Locus 5175

Sequence ID dm3.chr2R
Location 18,325,344 – 18,325,462
Length 118
Max. P 0.955228
window7103 window7104

overview

Window 3

Location 18,325,344 – 18,325,462
Length 118
Sequences 12
Columns 121
Reading direction forward
Mean pairwise identity 77.91
Shannon entropy 0.47481
G+C content 0.47018
Mean single sequence MFE -29.13
Consensus MFE -18.50
Energy contribution -17.98
Covariance contribution -0.52
Combinations/Pair 1.33
Mean z-score -1.69
Structure conservation index 0.64
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.955228
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18325344 118 + 21146708
AAUUUUCCACCCCCCCUCUAUCCACAACC--UGUUUGCCCAGUCGAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
...............(((..((((.....--((((((......)))))).))))...)))...-......((..((((((((((............))))))))))..))........... ( -26.40, z-score =  -2.03, R)
>droSim1.chr2R 16925571 116 + 19596830
AAUUUUCCACCCCC--UCGAUCCACAACC--UGUUUGCCCAGUCGAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
.............(--((((((((.....--((((((......)))))).)))).)))))...-......((..((((((((((............))))))))))..))........... ( -27.60, z-score =  -1.89, R)
>droSec1.super_9 1633998 115 + 3197100
AAUUUUCCACCCCC---CGAUCCACAACC--UGUUUGCCCAGUCGAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
..............---((((...(((..--...)))....))))((((((((....((((..-..))))((..((((((((((............))))))))))..)))).)))))).. ( -25.30, z-score =  -1.28, R)
>droYak2.chr2R 15794733 116 + 21139217
AAUUUUCCGCCCCC--UCGUUCCACAACC--UGCUUGCCCAGUCGAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
........((...(--((..((((.....--((((((......)))))).))))...)))...-......((..((((((((((............))))))))))..))......))... ( -28.10, z-score =  -1.66, R)
>droEre2.scaffold_4845 14968926 116 - 22589142
AAUGUGCCACCCCC--UCGGUCCACAACC--UGUUUGCCCAGUCGAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
..((((..(((...--..))).))))..(--((......)))...((((((((....((((..-..))))((..((((((((((............))))))))))..)))).)))))).. ( -28.70, z-score =  -0.82, R)
>droAna3.scaffold_13266 12454962 115 - 19884421
CCAUUGCCACCCCC--UGGUUGUACAACC--UGUUUGCCCAGCCAAGCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCAG-
(((((((.......--((((((..(((..--...)))..)))))).)))))))((((((((..-...)))((..((((((((((............))))))))))..)).)))))....- ( -32.90, z-score =  -2.24, R)
>dp4.chr3 8925938 107 + 19779522
-------CGCUCUC-----CACCACGACCC-UGUUUGCCCGAUCGGGGAAUGGAGUCGAGAUU-UGUUUUGUAUUGACCGCAAAUUUCAAUACAGCUUUGCGGUCGCCGCCCAAUUGCCAU
-------.((....-----.....((((.(-(((((.(((....))))))))).)))).....-......((..((((((((((............))))))))))..))......))... ( -28.90, z-score =  -0.46, R)
>droPer1.super_4 4247087 107 + 7162766
-------CGCACUC-----CACCACGACCC-UGUUUGCCCGACCGGGGAAUGGAGUCGAGAUU-UGUUUUGUAUUGACCGCAAAUUUCAAUACAGCUUUGCGGUCGCCGCCCAAUUGCCAU
-------.(((...-----.....((((.(-(((((.(((....))))))))).)))).....-......((..((((((((((............))))))))))..)).....)))... ( -30.00, z-score =  -0.89, R)
>droWil1.scaffold_180697 4145710 105 - 4168966
-----------CCU----ACUCCACUCUCGCUGUUUGCUCAAGCGUUCAAUGGAGUUGAGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUUGCCCAAUUGCCAU
-----------...----.(((.((((.((.((..(((....)))..)).)))))).)))...-......(((.((((((((((............)))))))))).)))........... ( -31.90, z-score =  -3.21, R)
>droVir3.scaffold_12875 19370372 108 + 20611582
-------CGUUCUU---AGCGCCAUGCUCC-UGUUUAUCCAGGCGUUCAAUAGAGUUGGGAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACACUUUUGCGGUCAGCGUCCAAUUGACU-
-------...((((---(((.....((.((-((......)))).))........)))))))..-......((..((((((((((............))))))))))))(((.....))).- ( -29.02, z-score =  -1.58, R)
>droMoj3.scaffold_6496 13072017 108 + 26866924
-------CCUUCUU---GGCACUAAAGUCC-UGUUUACCCAGCCGUUCAAUGGAGUUGGAAUU-UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGCCAGCGCUCAAUUGACC-
-------.......---((((....(((.(-((........(((((..(((.(.(((((((((-(((............)))))))))))).).)))..)))))))).)))....)).))- ( -23.10, z-score =   0.28, R)
>droGri2.scaffold_15245 6869233 114 + 18325388
------CCUCAUCCGCAGCAUUCCUGCUCCUUGUUUGCUCAGUCUUGCAAUGGAGUUGAAUUUGUGUUUUGCAUUGACCGCAAAUUUCAAUACAAAUUUGCGGUCAGCAUCCAAUUGUUU-
------.......(((((.((((..(((((....((((........)))).))))).)))))))))...(((..(((((((((((((......))))))))))))))))...........- ( -37.60, z-score =  -4.47, R)
>consensus
______CCACCCCC___CGCUCCACAACC__UGUUUGCCCAGUCGAGCAAUGGAGUUGAGAUU_UGUUUUGCAUUGACCGCAAAUUUCAAUACAGUUUUGCGGUCGUCGCCCAAUUGCUAU
..............................................(((((((....(((((...)))))((..((((((((((............))))))))))..)))).)))))... (-18.50 = -17.98 +  -0.52)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,325,344 – 18,325,462
Length 118
Sequences 12
Columns 121
Reading direction reverse
Mean pairwise identity 77.91
Shannon entropy 0.47481
G+C content 0.47018
Mean single sequence MFE -32.08
Consensus MFE -17.99
Energy contribution -16.88
Covariance contribution -1.12
Combinations/Pair 1.61
Mean z-score -1.38
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.716626
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18325344 118 - 21146708
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUCGACUGGGCAAACA--GGUUGUGGAUAGAGGGGGGGUGGAAAAUU
...(((....(....)(((((((((............)))))))))..)))......-.(((((..(((.(((.(.(((((.(.....).--))))).)))).)))..)))))........ ( -31.70, z-score =  -1.26, R)
>droSim1.chr2R 16925571 116 - 19596830
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUCGACUGGGCAAACA--GGUUGUGGAUCGA--GGGGGUGGAAAAUU
...(((....(....)(((((((((............)))))))))..)))......-....((.(((((.((((((....))))))...--((((...))))..--.))))).))..... ( -30.50, z-score =  -0.92, R)
>droSec1.super_9 1633998 115 - 3197100
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUCGACUGGGCAAACA--GGUUGUGGAUCG---GGGGGUGGAAAAUU
...(((....(....)(((((((((............)))))))))..)))......-.........((((((.(((((((..((((...--..)))))).)))---)).))))))..... ( -33.00, z-score =  -1.69, R)
>droYak2.chr2R 15794733 116 - 21139217
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUCGACUGGGCAAGCA--GGUUGUGGAACGA--GGGGGCGGAAAAUU
...((..(((.(((..(((((((((............)))))))))..)))......-..((((((((...((((((....))))))...--))))).))).)))--....))........ ( -32.30, z-score =  -1.19, R)
>droEre2.scaffold_4845 14968926 116 + 22589142
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUCGACUGGGCAAACA--GGUUGUGGACCGA--GGGGGUGGCACAUU
...((..(((.(((..(((((((((............)))))))))..)))....))-)......(((((.((((((....))))))...--((((...))))..--.))))).))..... ( -33.80, z-score =  -1.16, R)
>droAna3.scaffold_13266 12454962 115 + 19884421
-CUGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGCUUGGCUGGGCAAACA--GGUUGUACAACCA--GGGGGUGGCAAUGG
-.((((....(....)(((((((((............)))))))))..)))).....-.....((...(((((.(((((.((..(((...--..)))..)).)))--)).)))))...)). ( -35.00, z-score =  -1.43, R)
>dp4.chr3 8925938 107 - 19779522
AUGGCAAUUGGGCGGCGACCGCAAAGCUGUAUUGAAAUUUGCGGUCAAUACAAAACA-AAUCUCGACUCCAUUCCCCGAUCGGGCAAACA-GGGUCGUGGUG-----GAGAGCG-------
...((......)).(((((((((((.(......)...)))))))))...........-........(((((..((.(((((.(.....).-.))))).))))-----))).)).------- ( -33.20, z-score =  -0.75, R)
>droPer1.super_4 4247087 107 - 7162766
AUGGCAAUUGGGCGGCGACCGCAAAGCUGUAUUGAAAUUUGCGGUCAAUACAAAACA-AAUCUCGACUCCAUUCCCCGGUCGGGCAAACA-GGGUCGUGGUG-----GAGUGCG-------
...((......)).(((((((((((.(......)...)))))))))...........-.......((((((..((.((..(.(.....).-.)..)).))))-----)))))).------- ( -33.00, z-score =  -0.27, R)
>droWil1.scaffold_180697 4145710 105 + 4168966
AUGGCAAUUGGGCAACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCUCAACUCCAUUGAACGCUUGAGCAAACAGCGAGAGUGGAGU----AGG-----------
...(((....(....)(((((((((............)))))))))..)))......-.......((((((((...((((.(......)))))..))))))))----...----------- ( -30.90, z-score =  -2.31, R)
>droVir3.scaffold_12875 19370372 108 - 20611582
-AGUCAAUUGGACGCUGACCGCAAAAGUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUCCCAACUCUAUUGAACGCCUGGAUAAACA-GGAGCAUGGCGCU---AAGAACG-------
-.((...((((.(((((((((((((..(......)..))))))))).((((......-.........((....))...((((......))-)).))))))))))---))..)).------- ( -31.30, z-score =  -2.58, R)
>droMoj3.scaffold_6496 13072017 108 - 26866924
-GGUCAAUUGAGCGCUGGCCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA-AAUUCCAACUCCAUUGAACGGCUGGGUAAACA-GGACUUUAGUGCC---AAGAAGG-------
-((........(((.((((((((((............)))))))))).)))......-...........(((((((.(.(((......))-)..))))))))))---.......------- ( -25.60, z-score =   0.16, R)
>droGri2.scaffold_15245 6869233 114 - 18325388
-AAACAAUUGGAUGCUGACCGCAAAUUUGUAUUGAAAUUUGCGGUCAAUGCAAAACACAAAUUCAACUCCAUUGCAAGACUGAGCAAACAAGGAGCAGGAAUGCUGCGGAUGAGG------
-...........((((((((((((((((......)))))))))))))..))).........((((..(((.((((........))))....(.((((....)))).)))))))).------ ( -34.60, z-score =  -3.10, R)
>consensus
AUAGCAAUUGGGCGACGACCGCAAAACUGUAUUGAAAUUUGCGGUCAAUGCAAAACA_AAUCUCAACUCCAUUGCUCGACUGGGCAAACA__GGUUGUGGAGCG___GGGGGUGG______
...........((((((((((((((............)))))))))...............((((...............)))).........)))))....................... (-17.99 = -16.88 +  -1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:19 2011