Locus 9721

Sequence ID dm3.chr3R
Location 8,495,923 – 8,496,072
Length 149
Max. P 0.993126
window13331 window13332

overview

Window 1

Location 8,495,923 – 8,496,072
Length 149
Sequences 12
Columns 149
Reading direction forward
Mean pairwise identity 77.61
Shannon entropy 0.44401
G+C content 0.65607
Mean single sequence MFE -63.19
Consensus MFE -34.97
Energy contribution -34.68
Covariance contribution -0.29
Combinations/Pair 1.18
Mean z-score -2.01
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.34
SVM RNA-class probability 0.928359
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8495923 149 + 27905053
GGCGCAGUGAGUUGGCCAGCACCUCGGGCGACACGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAGACGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((......(((((((((((((.((.((....(((.(...((((((.(...(((((((.((....)).)))))))...).))))))...).)))...)).)).))))))))))))).(((.((.....)).)))...)))....... ( -75.60, z-score =  -2.56, R)
>droAna3.scaffold_13340 17017499 128 - 23697760
GGCGCAGUGAGUUGGCCAGCACUGGCGGCGAUCCACCCCGUUCCUUGAGCAGCUUCCUGCAGGACAACACG---------------------GGGCAGUCGGCCAAGGUGUUGGCCGAGGCGGCCAAAAAGGAUGUGCAGCGGAUCAGC
.(((((.((..((((((((((((...((((((...((((((((((...((((....))))))))....)))---------------------)))..))).)))..))))))))))))..)).((.....)).))))).((......)) ( -55.10, z-score =  -0.57, R)
>droEre2.scaffold_4770 4590936 149 - 17746568
GGCGCAGUGAGUUGGCCAGCACCUCGGGCGACACGCCCCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((......(((((((((((((.((.((((..(((((...((((((.(...(((((((.((....)).)))))))...).))))))...))))).)))).)).))))))))))))).(((.((.....)).)))...)))....... ( -85.60, z-score =  -4.75, R)
>droYak2.chr3R 12783120 149 + 28832112
GGCGCAGUGAGUUGGCCAGCACCUCGGGCGACACGCCCCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((......(((((((((((((.((.((((..(((((...((((((.(...(((((((.((....)).)))))))...).))))))...))))).)))).)).))))))))))))).(((.((.....)).)))...)))....... ( -85.60, z-score =  -4.75, R)
>droSec1.super_0 7631676 149 - 21120651
GGCGCAGUGAGUUGGCCAGCACCUCGGGCGACACGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGCAAUGGGUCAGGGUCAGGGGCAGUCAGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((......(((((((((((((..((((((..(((.(...((((((.(.....(((((.((....)).))))).....).))))))...).))).))).))).))))))))))))).(((.((.....)).)))...)))....... ( -74.30, z-score =  -2.29, R)
>droSim1.chr3R 14590330 149 - 27517382
GGCGCAGUGAGUUGGCCAGCACCUCGGGUGACACGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACCAGCAGGGAAUGGGUCAGGGUCAGGGGCAGUCAGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((......(((((((((((((.((.((((..(((.(...((((((.(...(((((((.((....)).)))))))...).))))))...).))).)))).)).))))))))))))).(((.((.....)).)))...)))....... ( -79.30, z-score =  -3.75, R)
>droWil1.scaffold_181130 2402678 125 + 16660200
GGCGUAGUGAGUUGGCCAGCACCGCGGGCGACAACGGACGUUCGCUGAGCAGCUUUCUGCACGA-GUCG-----------------------AGCGAGUCUGCCAAGGUUCUGGCCGAGGCGGCUAAAAAUGACGUGGAGCGGAUAAGC
.((.(((((..((((((((.(((...((((((......(((((((((.((((....)))).).)-).))-----------------------)))).))).)))..))).))))))))..).)))).......((.....)).....)) ( -44.30, z-score =   0.91, R)
>droPer1.super_19 397753 113 - 1869541
GGCGUAGUGAGUUGGCCAGCACCUCGGGGGCCAA------------GAGCAGCUUUCUGCAGGAGUCCA------------------------GCGAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGAUGUGCAGCGGAUCAGC
(((....((..(((((((((((((....((((..------------..((((....))))..((.((..------------------------..)).)))))).)))))))))))))..)))))......(((.((...)).)))... ( -48.10, z-score =  -0.88, R)
>dp4.chr2 25050732 113 - 30794189
GGCGUAGUGAGUUGGCCAGCACCUCGGGGGCCAA------------GAGCAGCUUUCUGCAGGAGUCCA------------------------GCGAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGAUGUGCAGCGGAUCAGC
(((....((..(((((((((((((....((((..------------..((((....))))..((.((..------------------------..)).)))))).)))))))))))))..)))))......(((.((...)).)))... ( -48.10, z-score =  -0.88, R)
>droVir3.scaffold_13047 11132014 125 - 19223366
GACGUAGUGAGCUGGCCAGCACCUCGGGCGAUAAGCCGAGAUCGCUCAGCAGCUUUCUGCAGGA-GACA-----------------------AGCGAAUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAACGAUGUGCAGCGCAUUAGC
....(((((.((((((((((((((.((.((((..((.(((....))).((((....)))).(..-..).-----------------------.))..)))).)).)))))))))))......((((.......)).))))).))))).. ( -54.40, z-score =  -2.12, R)
>droMoj3.scaffold_6540 28098995 125 + 34148556
GACGUAGUGAGCUGGCCAGCACCUCAGGCGACAAGCCGCGAUCGCUGAGCAGCUUCCUGCAGGA-GUCA-----------------------AGCGAUUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAUGACGUGCAGCGCAUCAGC
......(((.((((((((((((((..(....)..((((.(((((((((((((....))))....-.)).-----------------------)))))))))))..)))))))))))...(((..((....)).)))..))).))).... ( -50.50, z-score =  -0.10, R)
>droGri2.scaffold_15074 1531349 125 + 7742996
GACGUAGUGAGCUGGCCAGCACCACGGGCGAUAAGCCGCCAUCGCUGAGCAGUUUCCUGCAGGA-GACG-----------------------GGCGAAUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAACGAUGUGCAGCGCAUUAGC
....(((((.(((((((((((((..((.((((..(((((((....)).)).((((((....)))-))).-----------------------)))..)))).))..))))))))))......((((.......)).))))).))))).. ( -57.40, z-score =  -2.42, R)
>consensus
GGCGCAGUGAGUUGGCCAGCACCUCGGGCGACAAGCCGCGCUCCCUGAGCAGCUUCCUGCAGGACAACA_______________________GGCCAGUCGGCCAAGGUGCUGGCCGAGGCGGCCAAGAAGGACGUGCAGCGGAUCAGC
..(((.((....(((((((((((...(((...................((((....)))).(.....).................................)))..)))))))))))..(((.(.......).))))).)))....... (-34.97 = -34.68 +  -0.29)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,495,923 – 8,496,072
Length 149
Sequences 12
Columns 149
Reading direction reverse
Mean pairwise identity 77.61
Shannon entropy 0.44401
G+C content 0.65607
Mean single sequence MFE -59.69
Consensus MFE -32.70
Energy contribution -32.88
Covariance contribution 0.18
Combinations/Pair 1.18
Mean z-score -2.73
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.59
SVM RNA-class probability 0.993126
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 8495923 149 - 27905053
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGUCUGCCCCUGACCCUGACCCAUUCCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGCGGCGUGUCGCCCGAGGUGCUGGCCAACUCACUGCGCC
........((.(((((.((.....)).))....((((((((((((((.((.((((((((..((((((.(..((.(((((.((....)).))))).))..).)))))))).).)))).).)).)))))))))))))).......))))). ( -68.40, z-score =  -2.40, R)
>droAna3.scaffold_13340 17017499 128 + 23697760
GCUGAUCCGCUGCACAUCCUUUUUGGCCGCCUCGGCCAACACCUUGGCCGACUGCCC---------------------CGUGUUGUCCUGCAGGAAGCUGCUCAAGGAACGGGGUGGAUCGCCGCCAGUGCUGGCCAACUCACUGCGCC
((.(((((((.((.((.......)))).)).((((((((....))))))))..((((---------------------(((....((((((((....))))...)))))))))))))))))).(((((((..(.....).))))).)). ( -55.10, z-score =  -1.90, R)
>droEre2.scaffold_4770 4590936 149 + 17746568
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUGCCCCUGACCCUGACCCAUUCCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGGGGCGUGUCGCCCGAGGUGCUGGCCAACUCACUGCGCC
........((.(((((.((.....)).))....((((((((((((((.((((((((((...((((((.(..((.(((((.((....)).))))).))..).))))))...)))))).)))).)))))))))))))).......))))). ( -79.10, z-score =  -4.72, R)
>droYak2.chr3R 12783120 149 - 28832112
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUGCCCCUGACCCUGACCCAUUCCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGGGGCGUGUCGCCCGAGGUGCUGGCCAACUCACUGCGCC
........((.(((((.((.....)).))....((((((((((((((.((((((((((...((((((.(..((.(((((.((....)).))))).))..).))))))...)))))).)))).)))))))))))))).......))))). ( -79.10, z-score =  -4.72, R)
>droSec1.super_0 7631676 149 + 21120651
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCUGACUGCCCCUGACCCUGACCCAUUGCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGCGGCGUGUCGCCCGAGGUGCUGGCCAACUCACUGCGCC
........((.(((((.((.....)).))....((((((((((((((.(((((((((((..((((((.......(((((.((....)).))))).......)))))))).).)))).)))).)))))))))))))).......))))). ( -71.54, z-score =  -3.01, R)
>droSim1.chr3R 14590330 149 + 27517382
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCUGACUGCCCCUGACCCUGACCCAUUCCCUGCUGGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGCGGCGUGUCACCCGAGGUGCUGGCCAACUCACUGCGCC
........((.(((((.((.....)).))....((((((((((((((.(((((((((((..((((((.(..((.(((((.((....)).))))).))..).)))))))).).)))).)))).)))))))))))))).......))))). ( -71.30, z-score =  -3.64, R)
>droWil1.scaffold_181130 2402678 125 - 16660200
GCUUAUCCGCUCCACGUCAUUUUUAGCCGCCUCGGCCAGAACCUUGGCAGACUCGCU-----------------------CGAC-UCGUGCAGAAAGCUGCUCAGCGAACGUCCGUUGUCGCCCGCGGUGCUGGCCAACUCACUACGCC
((......(((.............)))......((((((.(((..(((.(((.((..-----------------------((..-((((((((....))))...)))).))..))..))))))...))).))))))..........)). ( -36.42, z-score =   0.51, R)
>droPer1.super_19 397753 113 + 1869541
GCUGAUCCGCUGCACAUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUCGC------------------------UGGACUCCUGCAGAAAGCUGCUC------------UUGGCCCCCGAGGUGCUGGCCAACUCACUACGCC
((......((.((.((.......)))).))...((((((((((((((((((.((..------------------------..)).))..((((....))))..------------..))))...))))))))))))..........)). ( -44.10, z-score =  -2.29, R)
>dp4.chr2 25050732 113 + 30794189
GCUGAUCCGCUGCACAUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUCGC------------------------UGGACUCCUGCAGAAAGCUGCUC------------UUGGCCCCCGAGGUGCUGGCCAACUCACUACGCC
((......((.((.((.......)))).))...((((((((((((((((((.((..------------------------..)).))..((((....))))..------------..))))...))))))))))))..........)). ( -44.10, z-score =  -2.29, R)
>droVir3.scaffold_13047 11132014 125 + 19223366
GCUAAUGCGCUGCACAUCGUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAUUCGCU-----------------------UGUC-UCCUGCAGAAAGCUGCUGAGCGAUCUCGGCUUAUCGCCCGAGGUGCUGGCCAGCUCACUACGUC
(((.....((.((.((.......)))).))...((((((((((((((.((((..(((-----------------------((.(-((..((((....)))).))))).....)))..)))).))))))))))))))))).......... ( -54.50, z-score =  -3.08, R)
>droMoj3.scaffold_6540 28098995 125 - 34148556
GCUGAUGCGCUGCACGUCAUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAAUCGCU-----------------------UGAC-UCCUGCAGGAAGCUGCUCAGCGAUCGCGGCUUGUCGCCUGAGGUGCUGGCCAGCUCACUACGUC
(((((.(((......((((....))))))).))(((((((((((..(..((.(((((-----------------------.((.-....((((....)))))))))))))((((....)))))..)))))))))))))).......... ( -54.90, z-score =  -1.70, R)
>droGri2.scaffold_15074 1531349 125 - 7742996
GCUAAUGCGCUGCACAUCGUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGAUUCGCC-----------------------CGUC-UCCUGCAGGAAACUGCUCAGCGAUGGCGGCUUAUCGCCCGUGGUGCUGGCCAGCUCACUACGUC
(((.....((.((.((.......)))).))...((((((((((.(((.((((..(((-----------------------.(((-((((((((....))))..)).)).))))))..)))).))).))))))))))))).......... ( -57.70, z-score =  -3.48, R)
>consensus
GCUGAUCCGCUGCACGUCCUUCUUGGCCGCCUCGGCCAGCACCUUGGCCGACUCCCC_______________________GGUUGUCCUGCAGGAAGCUGCUCAGGGAGCGCGGCGUGUCGCCCGAGGUGCUGGCCAACUCACUACGCC
((......((.((.((.......)))).))...((((((((((.(((.((...............................(....)..((((....))))..................)).))).))))))))))..........)). (-32.70 = -32.88 +   0.18)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:09:47 2011