Locus 8069

Sequence ID dm3.chr3L
Location 19,988,719 – 19,988,836
Length 117
Max. P 0.580039
window11103 window11104 window11105

overview

Window 3

Location 19,988,719 – 19,988,821
Length 102
Sequences 14
Columns 118
Reading direction forward
Mean pairwise identity 75.61
Shannon entropy 0.52201
G+C content 0.42402
Mean single sequence MFE -27.90
Consensus MFE -13.72
Energy contribution -13.33
Covariance contribution -0.39
Combinations/Pair 1.79
Mean z-score -1.28
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.580039
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19988719 102 + 24543557
---------------UCUUCUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
---------------................(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.09, R)
>droSim1.chr3L 19273067 102 + 22553184
---------------UCUUCUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
---------------................(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.09, R)
>droSec1.super_29 633646 102 + 700605
---------------UCUUCUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
---------------................(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.09, R)
>droWil1.scaffold_180727 938089 102 + 2741493
---------------UUUUUACAGGCAAUUUACGAUAUGCUAGGUGCAUGCUCAUCUAAUCGUCCAGCUGAUUCUGCAGAAGAGCGAGCA-AAAAAUAUUUUUGCUAAAAUGGAUGAA
---------------..................(((((((.....))))).))......((((((((((..(((....))).))).((((-(((.....)))))))....))))))). ( -25.70, z-score =  -1.21, R)
>droGri2.scaffold_15110 615749 102 - 24565398
---------------UCGUUUUAGGCAAUCUACGACAUGCUAGGAGCAUGCUCAUCAAAUCGUCCUGCUGACUCUGCAGAGGAGCGUGCA-AAAAAUAUAUUUGCUAAGAUGGAUGAA
---------------(((((((((.(((((((........)))).((((((((...........((((.......))))..)))))))).-..........))))))))))))..... ( -26.32, z-score =  -0.47, R)
>droMoj3.scaffold_6680 1484471 97 - 24764193
--------------------UCAGGCAAUCUAUGACAUGCUAGGCGCAUGCUCAUCAAAUCGUCCCGCUGAUUCAGCUGAGGAGCGAGCA-AAAAAUAUAUUUGCUAAGAUGGAUGAA
--------------------...........(((((((((.....))))).))))....((((((((((..(((....))).))))((((-((.......)))))).....)))))). ( -26.60, z-score =  -0.64, R)
>droYak2.chr3L 3617176 102 - 24197627
---------------UUCUCUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
---------------................(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.09, R)
>droEre2.scaffold_4784 19727794 102 + 25762168
---------------UUCUCUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
---------------................(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.09, R)
>droAna3.scaffold_13337 4009978 99 - 23293914
------------------UUUUAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGACUCAGCAGAAGAAAGAGCA-AAAAAUAUUUUUGCAAAAAUGGACGAA
------------------.............(((((((((.....))))).))))....(((((((((((...))))..........(((-(((.....)))))).....))))))). ( -28.20, z-score =  -2.69, R)
>droPer1.super_88 185418 104 - 213009
-------------UAUUGUUACAGGCAAUUUAUGAUAUGCUUGGAGCGUGCUCAUCCAAUCGUCCUGCAGACUCCGCGGAAGAACGAGCA-AAAAAUAUAUUUGCUAAGAUGGACGAA
-------------..(((((...(((((..(((....(((((((((....)))......((.(((.((.......))))).)).))))))-....)))...)))))......))))). ( -24.30, z-score =  -0.44, R)
>apiMel3.Group3 8692246 117 + 12341916
ACACUUUAAAUCGAUUUGUUUCAGGAUGCCGGUCUCGAGAGAAAGGAUUACCUUACGUAUAACGAUUUCAAGUUGAU-GAUGAAAGAGUACAAAGGCGAUUUCGUGGCAAUCGGUCUU
.........(((((((.((..(..((((((.(((((......((((....)))).(((.((((........))))))-)......))).))...))).)))..)..)))))))))... ( -25.10, z-score =   0.47, R)
>droVir3.scaffold_13049 7312017 102 - 25233164
---------------UUUUUUCAGGCAAUCUAUGACAUGCUAGGAGCAUGCUCAUCAAAUCGUCCCGCUGAUUCUGCAGAGGAGCGUGCA-AAAAAUAUAUUUGCUAAAAUGGAUGAA
---------------................(((((((((.....))))).))))....((((((((((..(((....))).)))).(((-((.......)))))......)))))). ( -24.80, z-score =  -0.38, R)
>anoGam1.chr2L 44041558 102 + 48795086
---------------UCUUCGCAGGCAAUAUACGACAUGCUGGGCGCGUGCUCAUCGAACAAACCGGCCGACUCGGCGGAGGAGCGCGCG-AAAAACAUCUUCGCCAAGAUGGAUGAA
---------------..(((((.((((..........))))..))((((((((..((.......))((((...))))....)))))))))-))...(((((((.....)).))))).. ( -33.00, z-score =  -0.43, R)
>triCas2.chrUn_22 88489 102 - 327011
---------------UUUUUCCAGGCUAUUUACGACAUGUUGGGCGCCUGUUCGUCCAACCGCCCUGCGGAUUCCGCCGAAGAGCGGGCA-AAGAACAUCUUCGCGAAAAUGGACGAG
---------------......(((((......(((....)))...))))).(((((((.((((.((.(((......))).)).))))((.-(((.....))).)).....))))))). ( -35.60, z-score =  -1.67, R)
>consensus
_______________UUUUUUCAGGCAAUUUAUGACAUGCUAGGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCA_AAAAAUAUUUUUGCAAAAAUGGACGAA
.................................(((((((.....))))).)).......(((((.((((...))))..........(((............)))......))))).. (-13.72 = -13.33 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,988,746 – 19,988,836
Length 90
Sequences 13
Columns 90
Reading direction forward
Mean pairwise identity 86.31
Shannon entropy 0.31107
G+C content 0.43162
Mean single sequence MFE -23.31
Consensus MFE -16.74
Energy contribution -16.93
Covariance contribution 0.19
Combinations/Pair 1.29
Mean z-score -1.45
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.572249
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19988746 90 + 24543557
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.30, R)
>droSim1.chr3L 19273094 90 + 22553184
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.30, R)
>droSec1.super_29 633673 90 + 700605
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.30, R)
>droWil1.scaffold_180727 938116 90 + 2741493
GGUGCAUGCUCAUCUAAUCGUCCAGCUGAUUCUGCAGAAGAGCGAGCAAAAAAUAUUUUUGCUAAAAUGGAUGAAAAUAAUGAUGGUCAA
......((..((((...((((((((((..(((....))).))).(((((((.....)))))))....))))))).......))))..)). ( -23.40, z-score =  -1.76, R)
>droGri2.scaffold_15110 615776 90 - 24565398
GGAGCAUGCUCAUCAAAUCGUCCUGCUGACUCUGCAGAGGAGCGUGCAAAAAAUAUAUUUGCUAAGAUGGAUGAAAAUAAUGAUGGUCAA
......((..(((((..((((((.(((..(((....))).)))..(((((.......)))))......))))))......)))))..)). ( -21.80, z-score =  -0.81, R)
>droMoj3.scaffold_6680 1484493 90 - 24764193
GGCGCAUGCUCAUCAAAUCGUCCCGCUGAUUCAGCUGAGGAGCGAGCAAAAAAUAUAUUUGCUAAGAUGGAUGAAAAUAACGAUGGUCAA
......((..((((...((((((((((..(((....))).))))((((((.......)))))).....)))))).......))))..)). ( -21.30, z-score =  -0.33, R)
>droYak2.chr3L 3617203 90 - 24197627
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.30, R)
>droEre2.scaffold_4784 19727821 90 + 25762168
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.30, R)
>droAna3.scaffold_13337 4010002 90 - 23293914
GGAGCGUGCUCAUCUAAUCGUCCAGCUGACUCAGCAGAAGAAAGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
.(((....)))......(((((((((((...))))..........((((((.....)))))).....)))))))................ ( -23.00, z-score =  -2.28, R)
>droPer1.super_88 185447 90 - 213009
GGAGCGUGCUCAUCCAAUCGUCCUGCAGACUCCGCGGAAGAACGAGCAAAAAAUAUAUUUGCUAAGAUGGACGAAAAUAAUGAUGGUCAA
.(((....)))......((((((...........(....)....((((((.......)))))).....))))))................ ( -18.20, z-score =   0.21, R)
>droVir3.scaffold_13049 7312044 90 - 25233164
GGAGCAUGCUCAUCAAAUCGUCCCGCUGAUUCUGCAGAGGAGCGUGCAAAAAAUAUAUUUGCUAAAAUGGAUGAAAAUAACGACGGUCAA
.(((....)))......((((((((((..(((....))).)))).(((((.......)))))......))))))................ ( -19.20, z-score =  -0.16, R)
>anoGam1.chr2L 44041585 90 + 48795086
GGCGCGUGCUCAUCGAACAAACCGGCCGACUCGGCGGAGGAGCGCGCGAAAAACAUCUUCGCCAAGAUGGAUGAAAAUAACGACGGUCAG
(((((((((((..((.......))((((...))))....))))))))(((.......))))))..(((.(.((.......)).).))).. ( -29.10, z-score =  -0.87, R)
>triCas2.chrUn_22 88516 90 - 327011
GGCGCCUGUUCGUCCAACCGCCCUGCGGAUUCCGCCGAAGAGCGGGCAAAGAACAUCUUCGCGAAAAUGGACGAGAACAACGACGGCCAA
(((.....((((((((.((((.((.(((......))).)).))))((.(((.....))).)).....))))))))..(......)))).. ( -32.00, z-score =  -1.37, R)
>consensus
GGAGCGUGCUCAUCUAAUCGUCCAGCUGAUUCAGCAGAAGAACGAGCAAAAAAUAUUUUUGCAAAAAUGGACGAAAAUAACGAUGGUCAA
......((..((((...((((((.((((...))))..........(((((.......)))))......)))))).......))))..)). (-16.74 = -16.93 +   0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,988,746 – 19,988,836
Length 90
Sequences 13
Columns 90
Reading direction reverse
Mean pairwise identity 86.31
Shannon entropy 0.31107
G+C content 0.43162
Mean single sequence MFE -22.75
Consensus MFE -14.44
Energy contribution -13.90
Covariance contribution -0.54
Combinations/Pair 1.45
Mean z-score -1.75
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540366
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 19988746 90 - 24543557
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.78, R)
>droSim1.chr3L 19273094 90 - 22553184
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.78, R)
>droSec1.super_29 633673 90 - 700605
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.78, R)
>droWil1.scaffold_180727 938116 90 - 2741493
UUGACCAUCAUUAUUUUCAUCCAUUUUAGCAAAAAUAUUUUUUGCUCGCUCUUCUGCAGAAUCAGCUGGACGAUUAGAUGAGCAUGCACC
.((....(((((....((.((((....(((((((.....))))))).(((.(((....)))..))))))).))...))))).....)).. ( -16.90, z-score =  -0.73, R)
>droGri2.scaffold_15110 615776 90 + 24565398
UUGACCAUCAUUAUUUUCAUCCAUCUUAGCAAAUAUAUUUUUUGCACGCUCCUCUGCAGAGUCAGCAGGACGAUUUGAUGAGCAUGCUCC
.......((((((...((.(((......(((((.......)))))..(((.(((....)))..))).))).))..))))))......... ( -20.30, z-score =  -1.55, R)
>droMoj3.scaffold_6680 1484493 90 + 24764193
UUGACCAUCGUUAUUUUCAUCCAUCUUAGCAAAUAUAUUUUUUGCUCGCUCCUCAGCUGAAUCAGCGGGACGAUUUGAUGAGCAUGCGCC
........(((.((.((((((.......(((((.......)))))(((.((((..((((...)))))))))))...)))))).))))).. ( -20.50, z-score =  -0.78, R)
>droYak2.chr3L 3617203 90 + 24197627
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.78, R)
>droEre2.scaffold_4784 19727821 90 - 25762168
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.78, R)
>droAna3.scaffold_13337 4010002 90 + 23293914
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCUUUCUUCUGCUGAGUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......(((((((.....((((((.....))))))..........((((...)))))))))))...))))..))...... ( -22.30, z-score =  -2.36, R)
>droPer1.super_88 185447 90 + 213009
UUGACCAUCAUUAUUUUCGUCCAUCUUAGCAAAUAUAUUUUUUGCUCGUUCUUCCGCGGAGUCUGCAGGACGAUUGGAUGAGCACGCUCC
...............((((((((.....(((((.......)))))(((((((...((((...))))))))))).))))))))........ ( -23.00, z-score =  -1.63, R)
>droVir3.scaffold_13049 7312044 90 + 25233164
UUGACCGUCGUUAUUUUCAUCCAUUUUAGCAAAUAUAUUUUUUGCACGCUCCUCUGCAGAAUCAGCGGGACGAUUUGAUGAGCAUGCUCC
.......((((((...((.(((......(((((.......))))).((((..((....))...))))))).))..))))))......... ( -18.70, z-score =  -0.58, R)
>anoGam1.chr2L 44041585 90 - 48795086
CUGACCGUCGUUAUUUUCAUCCAUCUUGGCGAAGAUGUUUUUCGCGCGCUCCUCCGCCGAGUCGGCCGGUUUGUUCGAUGAGCACGCGCC
...........(((((((..((.....)).))))))).....((((.((((....((((...))))(((.....)))..)))).)))).. ( -23.40, z-score =   1.08, R)
>triCas2.chrUn_22 88516 90 + 327011
UUGGCCGUCGUUGUUCUCGUCCAUUUUCGCGAAGAUGUUCUUUGCCCGCUCUUCGGCGGAAUCCGCAGGGCGGUUGGACGAACAGGCGCC
..(((.(((..(((..(((((((.....((((((.....))))))(((((((.(((......))).))))))).)))))))))))))))) ( -39.10, z-score =  -2.28, R)
>consensus
UUGACCAUCGUUAUUUUCGUCCAUUUUUGCAAAAAUAUUUUUUGCUCGUUCUUCUGCUGAAUCAGCUGGACGAUUAGAUGAGCACGCUCC
.((..((((.......((.(((......(((((.......)))))..........((((...)))).))).))...))))..))...... (-14.44 = -13.90 +  -0.54)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:38:51 2011