Locus 1865

Sequence ID dm3.chr2L
Location 14,456,974 – 14,457,076
Length 102
Max. P 0.966520
window2568 window2569

overview

Window 8

Location 14,456,974 – 14,457,076
Length 102
Sequences 12
Columns 110
Reading direction forward
Mean pairwise identity 83.99
Shannon entropy 0.33686
G+C content 0.42191
Mean single sequence MFE -30.71
Consensus MFE -18.64
Energy contribution -18.70
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -2.58
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.77
SVM RNA-class probability 0.966520
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14456974 102 + 23011544
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCU---UCAGCUGGCUGGCUACUGUCAGUCA-CUUGACCUUUUUUC----
..........(((.........((((((((...)))))))).((((((((..(((((((((..---.)))).)))))..))))))))))).-..............---- ( -33.40, z-score =  -3.27, R)
>droSim1.chr2L 14205553 102 + 22036055
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCU---UCAGCUGGCUGGCUACUGUCAGUCA-CUUGACCUUUUUUC----
..........(((.........((((((((...)))))))).((((((((..(((((((((..---.)))).)))))..))))))))))).-..............---- ( -33.40, z-score =  -3.27, R)
>droSec1.super_3 716010 102 + 7220098
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCU---UCAGCUGGCUGGCUACUGUCAGUCA-CUUGACCUUUUUUC----
..........(((.........((((((((...)))))))).((((((((..(((((((((..---.)))).)))))..))))))))))).-..............---- ( -33.40, z-score =  -3.27, R)
>droYak2.chr2L 14563560 102 + 22324452
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCU---UCAGCUGGCUGGCUACUGUCAGACA-CUUGACCUUUUUUC----
....(((((.(((((((..(..((((((((...))))))))..).((((...((((((.....---.))))))))))..))))))))))))-..............---- ( -32.10, z-score =  -2.97, R)
>droEre2.scaffold_4929 6212249 105 + 26641161
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCUGCUUCAGCUGCCUGGCUACUGUCAGUCA-CUUGACCUUUUUUC----
..........(((((((..(..((((((((...))))))))....(((((((((((....)))))))..))))...)..))))))).(((.-...)))........---- ( -33.30, z-score =  -3.09, R)
>droAna3.scaffold_12916 14816849 101 - 16180835
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCG----UUGCUGCCUGGCUACUGUCAGUCA-CUUGACCUUUUUUC----
..........(((((((..(..((((((((...))))))))..).(((..((((((......)----)))))..)))..))))))).(((.-...)))........---- ( -30.90, z-score =  -2.90, R)
>dp4.chr4_group1 1845315 105 - 5278887
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCAGCCGCUG---CUGUUG-CCGGCUUCUGUCAGUCA-CUUGACCUUUUUUUUUUC
..........(((((....(..((((((((...))))))))..)..(((..((((((((....)---))))))-)..))).))))).(((.-...)))............ ( -30.90, z-score =  -3.07, R)
>droPer1.super_5 1786359 105 + 6813705
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCAGCCGCUG---CUGUUG-CCGGCUUCUGUCAGUCA-CUUGACCUUUUUUUUUUC
..........(((((....(..((((((((...))))))))..)..(((..((((((((....)---))))))-)..))).))))).(((.-...)))............ ( -30.90, z-score =  -3.07, R)
>droWil1.scaffold_180764 2749417 98 + 3949147
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCCGCGG--------ACUUGGCUACUGUCAGUCAAUUUGACCUUUUUUU----
..........(((((((..(..((((((((...))))))))..)....(((((.((....))..--------)))))..))))))).(((.....)))........---- ( -25.80, z-score =  -2.00, R)
>droVir3.scaffold_12723 3076292 92 - 5802038
UAUUUGUUUCGACAGUUAACUUGAUGUGUUUAUGACACGUCUUGACAGUAAGUAGCUGCUGCG------GAC--UUGGCUACUGUCAGU-------GCGUGUUGACC---
........((((((((......((((((((...))))))))((((((((((((.((....)).------.))--)....))))))))).-------)).))))))..--- ( -27.10, z-score =  -1.19, R)
>droMoj3.scaffold_6500 16385530 98 - 32352404
UAUUUGUUUCGACAGUAAAGCUGAUGUGUUUAUGACACGUCUUGACAGUAAGUAGCUGCUGCG------GAC--CUGACUACUGUCUGUAG-CCGAGCGUGUUGACC---
........((((((((..((((((((((((...))))))))...((.....))))))((((((------(((--.........))))))))-)...)).))))))..--- ( -29.20, z-score =  -1.47, R)
>droGri2.scaffold_15126 782098 98 + 8399593
UAUUUGUUUCGACAGUAAAGUUGAUGUGUUUAUGACACGUCUUGACACUAAGUAGCCGCCGCA------GACUACUGGCUACUGUCCGU-----GUGCGUGUUGACCUU-
........((((((((......((((((((...))))))))...((((..((((((((.....------......))))))))....))-----)))).))))))....- ( -28.10, z-score =  -1.38, R)
>consensus
UAUUUGUUUCGACAGUAAACUUGAUGUGUUUAUGACACAUCUUGACAGUAAGUAGCUGCUGCU____CAGCUG_CUGGCUACUGUCAGUCA_CUUGACCUUUUUUC____
..........(((((((.....((((((((...)))))))).............((....)).................)))))))........................ (-18.64 = -18.70 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,456,974 – 14,457,076
Length 102
Sequences 12
Columns 110
Reading direction reverse
Mean pairwise identity 83.99
Shannon entropy 0.33686
G+C content 0.42191
Mean single sequence MFE -27.19
Consensus MFE -14.36
Energy contribution -14.47
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.28
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.773831
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 14456974 102 - 23011544
----GAAAAAAGGUCAAG-UGACUGACAGUAGCCAGCCAGCUGA---AGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((...-.))))((((((((..(((..((((.---..)))).)))..))))))))..(((((((.....)))))))..((((.......))))..... ( -30.00, z-score =  -3.00, R)
>droSim1.chr2L 14205553 102 - 22036055
----GAAAAAAGGUCAAG-UGACUGACAGUAGCCAGCCAGCUGA---AGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((...-.))))((((((((..(((..((((.---..)))).)))..))))))))..(((((((.....)))))))..((((.......))))..... ( -30.00, z-score =  -3.00, R)
>droSec1.super_3 716010 102 - 7220098
----GAAAAAAGGUCAAG-UGACUGACAGUAGCCAGCCAGCUGA---AGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((...-.))))((((((((..(((..((((.---..)))).)))..))))))))..(((((((.....)))))))..((((.......))))..... ( -30.00, z-score =  -3.00, R)
>droYak2.chr2L 14563560 102 - 22324452
----GAAAAAAGGUCAAG-UGUCUGACAGUAGCCAGCCAGCUGA---AGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----........(.((.(-((..(((((((((..(((..((((.---..)))).)))..))))))))).(((((((.....))))))).....))))).).......... ( -28.50, z-score =  -2.52, R)
>droEre2.scaffold_4929 6212249 105 - 26641161
----GAAAAAAGGUCAAG-UGACUGACAGUAGCCAGGCAGCUGAAGCAGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((...-.))))((((((((.(.(((((...(((.(((....))).))).)))))..(((((((.....)))))))..).)))))))).......... ( -33.90, z-score =  -3.46, R)
>droAna3.scaffold_12916 14816849 101 + 16180835
----GAAAAAAGGUCAAG-UGACUGACAGUAGCCAGGCAGCAA----CGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((...-.))))((((((((.(.(((((...----.((....))......)))))..(((((((.....)))))))..).)))))))).......... ( -28.70, z-score =  -2.75, R)
>dp4.chr4_group1 1845315 105 + 5278887
GAAAAAAAAAAGGUCAAG-UGACUGACAGAAGCCGG-CAACAG---CAGCGGCUGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
...........((((...-.))))(((((((((.((-((..((---.(((....))).))...))))..(((((((.....)))))))..)))).))))).......... ( -27.90, z-score =  -2.41, R)
>droPer1.super_5 1786359 105 - 6813705
GAAAAAAAAAAGGUCAAG-UGACUGACAGAAGCCGG-CAACAG---CAGCGGCUGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
...........((((...-.))))(((((((((.((-((..((---.(((....))).))...))))..(((((((.....)))))))..)))).))))).......... ( -27.90, z-score =  -2.41, R)
>droWil1.scaffold_180764 2749417 98 - 3949147
----AAAAAAAGGUCAAAUUGACUGACAGUAGCCAAGU--------CCGCGGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
----.......((((.....))))((((((((.(....--------....(((((.......)))))..(((((((.....)))))))..).)))))))).......... ( -28.20, z-score =  -3.84, R)
>droVir3.scaffold_12723 3076292 92 + 5802038
---GGUCAACACGC-------ACUGACAGUAGCCAA--GUC------CGCAGCAGCUACUUACUGUCAAGACGUGUCAUAAACACAUCAAGUUAACUGUCGAAACAAAUA
---(((.(((....-------..(((((((((...(--((.------.......)))..))))))))).((.((((.....)))).))..))).)))............. ( -18.40, z-score =  -0.49, R)
>droMoj3.scaffold_6500 16385530 98 + 32352404
---GGUCAACACGCUCGG-CUACAGACAGUAGUCAG--GUC------CGCAGCAGCUACUUACUGUCAAGACGUGUCAUAAACACAUCAGCUUUACUGUCGAAACAAAUA
---...........((((-(....((((((((...(--((.------.......)))..))))))))..((.((((.....)))).)).........)))))........ ( -20.40, z-score =  -0.10, R)
>droGri2.scaffold_15126 782098 98 - 8399593
-AAGGUCAACACGCAC-----ACGGACAGUAGCCAGUAGUC------UGCGGCGGCUACUUAGUGUCAAGACGUGUCAUAAACACAUCAACUUUACUGUCGAAACAAAUA
-...............-----...((((((((..(((.(((------(..((((.((....)))))).))))((((.....))))....))))))))))).......... ( -22.40, z-score =  -0.36, R)
>consensus
____GAAAAAAGGUCAAG_UGACUGACAGUAGCCAG_CAGCUG____AGCAGCAGCUACUUACUGUCAAGAUGUGUCAUAAACACAUCAAGUUUACUGUCGAAACAAAUA
........................((((((((................((((..........))))...((.((((.....)))).))....)))))))).......... (-14.36 = -14.47 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:40:20 2011