Locus 9063

Sequence ID	dm3.chr3R
Location	3,889,295 – 3,889,359
Length	64
Max. P	0.997040

overview

Window 4

Location	3,889,295 – 3,889,359
Length	64
Sequences	11
Columns	64
Reading direction	forward
Mean pairwise identity	77.77
Shannon entropy	0.48343
G+C content	0.49094
Mean single sequence MFE	-15.22
Consensus MFE	-8.92
Energy contribution	-9.10
Covariance contribution	0.18
Combinations/Pair	1.00
Mean z-score	-1.19
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.42
SVM RNA-class probability	0.689703
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3889295 64 + 27905053
CCCAAAAUAACCAACACUUGGCCAUCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGGACUC
.........((((....((((((.........))))))......)))).(((((....))))). ( -15.00, z-score =  -1.35, R)
>droPer1.super_0 11599551 58 - 11822988
CCCAAUAUAGCCAACACUUGGCCGGCCAAUUAGGGCAACUCAAGUGGUCAUCUCUCCC------
.........((((.....)))).(((((.((..(....)..)).))))).........------ ( -15.10, z-score =  -1.40, R)
>dp4.chr2 24394337 58 - 30794189
CCCAAUAUGGCCAACACUUGGCCAGCCAAUUAGGACAACUCAAGUGGUCAUCUCUCCC------
.......((((((.....))))))((((...((.....))....))))..........------ ( -13.20, z-score =  -0.92, R)
>droAna3.scaffold_13340 15160176 64 - 23697760
UUCGAAAUAACCAUCACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGGACUU
............(((((((((...(((.....)))....))))))))).(((((....))))). ( -16.10, z-score =  -1.46, R)
>droEre2.scaffold_4770 63484 64 - 17746568
UCCAAAAUAACCAACACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUCCAUGUGGACUC
..............(((((((...(((.....)))....)))))))...(((((....))))). ( -18.00, z-score =  -2.33, R)
>droYak2.chr3R 7968946 64 + 28832112
UCCAAAAUAACCAACACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGUACUC
.............((((((((((.........)))))).....((((.....)))))))).... ( -12.80, z-score =  -0.95, R)
>droSec1.super_0 3193102 64 - 21120651
UCCAAAAUAACCAACACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGGACUC
((((....(((...(((((((...(((.....)))....)))))))....)))....))))... ( -16.80, z-score =  -1.93, R)
>droSim1.chr3R 10156986 64 - 27517382
UCCAAAAUAACCAACACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGGACUC
((((....(((...(((((((...(((.....)))....)))))))....)))....))))... ( -16.80, z-score =  -1.93, R)
>droVir3.scaffold_13047 9912615 58 + 19223366
------ACAUCCUUCACUUGGCCAGCCAAUUAGGCCAACACUAGUGGCCAGAACGUGUGCUUUC
------((((..(((..((((....))))...(((((.......))))).))).))))...... ( -14.20, z-score =  -0.67, R)
>droMoj3.scaffold_6540 24685519 58 - 34148556
------ACAUCCUUCACUUGGCCAGCCAAUUAGGCCAACACAAGUGGGCAGAACGUGUGCUUUG
------........((((((....(((.....))).....))))))((((.......))))... ( -13.50, z-score =   0.25, R)
>droGri2.scaffold_14906 6639300 58 - 14172833
------ACAUCCUUCACUUGGCCAGCCAAUUAGGCCAACACAAGUGGGCAGAACGUGUGCUUGA
------...........((((((.........))))))..((((((.((.....)).)))))). ( -15.90, z-score =  -0.36, R)
>consensus
UCCAAAAUAACCAACACUUGGCCAGCCAAUUAGGCCAACUCAAGUGGUCAGUUCAUGUGGACUC
..............(((((((((.........))))).....)))).................. ( -8.92 =  -9.10 +   0.18)

alignment

secondary structure

dotplot

Window 5

Location	3,889,295 – 3,889,359
Length	64
Sequences	11
Columns	64
Reading direction	reverse
Mean pairwise identity	77.77
Shannon entropy	0.48343
G+C content	0.49094
Mean single sequence MFE	-23.43
Consensus MFE	-11.68
Energy contribution	-11.27
Covariance contribution	-0.40
Combinations/Pair	1.20
Mean z-score	-3.00
Structure conservation index	0.50
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.03
SVM RNA-class probability	0.997040
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3889295 64 - 27905053
GAGUCCACAUGAACUGACCACUUGAGUUGGCCUAAUUGGAUGGCCAAGUGUUGGUUAUUUUGGG
....(((....(((..((.(((((.(((..((.....))..))))))))))..)))....))). ( -19.80, z-score =  -1.66, R)
>droPer1.super_0 11599551 58 + 11822988
------GGGAGAGAUGACCACUUGAGUUGCCCUAAUUGGCCGGCCAAGUGUUGGCUAUAUUGGG
------((.........))...........((((((((((((((.....)))))))).)))))) ( -16.20, z-score =  -0.41, R)
>dp4.chr2 24394337 58 + 30794189
------GGGAGAGAUGACCACUUGAGUUGUCCUAAUUGGCUGGCCAAGUGUUGGCCAUAUUGGG
------......((..(((....).))..))(((((((((..((.....))..)))).))))). ( -17.60, z-score =  -0.92, R)
>droAna3.scaffold_13340 15160176 64 + 23697760
AAGUCCACAUGAACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGAUGGUUAUUUCGAA
.........((((.((((((((((.((..(((.....)))..)))))))...))))).)))).. ( -23.60, z-score =  -3.61, R)
>droEre2.scaffold_4770 63484 64 + 17746568
GAGUCCACAUGGACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGUUGGUUAUUUUGGA
...((((....(((..((.(((((.((..(((.....)))..)))))))))..)))....)))) ( -28.30, z-score =  -4.34, R)
>droYak2.chr3R 7968946 64 - 28832112
GAGUACACAUGAACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGUUGGUUAUUUUGGA
.......((..(((..((.(((((.((..(((.....)))..)))))))))..)))....)).. ( -24.30, z-score =  -3.67, R)
>droSec1.super_0 3193102 64 + 21120651
GAGUCCACAUGAACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGUUGGUUAUUUUGGA
...((((....(((..((.(((((.((..(((.....)))..)))))))))..)))....)))) ( -27.90, z-score =  -4.60, R)
>droSim1.chr3R 10156986 64 + 27517382
GAGUCCACAUGAACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGUUGGUUAUUUUGGA
...((((....(((..((.(((((.((..(((.....)))..)))))))))..)))....)))) ( -27.90, z-score =  -4.60, R)
>droVir3.scaffold_13047 9912615 58 - 19223366
GAAAGCACACGUUCUGGCCACUAGUGUUGGCCUAAUUGGCUGGCCAAGUGAAGGAUGU------
........(((((((...((((.(.((..(((.....)))..))).)))).)))))))------ ( -21.30, z-score =  -2.11, R)
>droMoj3.scaffold_6540 24685519 58 + 34148556
CAAAGCACACGUUCUGCCCACUUGUGUUGGCCUAAUUGGCUGGCCAAGUGAAGGAUGU------
........(((((((...((((((.((..(((.....)))..)))))))).)))))))------ ( -25.40, z-score =  -3.57, R)
>droGri2.scaffold_14906 6639300 58 + 14172833
UCAAGCACACGUUCUGCCCACUUGUGUUGGCCUAAUUGGCUGGCCAAGUGAAGGAUGU------
........(((((((...((((((.((..(((.....)))..)))))))).)))))))------ ( -25.40, z-score =  -3.49, R)
>consensus
GAGUCCACAUGAACUGACCACUUGAGUUGGCCUAAUUGGCUGGCCAAGUGUUGGUUAUUUUGGA
............(((...((((((.((((.((.....)).))))))))))..)))......... (-11.68 = -11.27 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:57:20 2011