Length 102
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 74.06
Shannon entropy 0.48383
G+C content 0.45783
Mean single sequence MFE -28.50
Consensus MFE -14.63
Energy contribution -15.70
Covariance contribution 1.07
Combinations/Pair 1.22
Mean z-score -1.72
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.86
SVM RNA-class probability 0.837281
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19127173 102 - 21146708
GCCCUUUCUGGCACUCUUUCUAUUCGGGCGACAGCUG-AAUUGUCGCAGAUAUUGACUUGUU------UAUGCGCUUUAAUUACCAUGCGGAGUGCCAAAAGUUCAAAU
(..((((.((((((((..((...((..(((((((...-..))))))).))....))......------....(((............)))))))))))))))..).... ( -29.70, z-score =  -2.14, R)
>droAna3.scaffold_13266 8220329 91 + 19884421
------------GCCCUCGCCCUCCGAGGGACUUCCAGCUGUCCCAUCGAUAUUGGCUUAUU------UAUGUGCUUUAAUUAGCAUGGCGAGAGUAAUAAACACAUUU
------------((.((((((...((((((((........))))).))).............------...(((((......))))))))))).))............. ( -29.10, z-score =  -3.31, R)
>droEre2.scaffold_4845 20495986 90 - 22589142
GCCCUUUCUGGCACUCUUGCUAUUCGGGCGACAGCUG-AAAACUCGCAGAUACUGGCU------------------UCAAUUACCCUGCGGAGUGCCAAAAGUUGGAGU
.((((((.((((((((......(((((.(....))))-))....(((((.........------------------.........)))))))))))))))))..))... ( -26.37, z-score =  -0.51, R)
>droYak2.chr2R 19092267 108 - 21139217
GCCCUUUCUGGCACUCUUUCUAUUCGGGCGACAGCUG-AGAACUCGCAGAUAUUGGCUUGUUUAUUAUUAUGCGCCUCAAUUACCAUGCGGAGUGCCAAAAGUUCAAAU
(..((((.(((((((((....(((.(((((.((..((-(((((..((........))..)))).)))...))))))).)))........)))))))))))))..).... ( -29.80, z-score =  -1.39, R)
>droSec1.super_9 2420832 103 - 3197100
GCCCUUUCUGGCACUCUUUCUAUUCGGGCGACAGCUGAAAAAGUCGCAGAUAUUGACUUGUU------UAUGCGCUUUAAUUACCAUGCGGAGUGCCAAAAGUUAAAAU
...((((.(((((((((....(((..((((.((..((((.((((((.......)))))).))------))))))))..)))........)))))))))))))....... ( -28.10, z-score =  -1.71, R)
>droSim1.chr2R 17709241 102 - 19596830
GCCCUUUCUGGCACUCUUUCUAUUCGGGGGACAGCUG-AAAAGUCGCAGAUAUUGACUUGUU------UAUGCGCUUUAAUUACCAUGCGGAGUGCCAAAAGUUCAAAU
(..((((.((((((((...((.(((((.......)))-)).)).((((...(((((..(((.------...)))..))))).....))))))))))))))))..).... ( -27.90, z-score =  -1.26, R)
>consensus
GCCCUUUCUGGCACUCUUUCUAUUCGGGCGACAGCUG_AAAACUCGCAGAUAUUGACUUGUU______UAUGCGCUUUAAUUACCAUGCGGAGUGCCAAAAGUUCAAAU
........((((((((..........(((....)))........((((...(((((..(((..........)))..))))).....))))))))))))........... (-14.63 = -15.70 +   1.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:09 2011