Locus 10864

Sequence ID dm3.chr3R
Location 17,123,616 – 17,123,736
Length 120
Max. P 0.999478
window14929 window14930

overview

Window 9

Location 17,123,616 – 17,123,717
Length 101
Sequences 8
Columns 109
Reading direction forward
Mean pairwise identity 61.26
Shannon entropy 0.74777
G+C content 0.51758
Mean single sequence MFE -34.98
Consensus MFE -13.63
Energy contribution -12.52
Covariance contribution -1.11
Combinations/Pair 1.80
Mean z-score -2.13
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.73
SVM RNA-class probability 0.994783
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17123616 101 + 27905053
-----CGCACU-CGGCCCGAUCCCGAUUGCAGCGUUAUUCGAAAGCUGUGUCUGCGACCGUGACUGAGAUCAUAUGCGUACAUAUAUCUAAUGUCCGGGGUCGUAGG--
-----.(((.(-(((.......)))).)))(((...........)))....((((((((.((((..((((.(((((....)))))))))...)).)).)))))))).-- ( -33.80, z-score =  -1.23, R)
>droSec1.super_38 395239 101 - 400794
-----CGCACU-CGGCCCGAUCCCGAUUGCAGCGUUAUUCGAAAGCUGUGUCUGCGACCAUGACUGAGAUUAUAUGCGUACAUAUAUCUAAUGUCCGGGGUCGUGGG--
-----......-...((((((((((.((((((...(((.(....)..))).))))))....(((..((((.(((((....)))))))))...))))))))))).)).-- ( -34.00, z-score =  -1.37, R)
>droYak2.chr3R 5923996 101 + 28832112
-----UGCACU-CGGCCCGAUCCAGAUUGCAGCGUUAUUCAAAAGCUGAGUCUGCGACCGUGACUGAGAUCAUAUGCGUAUAUAUAUCUAAUGUCCGGGGUCGUAGG--
-----....((-((((((..((((((((.((((...........)))))))))).)).((.(((..((((.(((((....)))))))))...))))))))))).)).-- ( -34.20, z-score =  -2.07, R)
>droEre2.scaffold_4770 13209467 101 - 17746568
-----UGCAUU-CGGCCCGAUCCCGAUUGCAGCGUUAUUCGAAUGCUGAGUCUGCGACCGUGACUGAGAUCAUAUGCGUAUAUAUAUCUAAUGUCCGGGGUCGUGGG--
-----.(((.(-(((.......)))).)))((((((.....))))))....(..(((((.((((..((((.(((((....)))))))))...)).)).)))))..).-- ( -33.80, z-score =  -1.00, R)
>droAna3.scaffold_13340 3784245 101 + 23697760
-----UGCACC--UAGCCAGCCGUCUAUGCAGCGUUUGGUGAAAGUUGUGCCCACGACCGUGACAGCGA-UAUAUAUAAUGUAAAAAUAUAUUUCGAUGGUCGUGGGUU
-----.(((.(--(.(((((.(((.......))).)))))...)).)))((((((((((((.....(((-.((((((.........)))))).))))))))))))))). ( -34.70, z-score =  -2.99, R)
>dp4.chr2 5623934 90 + 30794189
-----UGCACUUCGGCCCAUGUACGCGUUUGGCGU-ACGCGAAAGUUGUGGCUGCGACCCUGACUCAGCCUUAGUGU-----------UGAUUGUCGGGGUCGCGGC--
-----..(((..........((((((.....))))-))((....)).)))(((((((((((((((((((......))-----------)))..))))))))))))))-- ( -45.30, z-score =  -4.05, R)
>droPer1.super_19 1340694 90 + 1869541
-----UGCACUUCGGCCCAUGUACGCGUUUGGCGU-ACGCGAAAGUUGUGGCUGCGACCCUGACUCAGCCUUAGUGU-----------UGAUUGUCGGGGUCGCGGA--
-----........((((((.((((((.....))))-))((....)))).))))((((((((((((((((......))-----------)))..)))))))))))...-- ( -44.30, z-score =  -3.87, R)
>droWil1.scaffold_181130 16102510 89 + 16660200
UUCAGCACAUUUCAGUCAAGUCCAAUUUGCCGCGUGUGGUUCUAGUU-UGCCAGCGAUGAUGGUAUUG--UUAAU---------------AUUAUCGUUGUCAUGGG--
.....(((((....(.(((((...))))).)..))))).........-..((((((((((((((((..--...))---------------)))))))))))..))).-- ( -19.70, z-score =  -0.45, R)
>consensus
_____UGCACU_CGGCCCAAUCCCGAUUGCAGCGUUAUGCGAAAGCUGUGUCUGCGACCGUGACUGAGAUUAUAUGCGUA_AUAUAUCUAAUGUCCGGGGUCGUGGG__
.............................((((...........))))..(((((((((.((.................................)).))))))))).. (-13.63 = -12.52 +  -1.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 17,123,643 – 17,123,736
Length 93
Sequences 8
Columns 101
Reading direction forward
Mean pairwise identity 60.69
Shannon entropy 0.76741
G+C content 0.50536
Mean single sequence MFE -33.62
Consensus MFE -14.27
Energy contribution -14.27
Covariance contribution 0.00
Combinations/Pair 1.71
Mean z-score -2.61
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.93
SVM RNA-class probability 0.999478
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 17123643 93 + 27905053
GUUAUUCGAAAGCUGUGUCUGCGACCGUGACUGAGAUCAU----AUGCGUACAUAUAUCU-AAUGUCCG-GGGUCGUAGGCCAGCC-AGGGUGCUCGAUU-
..(((((....((((.((((((((((.((((..((((.((----(((....)))))))))-...)).))-.)))))))))))))).-.))))).......- ( -35.90, z-score =  -2.93, R)
>droSec1.super_38 395266 93 - 400794
GUUAUUCGAAAGCUGUGUCUGCGACCAUGACUGAGAUUAU----AUGCGUACAUAUAUCU-AAUGUCCG-GGGUCGUGGGCCAGCC-AGGGCGCUCGAUU-
.....((((..((((.(((..(((((..(((..((((.((----(((....)))))))))-...)))..-.)))))..)))))((.-...))))))))..- ( -34.20, z-score =  -2.24, R)
>droYak2.chr3R 5924023 93 + 28832112
GUUAUUCAAAAGCUGAGUCUGCGACCGUGACUGAGAUCAU----AUGCGUAUAUAUAUCU-AAUGUCCG-GGGUCGUAGGCCAGCC-AGGGUGCUCAAUU-
..(((((....((((.((((((((((.((((..((((.((----(((....)))))))))-...)).))-.)))))))))))))).-.))))).......- ( -32.70, z-score =  -2.81, R)
>droEre2.scaffold_4770 13209494 93 - 17746568
GUUAUUCGAAUGCUGAGUCUGCGACCGUGACUGAGAUCAU----AUGCGUAUAUAUAUCU-AAUGUCCG-GGGUCGUGGGCCAGCC-AGGGUACUCGAUU-
..(((((....((((.(((..(((((.((((..((((.((----(((....)))))))))-...)).))-.)))))..))))))).-.))))).......- ( -32.90, z-score =  -1.89, R)
>droAna3.scaffold_13340 3784271 101 + 23697760
GUUUGGUGAAAGUUGUGCCCACGACCGUGACAGCGAUAUAUAUAAUGUAAAAAUAUAUUUCGAUGGUCGUGGGUUGCAUAUCGACCCAGGGUCCCUCGAAU
((((((.(...((...((((((((((((.....(((.((((((.........)))))).))))))))))))))).)).....((((...))))).)))))) ( -32.00, z-score =  -2.24, R)
>dp4.chr2 5623962 82 + 30794189
-GUACGCGAAAGUUGUGGCUGCGACCCUGACUCAGCCUUA----GUGU-----------U-GAUUGUCG-GGGUCGCGGCCUGACC-AGGGUGCGUCGUUU
-((((.(....((((.((((((((((((((((((((....----..))-----------)-))..))))-))))))))))))))).-.).))))....... ( -43.70, z-score =  -4.92, R)
>droPer1.super_19 1340722 82 + 1869541
-GUACGCGAAAGUUGUGGCUGCGACCCUGACUCAGCCUUA----GUGU-----------U-GAUUGUCG-GGGUCGCGGACUGACC-AGGGUGCGUCGUUU
-(.(((((.......(((((((((((((((((((((....----..))-----------)-))..))))-))))))))).)))...-....)))))).... ( -37.34, z-score =  -3.13, R)
>droWil1.scaffold_181130 16102543 78 + 16660200
------------GUGUGGUU-CUAGUUUGCCAGCGAUGAUGGUAUUGUUAA----UAUUAUCGUUGUCAUGGGCGGCGUGC------AGGUUACAUCAUUU
------------(((((...-((.((.((((((((((((((.((....)).----))))))))))((.....)))))).))------.)).)))))..... ( -20.20, z-score =  -0.76, R)
>consensus
GUUAUUCGAAAGCUGUGUCUGCGACCGUGACUGAGAUCAU____AUGCGUA_AUAUAUCU_AAUGGCCG_GGGUCGCGGGCCAGCC_AGGGUGCUCCAUU_
...........((((.((((((((((.............................................))))))))))))))................ (-14.27 = -14.27 +   0.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:31:56 2011