Locus 2207

Sequence ID dm3.chr2L
Location 17,020,774 – 17,020,878
Length 104
Max. P 0.614378
window3046 window3047

overview

Window 6

Location 17,020,774 – 17,020,878
Length 104
Sequences 11
Columns 112
Reading direction forward
Mean pairwise identity 72.19
Shannon entropy 0.58871
G+C content 0.43540
Mean single sequence MFE -22.70
Consensus MFE -10.90
Energy contribution -10.88
Covariance contribution -0.02
Combinations/Pair 1.07
Mean z-score -1.04
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.614378
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17020774 104 + 23011544
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUUAAGGCACUG--GG--GGAGGCCAAGAAA-AUUCGAGGAGC---GGAAGAGACCUGGCUAAAA
............(((...((((.(..((((((.((....))...))))))..)))))..--..--)))((((..((..-..)).(((..(---....)...))))))).... ( -24.10, z-score =  -0.99, R)
>droSim1.chr2L 16702741 104 + 22036055
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUUAAGGCACUG--GG--GGAGGCCAAGAAA-AUUCGAGGAGC---GGAAGAGACCUGGCUAAAA
............(((...((((.(..((((((.((....))...))))))..)))))..--..--)))((((..((..-..)).(((..(---....)...))))))).... ( -24.10, z-score =  -0.99, R)
>droSec1.super_7 652938 104 + 3727775
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUUAAGGCACUG--GG--GGAGGCAAAGAAA-AUUCGAGGAGC---GGAAGAGACCUGGCUAAAA
...(((..((..(((...((((.(..((((((.((....))...))))))..)))))..--.)--))..)).......-.....(((..(---....)...))).))).... ( -22.50, z-score =  -0.92, R)
>droYak2.chr2R 17053650 104 - 21139217
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUUAAGGCACUG--GG--GGAGGCCAACAAA-AUUCGAGGAGC---GGAAGAAACCUGGCUAAAA
....((..((..(((...((((.(..((((((.((....))...))))))..)))))..--.)--))..))..))...-...(.(((..(---....)...))).)...... ( -22.60, z-score =  -0.51, R)
>droEre2.scaffold_4845 15372777 104 - 22589142
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUUAAGGCACUG--GG--GGAGGCCAACAAA-AUUCGAGGAGC---GGAAGAGACCUGGCUAAAA
....((..((..(((...((((.(..((((((.((....))...))))))..)))))..--.)--))..))..))...-...(.(((..(---....)...))).)...... ( -22.60, z-score =  -0.42, R)
>droAna3.scaffold_12916 12356978 105 - 16180835
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAGGCACAGA-GG--GGAGGCCACGGCACAUUCGAGGAA----GGAAGAGUCCUGGCUAAAA
............(((.((((((.(...(((((.((....))...)))))...))))))).-))--)..(((((.(((.(.(((......----))).).))).))))).... ( -26.90, z-score =  -2.04, R)
>dp4.chr4_group3 168802 111 - 11692001
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAGGCAGGAG-AGCCGGAGAGCGGUAGAGCUGUAGAGAACCGAGGCAAAAACCUGGCUAAAA
.(((........))).((.(((.(...(((((.((....))...)))))...)))).)).-((((......((((....((....)).))))(((......))))))).... ( -22.80, z-score =   0.18, R)
>droWil1.scaffold_180703 1133290 100 + 3946847
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAGGCAAAGGUAGACUGGUACUGGUUCAGGUACAGGUGGGUUUUGUGUGG------------
.(((........)))......((((((((..((((...((((.(((.((.......)).))))))).(((((......)))))..))))..)))))))).------------ ( -21.90, z-score =  -0.66, R)
>droMoj3.scaffold_6500 27412818 98 - 32352404
UGGAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAACGGCACAG--GGCACAGGUAGA-GAGCCAGCCUAGCAGUACUUAUGCAGA-----------
..(((((.((((....((((((.((..(((((.((....))...)))))..))))))))--(((...(((...-..))).)))))))..))))).......----------- ( -26.70, z-score =  -1.64, R)
>droVir3.scaffold_13246 986047 85 + 2672878
UGGAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAAGCACAG--AGCCCAGGUAC--GAACCAAAGCAGCAG-----------------------
..(((((...))))).((((((.....(((((.((....))...)))))....))))))--.((...(((..--..)))...)).....----------------------- ( -17.00, z-score =  -0.99, R)
>droGri2.scaffold_15252 960192 96 - 17193109
UGGAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAAGCACAG--AGCCCAGGUAAAAGAAGAAGAAGAAUAAGAGCCAAAA--------------
(((......((((((.((((((.....(((((.((....))...)))))....))))))--.((....)).............))))))...)))...-------------- ( -18.50, z-score =  -2.50, R)
>consensus
AGAAGUAAGUUAUUCAUUGUGCACGCAAACAUUACGGAAGUCAUAUGUUAAAGGCACAG__GG__GGAGGCCAAGAAA_AUUCGAGGAGC___GGAAGAGACCUGGCUAAAA
.(((........)))...((((.....(((((.((....))...)))))....))))....................................................... (-10.90 = -10.88 +  -0.02)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 17,020,774 – 17,020,878
Length 104
Sequences 11
Columns 112
Reading direction reverse
Mean pairwise identity 72.19
Shannon entropy 0.58871
G+C content 0.43540
Mean single sequence MFE -17.93
Consensus MFE -7.99
Energy contribution -8.03
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.15
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.18
SVM RNA-class probability 0.581153
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17020774 104 - 23011544
UUUUAGCCAGGUCUCUUCC---GCUCCUCGAAU-UUUCUUGGCCUCC--CC--CAGUGCCUUAAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.....((((((....(((.---.......))).-...))))))....--..--..(((((.((((((((((.....))).))))))).).)))).................. ( -21.20, z-score =  -2.47, R)
>droSim1.chr2L 16702741 104 - 22036055
UUUUAGCCAGGUCUCUUCC---GCUCCUCGAAU-UUUCUUGGCCUCC--CC--CAGUGCCUUAAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.....((((((....(((.---.......))).-...))))))....--..--..(((((.((((((((((.....))).))))))).).)))).................. ( -21.20, z-score =  -2.47, R)
>droSec1.super_7 652938 104 - 3727775
UUUUAGCCAGGUCUCUUCC---GCUCCUCGAAU-UUUCUUUGCCUCC--CC--CAGUGCCUUAAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.....((.(((....(((.---.......))).-...))).))....--..--..(((((.((((((((((.....))).))))))).).)))).................. ( -14.70, z-score =  -0.71, R)
>droYak2.chr2R 17053650 104 + 21139217
UUUUAGCCAGGUUUCUUCC---GCUCCUCGAAU-UUUGUUGGCCUCC--CC--CAGUGCCUUAAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.....(((((.....(((.---.......))).-....)))))....--..--..(((((.((((((((((.....))).))))))).).)))).................. ( -17.50, z-score =  -0.69, R)
>droEre2.scaffold_4845 15372777 104 + 22589142
UUUUAGCCAGGUCUCUUCC---GCUCCUCGAAU-UUUGUUGGCCUCC--CC--CAGUGCCUUAAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.....(((((.....(((.---.......))).-....)))))....--..--..(((((.((((((((((.....))).))))))).).)))).................. ( -17.50, z-score =  -0.73, R)
>droAna3.scaffold_12916 12356978 105 + 16180835
UUUUAGCCAGGACUCUUCC----UUCCUCGAAUGUGCCGUGGCCUCC--CC-UCUGUGCCUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
(((.((..((((....)))----)..)).)))((((((((((((...--..-...).)))...((((((((.....))).))))).))).)))))................. ( -19.90, z-score =  -1.52, R)
>dp4.chr4_group3 168802 111 + 11692001
UUUUAGCCAGGUUUUUGCCUCGGUUCUCUACAGCUCUACCGCUCUCCGGCU-CUCCUGCCUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
....((((((((....)))).)))).......((.....(((.....(((.-.....)))...((((((((.....))).))))).))).)).................... ( -19.10, z-score =  -0.40, R)
>droWil1.scaffold_180703 1133290 100 - 3946847
------------CCACACAAAACCCACCUGUACCUGAACCAGUACCAGUCUACCUUUGCCUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
------------................(((((.(((((...(((.((((....................))))...)))..))))).)))))................... ( -10.55, z-score =   0.07, R)
>droMoj3.scaffold_6500 27412818 98 + 32352404
-----------UCUGCAUAAGUACUGCUAGGCUGGCUC-UCUACCUGUGCC--CUGUGCCGUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUCCA
-----------...(((((.(((..(((.....)))..-..))).))))).--.((((((((.((((((((.....))).))))).))).)))))................. ( -23.90, z-score =  -1.64, R)
>droVir3.scaffold_13246 986047 85 - 2672878
-----------------------CUGCUGCUUUGGUUC--GUACCUGGGCU--CUGUGCUUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUCCA
-----------------------.....(((..(((..--..)))..))).--.(((((....((((((((.....))).))))).....)))))................. ( -17.70, z-score =  -0.93, R)
>droGri2.scaffold_15252 960192 96 + 17193109
--------------UUUUGGCUCUUAUUCUUCUUCUUCUUUUACCUGGGCU--CUGUGCUUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUCCA
--------------....(((((.......................)))))--.(((((....((((((((.....))).))))).....)))))................. ( -14.00, z-score =  -1.19, R)
>consensus
UUUUAGCCAGGUCUCUUCC___GCUCCUCGAAU_UUUCUUGGCCUCC__CC__CAGUGCCUUUAACAUAUGACUUCCGUAAUGUUUGCGUGCACAAUGAAUAACUUACUUCU
.......................................................(((((...((((((((.....))).)))))...).)))).................. ( -7.99 =  -8.03 +   0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:46:57 2011