Locus 8870

Sequence ID dm3.chr3R
Location 2,328,279 – 2,328,376
Length 97
Max. P 0.892005
window12170 window12171

overview

Window 0

Location 2,328,279 – 2,328,376
Length 97
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 86.71
Shannon entropy 0.22875
G+C content 0.49202
Mean single sequence MFE -33.15
Consensus MFE -25.87
Energy contribution -26.23
Covariance contribution 0.36
Combinations/Pair 1.05
Mean z-score -2.08
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.10
SVM RNA-class probability 0.892005
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2328279 97 + 27905053
AAUUAGUGCCAAGUGGUGAGGGCCAAAUGCCAGGGACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUCAACUCG----AGCAAAA--GGAGUU-------------
.....(((((..(..((((((...(((((((.((.......)).))))))).))))))..)....)).))).......(((((.----.......--.)))))------------- ( -31.00, z-score =  -1.90, R)
>droSim1.chr3R 2356869 97 + 27517382
AAUUAGUGCCAAGUGGUGAGGGCCAAAUGCCAGGGACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUCAACUCG----AGCAAAA--GGAGUU-------------
.....(((((..(..((((((...(((((((.((.......)).))))))).))))))..)....)).))).......(((((.----.......--.)))))------------- ( -31.00, z-score =  -1.90, R)
>droSec1.super_6 2414880 97 + 4358794
AAUUAGUGCCAAGUGGUGAGGGCCAAAUGCCAGGGACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUCAACUCG----AGCAAAA--GGAGUU-------------
.....(((((..(..((((((...(((((((.((.......)).))))))).))))))..)....)).))).......(((((.----.......--.)))))------------- ( -31.00, z-score =  -1.90, R)
>droYak2.chr3R 18247892 99 + 28832112
AAUUAGUGCCAAGUGGUGAGGGCCAAAUGCCAGGGACCUUGCCUGGCAUUUACCUCAUUGCACAAGGACACAUAACUUAACUGG----UCCAAAAACGGAGCU-------------
....(((.((..(..((((((...((((((((((.......)))))))))).))))))..)....((((.((.........)))----)))......)).)))------------- ( -38.70, z-score =  -3.52, R)
>droEre2.scaffold_4770 2574081 96 + 17746568
AAUUAGUGCCAAGUGGUGAGGGCCAAGUGCCAGG-ACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUUAACUCG----ACCAAAA--GGAGUU-------------
.....(((((..(..((((((...(((((((.((-......)).))))))).))))))..)....)).))).......(((((.----.......--.)))))------------- ( -31.30, z-score =  -2.28, R)
>droAna3.scaffold_13340 13555258 116 + 23697760
AAUUAGUGCCGAGUGGAGAGGGCCAAAAGGCAGGGACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUCAACUCGGGACUUGGGACUCGAGGCUGGGGAAAGGAAUG
.....(((((..(((.((((((((....((((((...)))))).))).....))))..).)))..)).)))....((((.((((((........))))))..)))).......... ( -35.90, z-score =  -0.97, R)
>consensus
AAUUAGUGCCAAGUGGUGAGGGCCAAAUGCCAGGGACCUUGCCAGGCAUUUACCUCAUUGCACAAGGACACAUAACUCAACUCG____AGCAAAA__GGAGUU_____________
.....(((((..(..((((((...(((((((.((.......)).))))))).))))))..)....)).)))............................................. (-25.87 = -26.23 +   0.36)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,328,279 – 2,328,376
Length 97
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 86.71
Shannon entropy 0.22875
G+C content 0.49202
Mean single sequence MFE -30.85
Consensus MFE -25.06
Energy contribution -25.73
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.654674
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2328279 97 - 27905053
-------------AACUCC--UUUUGCU----CGAGUUGAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGUCCCUGGCAUUUGGCCCUCACCACUUGGCACUAAUU
-------------(((((.--.(((...----.)))..)))))..(((.((..(((...(((((((((((((.((.......)).))))))))..))))).)))..)))))..... ( -31.00, z-score =  -1.79, R)
>droSim1.chr3R 2356869 97 - 27517382
-------------AACUCC--UUUUGCU----CGAGUUGAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGUCCCUGGCAUUUGGCCCUCACCACUUGGCACUAAUU
-------------(((((.--.(((...----.)))..)))))..(((.((..(((...(((((((((((((.((.......)).))))))))..))))).)))..)))))..... ( -31.00, z-score =  -1.79, R)
>droSec1.super_6 2414880 97 - 4358794
-------------AACUCC--UUUUGCU----CGAGUUGAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGUCCCUGGCAUUUGGCCCUCACCACUUGGCACUAAUU
-------------(((((.--.(((...----.)))..)))))..(((.((..(((...(((((((((((((.((.......)).))))))))..))))).)))..)))))..... ( -31.00, z-score =  -1.79, R)
>droYak2.chr3R 18247892 99 - 28832112
-------------AGCUCCGUUUUUGGA----CCAGUUAAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCAGGCAAGGUCCCUGGCAUUUGGCCCUCACCACUUGGCACUAAUU
-------------.(.((((....))))----.).....(((((.(((.((..(((...((((((((((((((((.......)))))))))))..))))).)))..)))))))))) ( -35.80, z-score =  -2.51, R)
>droEre2.scaffold_4770 2574081 96 - 17746568
-------------AACUCC--UUUUGGU----CGAGUUAAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGU-CCUGGCACUUGGCCCUCACCACUUGGCACUAAUU
-------------(((((.--.......----.))))).(((((.(((.((..(((...((((((((.((((.((......-)).)))).)))..))))).)))..)))))))))) ( -26.70, z-score =  -0.37, R)
>droAna3.scaffold_13340 13555258 116 - 23697760
CAUUCCUUUCCCCAGCCUCGAGUCCCAAGUCCCGAGUUGAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGUCCCUGCCUUUUGGCCCUCUCCACUCGGCACUAAUU
............((((.(((.(.(....).).)))))))(((((.(((((...(((....((((.....(((.((((.(....)))))....)))))))..)))..)))))))))) ( -29.60, z-score =  -0.94, R)
>consensus
_____________AACUCC__UUUUGCU____CGAGUUGAGUUAUGUGUCCUUGUGCAAUGAGGUAAAUGCCUGGCAAGGUCCCUGGCAUUUGGCCCUCACCACUUGGCACUAAUU
.............(((((...............))))).(((((.(((.((..(((...(((((((((((((.((.......)).))))))))..))))).)))..)))))))))) (-25.06 = -25.73 +   0.67)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:53:40 2011