Locus 5979

Sequence ID dm3.chr3L
Location 2,880,788 – 2,880,950
Length 162
Max. P 0.944741
window8225 window8226

overview

Window 5

Location 2,880,788 – 2,880,950
Length 162
Sequences 8
Columns 169
Reading direction forward
Mean pairwise identity 74.68
Shannon entropy 0.53554
G+C content 0.41146
Mean single sequence MFE -39.13
Consensus MFE -20.94
Energy contribution -22.46
Covariance contribution 1.52
Combinations/Pair 1.25
Mean z-score -1.37
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.93
SVM RNA-class probability 0.855050
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2880788 162 + 24543557
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA-AGCAGCCACAAUAAAAAGACGUGCGGCAAAGGAAACCAGAAAUGUAUCUGACAGUUGGUGCUGCAGAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAGAACAUGAAUAGAAAAAUAAA------
((((((((((((((.......)))))))))(((((..(((((-.((.(((.((...........)).))).......(((((...(((.....))).))))))))))))......((....))))))).......))))).......................------ ( -41.40, z-score =  -1.69, R)
>droSim1.chr3L 2433756 162 + 22553184
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA-AGCAGCCACAAUAAAAAGACGUGCGGCAAAGGAAACCAGAAAUGUAUCUGACAGUUGGUGCUGCAGAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAAAACAUGAACAGAAAAAUAAA------
((((((((((((((.......)))))))))(((((..(((((-.((.(((.((...........)).))).......(((((...(((.....))).))))))))))))......((....))))))).......))))).......................------ ( -41.40, z-score =  -1.60, R)
>droSec1.super_2 2900928 162 + 7591821
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA-AGCAGCCACAAUAAAAAGACGUGCGGCAAAGGAAACCAGAAAUGUAUCUGACAUUUGGUGCUGCAGAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAAAACAUGAACAGAAAAAUAAA------
((((((((((((((.......)))))))))(((((..(((((-.((.(((.((...........)).))).......((((..(((((.....))))))))))))))))......((....))))))).......))))).......................------ ( -40.90, z-score =  -1.56, R)
>droYak2.chr3L 15147716 168 - 24197627
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA-AGCAGCUACAAUAAAAAGACGUGCGGCAAAGGAAACCAGAAAUGUAUCUGACAGUUGGCGCUGCAGAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAAAACAUGAACAGAAAAAUAAAUAAACA
((.(((((((((((.......))))))))))).))..(((..-..)))...............((((((((..(....)...(((((..((((.((((....))))))))..)))))...............))).)))))............................ ( -39.50, z-score =  -1.06, R)
>droEre2.scaffold_4784 2907565 168 + 25762168
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA-AGCAGCCACAAUAAAAAGACGUGCGGCAAGGCAAACCAGAAAUGUAUCUGACAGUUGGUGCUGCACAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAAAACAUGAACAGAAAAAUAAAUAAAAA
((((((((((((((.......)))))))))(((((..(((..-..)))...............((((((((.(((....((((......))))...)))..))))))))..............))))).......)))))............................. ( -42.40, z-score =  -1.48, R)
>droAna3.scaffold_13337 14086429 162 - 23293914
UGCGUGUCCUUUGCGAGGACAGCAAAGGACAUUCACAUCGCA-UGUAGCCACAAUACAAAGGAAAGCGGCAAAGGAAACCAGAAAUGUAUCUGACAGUUGCAGCAGU-UAAGUAUUUGAAAAAUGAACGAAAAGCGAGCA-AGGAUACGAAAAGGCAAAGAUAUC----
((((((((((((((.......)))))))))).......))))-....(((...............((.((((.(....)((((......))))....)))).))...-...((((((......((..((.....))..))-.)))))).....))).........---- ( -38.81, z-score =  -1.85, R)
>droWil1.scaffold_180698 351708 157 - 11422946
UGCGUGCCCUUUGUCAGGACAGCAAAGGACAUUCACAAUGCAGUUCAGUGGUA-----AGAGUUCAGGGAAAUACGAGAGAACAAAAUUUCUGACAGUUGCCAAGUGCCGCAUAUUUGAAAGAGAAGCGAAGCAAAAAAAAACUAUAUGUCCUAGAAAUAAA-------
(((.((.(((.....))).))))).((((((((((..((((.((....(((((-----(..((.(((..(....(....).......)..)))))..))))))...)).))))...))))......((...))..............)))))).........------- ( -33.20, z-score =  -0.22, R)
>droGri2.scaffold_15110 19448938 122 + 24565398
UGUGUGUCCUUUACCAGG-CAACAAAGGACAUUCACAUCGCA-UGCGGCAAC------------UGCAGCAACAACAACGUGAAA-GUAUCUGACAGUUGCAGCA----AAGUAUUUGAAAAAUGAAAGAAACGCGCGCGA----------------------------
((((((((((((....(.-...)))))))))..))))((((.-(((((((((------------(((((..((............-))..))).)))))))..((----(.....)))..............)))).))))---------------------------- ( -35.40, z-score =  -1.49, R)
>consensus
UGCGUGUCCUUUGUGAGGACAGCAAAGGACAUUCACACUGCA_AGCAGCCACAAUAAAAAGACGUGCGGCAAAGGAAACCAGAAAUGUAUCUGACAGUUGGUGCUGCAGAAGUAUUUGAAAAAUGAAUGAAAUGUGCGCACAAAACAUGAACAGAAAAAUAAA______
((((((((((((((.......))))))))).((((..((((...)))).................(((.(((.......((((......))))....))).)))............))))...............)))))............................. (-20.94 = -22.46 +   1.52)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,880,788 – 2,880,950
Length 162
Sequences 8
Columns 169
Reading direction reverse
Mean pairwise identity 74.68
Shannon entropy 0.53554
G+C content 0.41146
Mean single sequence MFE -38.35
Consensus MFE -19.73
Energy contribution -19.78
Covariance contribution 0.05
Combinations/Pair 1.45
Mean z-score -1.79
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 2880788 162 - 24543557
------UUUAUUUUUCUAUUCAUGUUCUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUCUGCAGCACCAACUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCACGUCUUUUUAUUGUGGCUGCU-UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
------.......................((((......................(((..((((((((.......(((((......)))))........((((((...........))))))))).-))))).)))..(((((((((.((....))))))))))))))) ( -39.80, z-score =  -2.41, R)
>droSim1.chr3L 2433756 162 - 22553184
------UUUAUUUUUCUGUUCAUGUUUUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUCUGCAGCACCAACUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCACGUCUUUUUAUUGUGGCUGCU-UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
------.......................((((......................(((..((((((((.......(((((......)))))........((((((...........))))))))).-))))).)))..(((((((((.((....))))))))))))))) ( -39.80, z-score =  -2.03, R)
>droSec1.super_2 2900928 162 - 7591821
------UUUAUUUUUCUGUUCAUGUUUUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUCUGCAGCACCAAAUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCACGUCUUUUUAUUGUGGCUGCU-UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
------.......................((((......................(((..((((((((.......(((((......)))))........((((((...........))))))))).-))))).)))..(((((((((.((....))))))))))))))) ( -39.80, z-score =  -1.98, R)
>droYak2.chr3L 15147716 168 + 24197627
UGUUUAUUUAUUUUUCUGUUCAUGUUUUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUCUGCAGCGCCAACUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCACGUCUUUUUAUUGUAGCUGCU-UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
.................((((((.....((((...........................(((((((......))).)))).........(((.......)))))))..............((((..-..))))))))))((((((((.((....))))))))))..... ( -36.00, z-score =  -0.77, R)
>droEre2.scaffold_4784 2907565 168 - 25762168
UUUUUAUUUAUUUUUCUGUUCAUGUUUUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUGUGCAGCACCAACUGUCAGAUACAUUUCUGGUUUGCCUUGCCGCACGUCUUUUUAUUGUGGCUGCU-UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
.................((((((.....(((((((((......................))))).))))..(((((((((......))))....((...((((((...........)))))).)).-.)))))))))))((((((((.((....))))))))))..... ( -44.25, z-score =  -2.44, R)
>droAna3.scaffold_13337 14086429 162 + 23293914
----GAUAUCUUUGCCUUUUCGUAUCCU-UGCUCGCUUUUCGUUCAUUUUUCAAAUACUUA-ACUGCUGCAACUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCUUUCCUUUGUAUUGUGGCUACA-UGCGAUGUGAAUGUCCUUUGCUGUCCUCGCAAAGGACACGCA
----(((((............)))))..-(((((((...((((..........(((((...-...((.((((...(((((......)))))......)))).))........))))).........-.)))).)))).((((((((((.......)))))))))).))) ( -37.79, z-score =  -2.36, R)
>droWil1.scaffold_180698 351708 157 + 11422946
-------UUUAUUUCUAGGACAUAUAGUUUUUUUUUGCUUCGCUUCUCUUUCAAAUAUGCGGCACUUGGCAACUGUCAGAAAUUUUGUUCUCUCGUAUUUCCCUGAACUCU-----UACCACUGAACUGCAUUGUGAAUGUCCUUUGCUGUCCUGACAAAGGGCACGCA
-------.........(((((((................((((...............))))(((...(((....((((.......((((..............))))...-----.....))))..)))...))).))))))).(((((((((.....)))))).))) ( -34.36, z-score =  -1.25, R)
>droGri2.scaffold_15110 19448938 122 - 24565398
----------------------------UCGCGCGCGUUUCUUUCAUUUUUCAAAUACUU----UGCUGCAACUGUCAGAUAC-UUUCACGUUGUUGUUGCUGCA------------GUUGCCGCA-UGCGAUGUGAAUGUCCUUUGUUG-CCUGGUAAAGGACACACA
----------------------------(((((((((.......)...............----(((.(((((((.(((..((-............))..)))))------------))))).)))-.))).))))).(((((((((...-.....))))))))).... ( -35.00, z-score =  -1.11, R)
>consensus
______UUUAUUUUUCUGUUCAUGUUUUGUGCGCACAUUUCAUUCAUUUUUCAAAUACUUCUGCAGCACCAACUGUCAGAUACAUUUCUGGUUUCCUUUGCCGCACGUCUUUUUAUUGUGGCUGCU_UGCAGUGUGAAUGUCCUUUGCUGUCCUCACAAAGGACACGCA
..............................(((((((((.((.................................(((((......)))))........((.((................)).))..)).))))))..(((((((((.((....)))))))))))))). (-19.73 = -19.78 +   0.05)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:58:56 2011