Locus 1538

Sequence ID dm3.chr2L
Location 11,916,763 – 11,916,892
Length 129
Max. P 0.989146
window2099 window2100 window2101

overview

Window 9

Location 11,916,763 – 11,916,876
Length 113
Sequences 9
Columns 119
Reading direction forward
Mean pairwise identity 83.32
Shannon entropy 0.34787
G+C content 0.42269
Mean single sequence MFE -28.36
Consensus MFE -22.09
Energy contribution -22.21
Covariance contribution 0.12
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933167
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11916763 113 + 23011544
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGGCGGACAUCGGGUGGAUAUAUCUACAAUACUG
------....((((....(((((((((((.(((........)))))).))))))))(..((((((((.....))))))))..)...))))........(((((....)))))....... ( -28.30, z-score =  -2.59, R)
>droSim1.chr2L 11723961 113 + 22036055
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGUCGGACAUCGGGUGGAUAUAUCCACUAUAUUG
------....((((....(((((((((((.(((........)))))).))))))))(..((((((((.....))))))))..)..)).)).......((((((....))))))...... ( -28.00, z-score =  -2.59, R)
>droSec1.super_16 116095 113 + 1878335
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCAACAGGGCGGACAUCGGGUGGAUAUAUCCACUAUAUUG
------....((((....(((((((((((.(((........)))))).))))))))...((((((((.....))))))))......)))).......((((((....))))))...... ( -31.30, z-score =  -3.81, R)
>droYak2.chr2L 8336663 112 + 22324452
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGGCGGACAUCGGCUGGAUCUA-CUACUAUACUU
------.....(((((.....)).......(((.((((((..((.......))......((((((((.....)))))))).))))))...)))...)))........-........... ( -24.30, z-score =  -1.25, R)
>droEre2.scaffold_4929 13144297 107 - 26641161
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGGCGGACAUCGGCUGGAUAUA-CUACUG-----
------....((((....(((((((((((.(((........)))))).))))))))(..((((((((.....))))))))..)...)))).....(((.(((.....-))))))----- ( -24.80, z-score =  -1.48, R)
>droAna3.scaffold_12943 2689681 97 - 5039921
------UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGGCGGACAUCACAGCGA----------------
------....((((....(((((((((((.(((........)))))).))))))))(..((((((((.....))))))))..)...)))).............---------------- ( -24.20, z-score =  -2.30, R)
>dp4.chr4_group3 9236871 109 + 11692001
------UGAGCGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACGGGGCGAGC-CGGGCUGCAGGA---UGCUGGACAG
------.....((((((((((((....((((((.((.(((..((.......))......((((((((.....)))))))).))))))))))).-......))))))---)).))).).. ( -31.10, z-score =  -0.37, R)
>droPer1.super_8 428115 109 + 3966273
------UGAGCGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACGGGGCGGGC-CCGGCUGCAGGA---UGCUGGACAG
------.....((((((((((((((((((.(((........)))))))))(((...(..((((((((.....))))))))..)((((.....)-))))))))))))---)).))).).. ( -33.70, z-score =  -0.96, R)
>droWil1.scaffold_180708 2601910 119 + 12563649
GUAGAAAAAAUGCGGCAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGAUGGGGCGGAGGCUAGUGGUUGAUAGCCUGAACAACG
((((((((((((...)))))).)))))).......(((((((((.((....)).(((((((......(((((((.....)))))))(((....))))))))))....))))).)))).. ( -29.50, z-score =  -0.42, R)
>consensus
______UAAACGCCACAUUUUGUUUUACUCGUCACUUGUCAGGCAGUAAAAGCAAAUUACUUAAAGUUCAUUGCUUUAAGCGACAGGGCGGACAUCGGCUGGAUAUA_CUACUAUACUG
..........((((....(((((((((((.(((........)))))).))))))))...((((((((.....))))))))......))))............................. (-22.09 = -22.21 +   0.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,916,763 – 11,916,876
Length 113
Sequences 9
Columns 119
Reading direction reverse
Mean pairwise identity 83.32
Shannon entropy 0.34787
G+C content 0.42269
Mean single sequence MFE -24.64
Consensus MFE -19.32
Energy contribution -19.33
Covariance contribution 0.01
Combinations/Pair 1.07
Mean z-score -1.05
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.11
SVM RNA-class probability 0.550162
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11916763 113 - 23011544
CAGUAUUGUAGAUAUAUCCACCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
..........(((((.........)))))((((.....((((((((.......))))))))..((((((((((((........))))).))))))).........))))....------ ( -22.20, z-score =  -0.70, R)
>droSim1.chr2L 11723961 113 - 22036055
CAAUAUAGUGGAUAUAUCCACCCGAUGUCCGACCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
.......(((((....)))))..((((((((...(((.((((((((.......))))))))..((((((((((((........))))).))))))))))...)).))))))..------ ( -25.70, z-score =  -1.82, R)
>droSec1.super_16 116095 113 - 1878335
CAAUAUAGUGGAUAUAUCCACCCGAUGUCCGCCCUGUUGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
.......(((((....)))))..((((.((((....((((((((((.......))))))))))((((((((((((........))))).))))))).......))))))))..------ ( -29.30, z-score =  -3.01, R)
>droYak2.chr2L 8336663 112 - 22324452
AAGUAUAGUAG-UAGAUCCAGCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
...........-...........((((.((((......((((((((.......))))))))..((((((((((((........))))).))))))).......))))))))..------ ( -21.90, z-score =  -0.07, R)
>droEre2.scaffold_4929 13144297 107 + 26641161
-----CAGUAG-UAUAUCCAGCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
-----......-.(((((.....))))).((((.....((((((((.......))))))))..((((((((((((........))))).))))))).........))))....------ ( -22.10, z-score =  -0.54, R)
>droAna3.scaffold_12943 2689681 97 + 5039921
----------------UCGCUGUGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA------
----------------.......((((.((((......((((((((.......))))))))..((((((((((((........))))).))))))).......))))))))..------ ( -21.80, z-score =  -0.98, R)
>dp4.chr4_group3 9236871 109 - 11692001
CUGUCCAGCA---UCCUGCAGCCCG-GCUCGCCCCGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGCUCA------
..(((..((.---.......))..)-)).((((.(((.((((((((.......))))))))..((((((((((((........))))).))))))).....))).))))....------ ( -25.20, z-score =   0.03, R)
>droPer1.super_8 428115 109 - 3966273
CUGUCCAGCA---UCCUGCAGCCGG-GCCCGCCCCGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGCUCA------
..((((.((.---.......)).))-)).((((.(((.((((((((.......))))))))..((((((((((((........))))).))))))).....))).))))....------ ( -29.30, z-score =  -0.85, R)
>droWil1.scaffold_180708 2601910 119 - 12563649
CGUUGUUCAGGCUAUCAACCACUAGCCUCCGCCCCAUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGCCGCAUUUUUUCUAC
........((((((........))))))..((..(((.((((((((.......))))))))..((((((((((((........))))).))))))).....)))..))........... ( -24.30, z-score =  -1.51, R)
>consensus
CAGUAUAGUAG_UAUAUCCAGCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUGACAAGUGACGAGUAAAACAAAAUGUGGCGUUUA______
.............................((((.(((.((((((((.......))))))))..((((((((((((........))))).))))))).....))).)))).......... (-19.32 = -19.33 +   0.01)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,916,796 – 11,916,892
Length 96
Sequences 9
Columns 112
Reading direction reverse
Mean pairwise identity 69.15
Shannon entropy 0.60439
G+C content 0.48175
Mean single sequence MFE -20.34
Consensus MFE -8.07
Energy contribution -8.07
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.35
SVM RNA-class probability 0.989146
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11916796 96 - 23011544
-------------CCCACCCCCUAUG---GAGCAGUAUUGUAGAUAUAUCCACCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-------------.(((.......))---).((((((..(((((((((((.....)))))..........((((((((.......)))))))).))))))...))))))... ( -21.30, z-score =  -3.10, R)
>droSim1.chr2L 11723994 96 - 22036055
-------------CCCACCCCCUAUG---GAGCAAUAUAGUGGAUAUAUCCACCCGAUGUCCGACCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-------------............(---((((((.(((((((((((.........)))))))..)))).((((((((.......))))))))...)))))))......... ( -18.00, z-score =  -1.57, R)
>droSec1.super_16 116128 96 - 1878335
-------------CCCACCCCCUUUA---GAGCAAUAUAGUGGAUAUAUCCACCCGAUGUCCGCCCUGUUGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-------------.............---((((((((..((((((((.........))))))))..))))))))(((((((...((.....))...)))))))......... ( -24.10, z-score =  -4.63, R)
>droYak2.chr2L 8336696 98 - 22324452
-------------CCCAACCCCCAUGGUAGAGAAGUAUAGUAG-UAGAUCCAGCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-------------............((((((((((((......-..(((...((.(....).))...)))((((((((.......))))))))....))))))).))))).. ( -21.70, z-score =  -2.45, R)
>droEre2.scaffold_4929 13144330 90 + 26641161
-------------CCCAACCCCCAUG--------GAGCAGUAG-UAUAUCCAGCCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-------------.(((.......))--------).(((((((-.(((((.....))))).)((...((..(((((((.......)))))))..))..))...))))))... ( -20.10, z-score =  -2.50, R)
>droAna3.scaffold_12943 2689714 76 + 5039921
-----------------------------------CCCAGCCCCUGU-UCGCUGUGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-----------------------------------..((((......-..))))........((...((..(((((((.......)))))))..))..))............ ( -12.70, z-score =  -1.33, R)
>dp4.chr4_group3 9236904 93 - 11692001
-----------------CCCCUCUCCUGCAUGUGCUGUCCAG--CAUCCUGCAGCCCGGCUCGCCCCGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-----------------........(((((.(((((....))--)))..)))))...(((..((......))..(((((((...((.....))...)))))))....))).. ( -22.20, z-score =  -2.12, R)
>droPer1.super_8 428148 93 - 3966273
-----------------CCCCUCUCCUGCAUGUGCUGUCCAG--CAUCCUGCAGCCGGGCCCGCCCCGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
-----------------........(((((.(((((....))--)))..))))).((((.....))))..((..(((((((...((.....))...)))))))....))... ( -24.40, z-score =  -2.06, R)
>droWil1.scaffold_180708 2601949 112 - 12563649
CUCACCCACAACCACCGUCUUACCCCACGAAACGUUGUUCAGGCUAUCAACCACUAGCCUCCGCCCCAUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
.......(((((...(((........)))....)))))..((((((........))))))..........((..(((((((...((.....))...)))))))....))... ( -18.60, z-score =  -2.36, R)
>consensus
_____________CCCACCCCCCAUG___GAGCAGUAUAGUGG_UAUAUCCAACCGAUGUCCGCCCUGUCGCUUAAAGCAAUGAACUUUAAGUAAUUUGCUUUUACUGCCUG
......................................................................((..(((((((...((.....))...)))))))....))... ( -8.07 =  -8.07 +   0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:33:52 2011