Locus 7396

Sequence ID dm3.chr3L
Location 14,554,299 – 14,554,423
Length 124
Max. P 0.957700
window10183 window10184

overview

Window 3

Location 14,554,299 – 14,554,397
Length 98
Sequences 12
Columns 114
Reading direction forward
Mean pairwise identity 76.63
Shannon entropy 0.48917
G+C content 0.43149
Mean single sequence MFE -23.58
Consensus MFE -12.29
Energy contribution -12.47
Covariance contribution 0.17
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.64
SVM RNA-class probability 0.957700
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14554299 98 + 24543557
CCCCUUUUCUCCGCUCGC----------CACUUGU-ACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCC-----
.((((((..((.((..((----------.......-.......))..)).))..)).))))..((((((((......))))))))........................----- ( -17.84, z-score =  -1.14, R)
>droSim1.chr3L 13880006 98 + 22553184
CCCCUUUUCUCCGCUCGC----------CACUUGU-ACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCC-----
.((((((..((.((..((----------.......-.......))..)).))..)).))))..((((((((......))))))))........................----- ( -17.84, z-score =  -1.14, R)
>droSec1.super_0 6679617 98 + 21120651
CCCCUUUUCUCCGCUCGC----------CACUUGU-ACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCC-----
.((((((..((.((..((----------.......-.......))..)).))..)).))))..((((((((......))))))))........................----- ( -17.84, z-score =  -1.14, R)
>droYak2.chr3L 14640573 98 + 24197627
CCCCUUUUCACCGCUCGC----------CACUUGU-GCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCC-----
............((.((.----------....)).-))...((((..(((....)))..))))((((((((......))))))))........................----- ( -19.80, z-score =  -1.75, R)
>droEre2.scaffold_4784 14523954 103 + 25762168
CCCCUUUUCUCCGCUCGC----------CACUUGG-GCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUUCC
..................----------....(((-((...((((..(((....)))..))))((((((((......)))))))).......)))))................. ( -25.10, z-score =  -2.90, R)
>droAna3.scaffold_13337 18756910 98 - 23293914
CCCCUUUUUUGUGCUCGC----------CACUUGU-ACAAAUUGCUGGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGUCGACUUUUCUUUUCC-----
.......(((((((....----------.....))-)))))(((((.(((....))).)))))((((((((......))))))))........................----- ( -23.50, z-score =  -2.09, R)
>droPer1.super_41 603655 107 + 728894
CCCCUUUUUGCCUGCCUUGCCACUCACUCAGUCGU-ACAAAU-GCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCGUUGC-----
.......((((((((..((.....)).((((.((.-.(....-)..))))))...))))))))((((((((......)))))))).......((.((.......)).))----- ( -26.40, z-score =  -2.46, R)
>dp4.chrXR_group6 7250719 107 + 13314419
CCCCUUUUUGCCUGCCUUGCCACUCACUCAGUCGU-ACAAAU-GCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCGUUGC-----
.......((((((((..((.....)).((((.((.-.(....-)..))))))...))))))))((((((((......)))))))).......((.((.......)).))----- ( -26.40, z-score =  -2.46, R)
>droWil1.scaffold_181136 508739 99 - 2313701
CCCUCUAAAGUCAGUAGU----------CACUUGGGACAAAUUGCUCGCUGAUUAGCAAGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGCAAACUUUCUCUUUCU-----
......(((((..(((((----------(......)))...(((((.(((....))).)))))((((((((......))))))))......)))..)))))........----- ( -23.80, z-score =  -2.49, R)
>droVir3.scaffold_13049 16637893 100 + 25233164
CCCUUUUGGGGCAGCCUUG----UCAGCCAGUUGU-ACAAAUUGCUCGCUGAUUAGCAGGCAAGCGCAUGAAAUUAAUCAUAUGCAAAUACGAGUAUGCUACCAC---------
(((....)))(((((((.(----(((((.(((.((-....)).))).))))))....))))..(((.((((......)))).)))...........)))......--------- ( -28.70, z-score =  -1.16, R)
>droMoj3.scaffold_6680 4685311 85 - 24764193
CCCUUUGUCGGCAGCCUUG----UCAGGCAGUUGU-ACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUA------------------------
...(((((((((.((((..----..)))).)))).-)))))((((..(((....)))..))))((((((((......)))))))).....------------------------ ( -29.60, z-score =  -3.28, R)
>droGri2.scaffold_15110 8093102 92 - 24565398
CCCCUU----UCGGUUGG----------CAGUUGU-ACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUA--GCCAAGUAUCCUUCCAU-----
......----(((((.((----------(((((..-...))))))).)))))......(((..((((((((......)))))))).....--)))..............----- ( -26.20, z-score =  -2.69, R)
>consensus
CCCCUUUUCGCCGCUCGC__________CACUUGU_ACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCAACUUUUCUUUUCC_____
.........................................(((((........)))))....((((((((......))))))))............................. (-12.29 = -12.47 +   0.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,554,320 – 14,554,423
Length 103
Sequences 11
Columns 116
Reading direction forward
Mean pairwise identity 75.62
Shannon entropy 0.50563
G+C content 0.40086
Mean single sequence MFE -24.48
Consensus MFE -12.22
Energy contribution -12.41
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -1.33
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.20
SVM RNA-class probability 0.591863
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 14554320 103 + 24543557
--------UUGUACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUGACGC-----GAAUUUGUUGCUGUCGUGG
--------..((((((((((((((((....)))((((((((((((((......)))))))).......(....).......)))))))).))-----.)))))).)))........ ( -24.00, z-score =  -0.86, R)
>droSim1.chr3L 13880027 103 + 22553184
--------UUGUACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUCGACGC-----GAAUUUGUUGCUGUCGUGG
--------.((.((.......((.(((.....))).)).((((((((......)))))))).......)).))..........((.((((((-----((.....)))).)))).)) ( -25.20, z-score =  -1.19, R)
>droSec1.super_0 6679638 103 + 21120651
--------UUGUACAAAUUGCUCGCUGAUUAGCAGGGAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUCGACGC-----GAAUUUGUUGCUGUCGUGG
--------.((.((.......((.(((.....))).)).((((((((......)))))))).......)).))..........((.((((((-----((.....)))).)))).)) ( -25.20, z-score =  -1.19, R)
>droYak2.chr3L 14640594 103 + 24197627
--------UUGUGCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUGACGC-----GAAUUUGUUGCUGUCGUGG
--------.((..(...((((..(((....)))..))))((((((((......)))))))).......)..))..........((.((((((-----((.....)))).)))).)) ( -27.40, z-score =  -1.63, R)
>droEre2.scaffold_4784 14523975 108 + 25762168
--------UUGGGCAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUUCCUUGAAGCGAAUUUGUUGCUGUCGUGG
--------.(((((...((((..(((....)))..))))((((((((......)))))))).......)))))...............((.((((((((.....))))).))).)) ( -31.20, z-score =  -2.51, R)
>droAna3.scaffold_13337 18756931 105 - 23293914
--------UUGUACAAAUUGCUGGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUGUCGACUUUUCUUUUCCUUGACGCC---CAAUGUUGUUGCUGUCGUGG
--------(((.((((.(((((.(((....))).)))))((((((((......)))))))).....)))))))..........((.((((((.---((....))..)).)))).)) ( -25.40, z-score =  -0.91, R)
>droPer1.super_41 603678 104 + 728894
UCACUCAGUCGUACAAAU-GCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCGUUGCUC-----------AAGUUGUUGAUGUCCUUG
.......((((.((((.(-((..(((....)))..))).((((((((......)))))))).......((.((.......)).))..-----------...))))))))....... ( -22.60, z-score =  -0.75, R)
>dp4.chrXR_group6 7250742 104 + 13314419
UCACUCAGUCGUACAAAU-GCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGCCACUUUUUCCGUUGCUC-----------AAGUUGUUGAUGUCCUUG
.......((((.((((.(-((..(((....)))..))).((((((((......)))))))).......((.((.......)).))..-----------...))))))))....... ( -22.60, z-score =  -0.75, R)
>droWil1.scaffold_181136 508760 104 - 2313701
-------UUGGGACAAAUUGCUCGCUGAUUAGCAAGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUUG-CAAACUUUCUCUUUCUUUUUUUAU----AGCUUCUUUCUGUGUCGC
-------....((((..(((((.(((....))).)))))((((((((......))))))))........-........................----............)))).. ( -22.30, z-score =  -1.15, R)
>droVir3.scaffold_13049 16637920 80 + 25233164
--------UUGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGCAUGAAAUUAAUCAUAUGCAAAUA----CGAGUAUGCUACCACUUUGCGC------------------------
--------..((((...((((..(((....)))..))))(((.((((......)))).))).....----...))))((.........))..------------------------ ( -17.00, z-score =   0.33, R)
>droGri2.scaffold_15110 8093119 81 - 24565398
--------UUGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAGC--CAAGUAUCCUUCCAUUUGGCG-------------------------
--------.........((((..(((....)))..))))((((((((......)))))))).....((--(((((........))))))).------------------------- ( -26.40, z-score =  -4.04, R)
>consensus
________UUGUACAAAUUGCUCGCUGAUUAGCAGGCAAGCGUAUGAAAUUAAUCAUAUGCAAAUAUCGUCCACUUUUCUUUUCCUUGACGC______AAUUUGUUGCUGUCGUGG
.................(((((........)))))....((((((((......))))))))....................................................... (-12.22 = -12.41 +   0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:26:07 2011