Locus 11863

Sequence ID dm3.chr3R
Location 24,266,944 – 24,267,035
Length 91
Max. P 0.874303
window16305 window16306

overview

Window 5

Location 24,266,944 – 24,267,035
Length 91
Sequences 12
Columns 113
Reading direction forward
Mean pairwise identity 66.83
Shannon entropy 0.68313
G+C content 0.44313
Mean single sequence MFE -25.67
Consensus MFE -10.38
Energy contribution -10.26
Covariance contribution -0.12
Combinations/Pair 1.29
Mean z-score -1.40
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.98
SVM RNA-class probability 0.866050
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24266944 91 + 27905053
-CGAAAGUUGAGUCAAAGGUUUUUCGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG-GGCAGCAACCAUCCAGAACUCCC--------------------
-.((((...(((((((((........)))))))))((((.....))))....))))..........(((-((.........))))).......-------------------- ( -20.40, z-score =  -0.64, R)
>droSim1.chr3R 23954668 89 + 27517382
---CGAGUUGAGUCAAAGGUUUUUCGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG-GGCAGCAACCACCCAGAACUCCC--------------------
---.((((((((((((((........)))))))))((((.....))))..................(((-((.........))))))))))..-------------------- ( -25.40, z-score =  -2.42, R)
>droSec1.super_22 870458 91 + 1066717
-CGAAAGUUGAGUCAAAGGUUUUUCGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG-GGCAGCAACCACCCAGAACUCCC--------------------
-.((((...(((((((((........)))))))))((((.....))))....))))..........(((-((.........))))).......-------------------- ( -23.20, z-score =  -1.57, R)
>droYak2.chr3R 6600283 98 - 28832112
-CUAAAGUUGAGUCAAAGGUUUUUCGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG-GGCAGCAACCACCCAGAGAAAUUGGGGCCC-------------
-........(((((((((........)))))))))((((.....))))...((..((....((...(((-((.........)))))))....))..))..------------- ( -25.60, z-score =  -0.66, R)
>droEre2.scaffold_4820 6697164 94 - 10470090
-CUAAAGUUGAGUCAAAGGUUUUUCGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG-GGCAGCAACCACCCAGAACUGCCCCC-----------------
-....(((((((((((((........)))))))))((((.....))))................))))(-(((((.............))))))..----------------- ( -25.22, z-score =  -2.19, R)
>droAna3.scaffold_13340 17066793 85 + 23697760
-CAAAAGUUGAGUCAAAGGUUUU-CGCUUUGACUCGUAAUUAAUUUGCUUUGUUCCGUCCGCUUGGCCG-GGCAGCCAUCAGCGGGUG-------------------------
-((((....(((((((((.....-..)))))))))((((.....))))))))...(..(((((((((..-....))))..)))))..)------------------------- ( -28.50, z-score =  -2.45, R)
>dp4.chr2 20528376 103 - 30794189
-UAAAAGUUGAGUCAAAGGUUUU-CUCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUGCGCUUCGCUG-GGCAAUAGACAUAGGCCAUAGACGGUCCCCCGCGUC-------
-........((((((((((....-.))))))))))...........(((((((((..(((.(......)-.)))..))))).))))....((((........))))------- ( -26.90, z-score =  -1.17, R)
>droPer1.super_0 10215730 101 + 11822988
-CAAAAGUUGAGUCAAAGGUUUU-CUCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUGCGCUUCGCUG-GGCAAUAGACAUAGGCAAUAGACGGUCCCCCGUC---------
-........((((((((((....-.)))))))))).........(((((((((((..(((.(......)-.)))..))))).))))))..(((((....)))))--------- ( -32.30, z-score =  -3.49, R)
>droWil1.scaffold_181089 8937255 92 + 12369635
UGUUUGGCCCAGUCAAAAGGUU--GCCUUUGACUUGCAAUUAAUUCGCUUUGUUUUUCACGCUUGACUG-GACAACACAAACACAGAUAGAGCGA------------------
......((..(((((((.((..--.))))))))).)).......(((((((((...(((....)))(((-.............))))))))))))------------------ ( -19.02, z-score =   0.21, R)
>droMoj3.scaffold_6540 17014170 109 + 34148556
-UGUUCAUGGAGUCAAA-GGUU--CGCUUUGACUUGCAAUUAAUUUGCUUUGUUUUUUGCACUUGACUGCGCUUGGACAGACUUACAAGCUGCCAGGCAGAUAGAUAGAAGGA
-(.(((...((((((((-(...--..)))))))))((((.....))))(((((((...(((......)))((((((.(((.((....))))))))))))))))))..))).). ( -31.80, z-score =  -1.38, R)
>droVir3.scaffold_12822 3703560 105 + 4096053
-UGUUCAUGGAGUCAAA-GGUU--CGCUUUGACUUGCAAUUAAUUUGCUUUGUUUUUUGCACUUGACUGCGCCCGGACAGACUUACAAGCGCUCAUCCGGACAGAUAGA----
-(((((...((((((((-(...--..)))))))))((((..(((.......)))..))))...(((..((((..(..........)..)))))))...)))))......---- ( -24.40, z-score =   0.15, R)
>droGri2.scaffold_14906 1304625 105 + 14172833
-UUUUAGUAAAGUCAAA-GGUU--CCCUUUGACUUGCAAUUAAUUUGCUUUGUUUUUUGCACUUGACUGCGCCUGGACAAACAGACAAGACGUCGAACAGACAGAAAGA----
-.....((((.((((((-((..--.))))))))))))......((((.(((((((..((((......))))...)))))))))))......(((.....))).......---- ( -25.30, z-score =  -1.23, R)
>consensus
_CGAAAGUUGAGUCAAAGGUUUU_CGCUUUGACUCGUAAUUAAUUUGCUUUGUUUCAUCCGCUUGACUG_GGCAGCAAACACCCAGAACACCC____________________
.........((((((((.((.....))))))))))((((.....))))................................................................. (-10.38 = -10.26 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 24,266,944 – 24,267,035
Length 91
Sequences 12
Columns 113
Reading direction reverse
Mean pairwise identity 66.83
Shannon entropy 0.68313
G+C content 0.44313
Mean single sequence MFE -26.58
Consensus MFE -8.03
Energy contribution -7.98
Covariance contribution -0.05
Combinations/Pair 1.20
Mean z-score -2.02
Structure conservation index 0.30
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874303
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24266944 91 - 27905053
--------------------GGGAGUUCUGGAUGGUUGCUGCC-CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCGAAAAACCUUUGACUCAACUUUCG-
--------------------(..((((...(((..(((((...-...(((......))).....)))))....)))..(((((((((........)))))))))))))..).- ( -24.30, z-score =  -1.61, R)
>droSim1.chr3R 23954668 89 - 27517382
--------------------GGGAGUUCUGGGUGGUUGCUGCC-CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCGAAAAACCUUUGACUCAACUCG---
--------------------..((((((((((..(...)..))-)))....((............))...........(((((((((........)))))))))))))).--- ( -27.40, z-score =  -2.43, R)
>droSec1.super_22 870458 91 - 1066717
--------------------GGGAGUUCUGGGUGGUUGCUGCC-CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCGAAAAACCUUUGACUCAACUUUCG-
--------------------(..(((((((((..(...)..))-)))....((............))...........(((((((((........)))))))))))))..).- ( -28.50, z-score =  -2.59, R)
>droYak2.chr3R 6600283 98 + 28832112
-------------GGGCCCCAAUUUCUCUGGGUGGUUGCUGCC-CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCGAAAAACCUUUGACUCAACUUUAG-
-------------((((..((((..(.....)..))))..)))-)......((............))...........(((((((((........)))))))))........- ( -24.00, z-score =  -0.69, R)
>droEre2.scaffold_4820 6697164 94 + 10470090
-----------------GGGGGCAGUUCUGGGUGGUUGCUGCC-CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCGAAAAACCUUUGACUCAACUUUAG-
-----------------..(((((((.((....))..))))))-)......((............))...........(((((((((........)))))))))........- ( -26.60, z-score =  -1.38, R)
>droAna3.scaffold_13340 17066793 85 - 23697760
-------------------------CACCCGCUGAUGGCUGCC-CGGCCAAGCGGACGGAACAAAGCAAAUUAAUUACGAGUCAAAGCG-AAAACCUUUGACUCAACUUUUG-
-------------------------...(((((..(((((...-.)))))))))).......................(((((((((.(-....))))))))))........- ( -27.40, z-score =  -3.69, R)
>dp4.chr2 20528376 103 + 30794189
-------GACGCGGGGGACCGUCUAUGGCCUAUGUCUAUUGCC-CAGCGAAGCGCAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGAG-AAAACCUUUGACUCAACUUUUA-
-------...((((....))))((.((...(((((((.((((.-..)))))).)))))...)).))............(((((((((..-.....)))))))))........- ( -26.00, z-score =  -1.43, R)
>droPer1.super_0 10215730 101 - 11822988
---------GACGGGGGACCGUCUAUUGCCUAUGUCUAUUGCC-CAGCGAAGCGCAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGAG-AAAACCUUUGACUCAACUUUUG-
---------(((((....)))))..((((...(((....(((.-(......).)))....)))..)))).........(((((((((..-.....)))))))))........- ( -30.40, z-score =  -3.66, R)
>droWil1.scaffold_181089 8937255 92 - 12369635
------------------UCGCUCUAUCUGUGUUUGUGUUGUC-CAGUCAAGCGUGAAAAACAAAGCGAAUUAAUUGCAAGUCAAAGGC--AACCUUUUGACUGGGCCAAACA
------------------............((((((....(((-((((((((.............((((.....))))..((.....))--.....))))))))))))))))) ( -22.80, z-score =  -0.94, R)
>droMoj3.scaffold_6540 17014170 109 - 34148556
UCCUUCUAUCUAUCUGCCUGGCAGCUUGUAAGUCUGUCCAAGCGCAGUCAAGUGCAAAAAACAAAGCAAAUUAAUUGCAAGUCAAAGCG--AACC-UUUGACUCCAUGAACA-
...............((.((((((((....)).))).))).))(((((....(((..........))).....))))).((((((((..--...)-))))))).........- ( -24.10, z-score =  -1.28, R)
>droVir3.scaffold_12822 3703560 105 - 4096053
----UCUAUCUGUCCGGAUGAGCGCUUGUAAGUCUGUCCGGGCGCAGUCAAGUGCAAAAAACAAAGCAAAUUAAUUGCAAGUCAAAGCG--AACC-UUUGACUCCAUGAACA-
----.......((((((((..((........))..))))))))(((((....(((..........))).....))))).((((((((..--...)-))))))).........- ( -31.30, z-score =  -2.59, R)
>droGri2.scaffold_14906 1304625 105 - 14172833
----UCUUUCUGUCUGUUCGACGUCUUGUCUGUUUGUCCAGGCGCAGUCAAGUGCAAAAAACAAAGCAAAUUAAUUGCAAGUCAAAGGG--AACC-UUUGACUUUACUAAAA-
----.......(((.....)))((((((.((((..((....)))))).)))).))..........((((.....))))((((((((((.--..))-))))))))........- ( -26.20, z-score =  -1.95, R)
>consensus
____________________GGCAGUUCUGGGUGUUUGCUGCC_CAGUCAAGCGGAUGAAACAAAGCAAAUUAAUUACGAGUCAAAGCG_AAAACCUUUGACUCAACUUUAG_
...................................................((............))...........((((((((..........))))))))......... ( -8.03 =  -7.98 +  -0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:07 2011