Locus 2674

Sequence ID	dm3.chr2L
Location	20,953,569 – 20,953,645
Length	76
Max. P	0.747095

overview

Window 7

Location	20,953,569 – 20,953,645
Length	76
Sequences	9
Columns	84
Reading direction	forward
Mean pairwise identity	68.37
Shannon entropy	0.64522
G+C content	0.54202
Mean single sequence MFE	-22.87
Consensus MFE	-10.12
Energy contribution	-9.17
Covariance contribution	-0.96
Combinations/Pair	1.79
Mean z-score	-1.14
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.747095
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20953569 76 + 23011544
ACUAGGCGAGAAAGCCCGGCCAUCUCGCCGUGUGUUAUUUGCCC-CCAAAUGGAGAAAUG--AACAGGCUGGAUGUGUG-----
....(((......)))..(((((((.(((.(((.((((((..((-......))..)))))--))))))).))))).)).----- ( -22.80, z-score =  -1.25, R)
>droSim1.chr2L_random 844034 76 + 909653
ACUAGGCGAGAAAGCCCGGCCAUCUCGCCGUGUGUUAUUUGCCC-CCAAAUGGAGAAAUG--AACAGUCUGGAUGUGUG-----
.((((((((((..((...))..))))))).(((.((((((..((-......))..)))))--))))...))).......----- ( -18.80, z-score =  -0.47, R)
>droSec1.super_18 886654 76 + 1342155
ACUAGGCGAGAAAGCCCGGCCAUCUCGCCGUGUGUUAUUUGCCC-CCAAAUGGAGAAAUG--AACAGGCUGGAUGUGUG-----
....(((......)))..(((((((.(((.(((.((((((..((-......))..)))))--))))))).))))).)).----- ( -22.80, z-score =  -1.25, R)
>droYak2.chr2R 19339237 76 - 21139217
ACUAGGCGAGAAAGCCCGGCCAUCUCGCCGUGUGUUAUUUGCCC-CCAAAUGGAGAAAUG--AACAGGCCGGAAGUGCG-----
....(((((((..((...))..))))))).(((.((((((..((-......))..)))))--)))).(((....).)).----- ( -22.50, z-score =  -0.86, R)
>droEre2.scaffold_4845 19071388 74 - 22589142
GCUAGGCGAGAAAGCCCGGCCAUC--GCCGUGUGUUACUUGCCC-CCAAAUGGAGAAAUG--AACGGGCCGGCUGCGCG-----
....(((......)))((((....--)))).((((..((.((((-((....))(....).--...)))).))..)))).----- ( -23.40, z-score =   0.47, R)
>droAna3.scaffold_12943 1268576 78 - 5039921
ACUAGGCGAGAAAGCCCGACCAUCUAGUCGUGUGUUAUUUGCACACCAAAUGGAGAAAUG--AACAGAGCCG-UGAAAGUC---
....(((..........(((......)))((((((.....))))))..............--......))).-........--- ( -15.50, z-score =  -0.35, R)
>dp4.chr4_group1 88408 84 - 5278887
ACUAGGCUUUCUCGCCUCGCCAUCUCUUGGUCUGCUAUUUGCACACCAAAUGGAGAAAUGGCAACAAGCAGAAGGACCUUCGAA
...(((((((((.((...(((((((((((((.(((.....))).))))...)))))..)))).....)))))))).)))..... ( -28.90, z-score =  -3.15, R)
>droPer1.super_5 26860 84 + 6813705
ACUAGGCUUUCUCGCCUCGCCAUCUCUUGGUCUGCUAUUUGCACACCAAAUGGAGAAAUGGCAACAAGCAGAAGGACUUUCGAA
...(((((((((.((...(((((((((((((.(((.....))).))))...)))))..)))).....)))))))).)))..... ( -26.20, z-score =  -2.35, R)
>droWil1.scaffold_180772 3823017 60 - 8906247
-------------GCUAGGCUUUCUCGCCUUGCCUCUCCUCGAC-CUGGGUGAAACGAGGG-GGGGAGGUGGAUG---------
-------------....(((......)))(..((((((((...(-((.(......).))))-)))))))..)...--------- ( -24.90, z-score =  -1.01, R)
>consensus
ACUAGGCGAGAAAGCCCGGCCAUCUCGCCGUGUGUUAUUUGCCC_CCAAAUGGAGAAAUG__AACAGGCUGGAUGUGUG_____
....(((......)))((((......))))....(((((((.....)))))))............................... (-10.12 =  -9.17 +  -0.96)

alignment

secondary structure

dotplot

Window 8

Location	20,953,569 – 20,953,645
Length	76
Sequences	9
Columns	84
Reading direction	reverse
Mean pairwise identity	68.37
Shannon entropy	0.64522
G+C content	0.54202
Mean single sequence MFE	-24.18
Consensus MFE	-7.82
Energy contribution	-7.59
Covariance contribution	-0.23
Combinations/Pair	1.62
Mean z-score	-1.64
Structure conservation index	0.32
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.19
SVM RNA-class probability	0.586804
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20953569 76 - 23011544
-----CACACAUCCAGCCUGUU--CAUUUCUCCAUUUGG-GGGCAAAUAACACACGGCGAGAUGGCCGGGCUUUCUCGCCUAGU
-----....((((..(((((((--.((((((((.....)-))).))))))))...)))..))))((..(((......)))..)) ( -23.70, z-score =  -1.78, R)
>droSim1.chr2L_random 844034 76 - 909653
-----CACACAUCCAGACUGUU--CAUUUCUCCAUUUGG-GGGCAAAUAACACACGGCGAGAUGGCCGGGCUUUCUCGCCUAGU
-----.............((((--.((((((((.....)-))).))))))))...(((((((.(((...))).))))))).... ( -22.60, z-score =  -1.83, R)
>droSec1.super_18 886654 76 - 1342155
-----CACACAUCCAGCCUGUU--CAUUUCUCCAUUUGG-GGGCAAAUAACACACGGCGAGAUGGCCGGGCUUUCUCGCCUAGU
-----....((((..(((((((--.((((((((.....)-))).))))))))...)))..))))((..(((......)))..)) ( -23.70, z-score =  -1.78, R)
>droYak2.chr2R 19339237 76 + 21139217
-----CGCACUUCCGGCCUGUU--CAUUUCUCCAUUUGG-GGGCAAAUAACACACGGCGAGAUGGCCGGGCUUUCUCGCCUAGU
-----.............((((--.((((((((.....)-))).))))))))...(((((((.(((...))).))))))).... ( -22.60, z-score =  -0.39, R)
>droEre2.scaffold_4845 19071388 74 + 22589142
-----CGCGCAGCCGGCCCGUU--CAUUUCUCCAUUUGG-GGGCAAGUAACACACGGC--GAUGGCCGGGCUUUCUCGCCUAGC
-----.(((.((..((((((((--.((((((((.....)-))).)))))))....(((--....))))))))..)))))..... ( -26.70, z-score =  -0.56, R)
>droAna3.scaffold_12943 1268576 78 + 5039921
---GACUUUCA-CGGCUCUGUU--CAUUUCUCCAUUUGGUGUGCAAAUAACACACGACUAGAUGGUCGGGCUUUCUCGCCUAGU
---........-.(((......--.......((((((((((((.........))).)))))))))..(((....)))))).... ( -17.30, z-score =  -0.64, R)
>dp4.chr4_group1 88408 84 + 5278887
UUCGAAGGUCCUUCUGCUUGUUGCCAUUUCUCCAUUUGGUGUGCAAAUAGCAGACCAAGAGAUGGCGAGGCGAGAAAGCCUAGU
.....((((..(((((((..(((((((((((.....((((.(((.....))).)))))))))))))))))).)))).))))... ( -34.00, z-score =  -3.90, R)
>droPer1.super_5 26860 84 - 6813705
UUCGAAAGUCCUUCUGCUUGUUGCCAUUUCUCCAUUUGGUGUGCAAAUAGCAGACCAAGAGAUGGCGAGGCGAGAAAGCCUAGU
......((.(.(((((((..(((((((((((.....((((.(((.....))).)))))))))))))))))).)))).).))... ( -29.90, z-score =  -3.03, R)
>droWil1.scaffold_180772 3823017 60 + 8906247
---------CAUCCACCUCCCC-CCCUCGUUUCACCCAG-GUCGAGGAGAGGCAAGGCGAGAAAGCCUAGC-------------
---------......((((...-.(((((..((.....)-).))))).))))..((((......))))...------------- ( -17.10, z-score =  -0.89, R)
>consensus
_____CACACAUCCAGCCUGUU__CAUUUCUCCAUUUGG_GGGCAAAUAACACACGGCGAGAUGGCCGGGCUUUCUCGCCUAGU
..................((((.........((....)).........))))...(((......)))((((......))))... ( -7.82 =  -7.59 +  -0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:55:38 2011