Locus 15758

Sequence ID dm3.chrX
Location 20,847,273 – 20,847,378
Length 105
Max. P 0.984697
window21715 window21716

overview

Window 5

Location 20,847,273 – 20,847,378
Length 105
Sequences 8
Columns 120
Reading direction forward
Mean pairwise identity 80.95
Shannon entropy 0.37089
G+C content 0.54917
Mean single sequence MFE -35.88
Consensus MFE -27.21
Energy contribution -28.29
Covariance contribution 1.08
Combinations/Pair 1.36
Mean z-score -2.21
Structure conservation index 0.76
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.18
SVM RNA-class probability 0.984697
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20847273 105 + 22422827
GAGACAGCAAGUAGACACAGA-UCCAGCAGGCGACGUCG-GCACUUUUGGUCCACUUGCCCGGCAAUUGGACCAUUUCGUUGAGCGCUUCACAGCGCUCAAGUUGCC-------------
..(((.((..((.((......-))..))..))...)))(-(((....(((((((.((((...)))).))))))).....(((((((((....)))))))))..))))------------- ( -37.90, z-score =  -2.57, R)
>droSim1.chrX 16015787 105 + 17042790
GAGACAGAAAGUAGACACAGA-UCCAACAGGCGACGUCG-GCACUUUUGGUCCACUUGCCCGGCAAUUGGACCAUUUCGUUGAGCGCUUCACAGCGCUCAAGUUGCC-------------
.....................-.......((((((....-.......(((((((.((((...)))).))))))).....(((((((((....)))))))))))))))------------- ( -37.60, z-score =  -2.97, R)
>droSec1.super_8 3130350 105 + 3762037
GAGACAGAAAGUAGACACAGA-UCCAACAGGCGACGUCG-GCACUUUUGGUCCACUUGCCCGGCAAUUGGGCCAUUUCGUUGAGCGCUUCACAGCGCUCAAGUUGCC-------------
.....................-.......((((((....-.......(((((((.((((...)))).))))))).....(((((((((....)))))))))))))))------------- ( -37.00, z-score =  -2.29, R)
>droYak2.chrX 20058716 105 + 21770863
GAGACAGAAAGUAGACACAGA-UCCAACAGGCGACGUCG-GCACUUUUGGUCCACUUGCCCGGCAAUUGGACCAUUUCGUUGAGCGCUUCACGGCGCUCAAGUUGCC-------------
.....................-.......((((((....-.......(((((((.((((...)))).))))))).....(((((((((....)))))))))))))))------------- ( -37.60, z-score =  -2.51, R)
>droEre2.scaffold_4690 17420945 105 + 18748788
GAGACAGAAAGUAGACACAGA-UCCAACAGGCAACGUCG-GCACUUUUGGUCCACUUGCCCGGCAAUUGGACCAUUUCGUUGAGCGCUUCACAGCGCUCAAGUUGCC-------------
.....................-.......((((((....-.......(((((((.((((...)))).))))))).....(((((((((....)))))))))))))))------------- ( -37.90, z-score =  -3.39, R)
>droAna3.scaffold_13334 1381587 101 + 1562580
GAGACAGAAAGUAGAC----A-UCCAACAGGCGACGUCG-GCACUUUUGGUCCACUUGGCCGGCAAUUGGACCAUUUCGGUGAGCGCUUCACAGCGCUCAAGUUGUC-------------
..((((((((((.(((----.-((........)).))).-)).....(((((((.(((.....))).)))))))))))..((((((((....))))))))...))))------------- ( -35.10, z-score =  -1.98, R)
>dp4.chrXL_group1e 9482001 105 + 12523060
GAUAUAUAGAGAAGACGUAGA-UCCAACAGGCGACGUCG-GCACUUUUGGUCCACUUGGCCGGCAAUUGGACCAUUUUGGUGAGCGCUUCACAGCCUUCAAGUUGCC-------------
.............(((((...-.((....))..)))))(-((((((.(((((((.(((.....))).))))))).......(((.(((....))).)))))).))))------------- ( -29.90, z-score =  -0.68, R)
>droPer1.super_22 962615 120 - 1688296
UAUCGAUUGUGUAGGGGAUGACUUCCACAGCGUGUGUCGCACGCUUUUGCCCCAUUCGGCCGCCAUUUGUCCCUUUGCGGAGGCCGUUACCAGCCUUUCAAGUCAAACCCCCCCCCCCCC
.............((((.((((((....((((((.....))))))...((......(((((.((..............)).)))))......)).....))))))..))))......... ( -34.04, z-score =  -1.26, R)
>consensus
GAGACAGAAAGUAGACACAGA_UCCAACAGGCGACGUCG_GCACUUUUGGUCCACUUGCCCGGCAAUUGGACCAUUUCGUUGAGCGCUUCACAGCGCUCAAGUUGCC_____________
.............................((((((............(((((((.((((...)))).)))))))......((((((((....)))))))).))))))............. (-27.21 = -28.29 +   1.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,847,273 – 20,847,378
Length 105
Sequences 8
Columns 120
Reading direction reverse
Mean pairwise identity 80.95
Shannon entropy 0.37089
G+C content 0.54917
Mean single sequence MFE -40.00
Consensus MFE -23.91
Energy contribution -26.09
Covariance contribution 2.17
Combinations/Pair 1.22
Mean z-score -2.67
Structure conservation index 0.60
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.15
SVM RNA-class probability 0.984055
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 20847273 105 - 22422827
-------------GGCAACUUGAGCGCUGUGAAGCGCUCAACGAAAUGGUCCAAUUGCCGGGCAAGUGGACCAAAAGUGC-CGACGUCGCCUGCUGGA-UCUGUGUCUACUUGCUGUCUC
-------------((((.((((((((((....))))))).......(((((((.((((...)))).))))))).))))))-)((((..((..(.((((-(....))))))..)))))).. ( -42.90, z-score =  -3.29, R)
>droSim1.chrX 16015787 105 - 17042790
-------------GGCAACUUGAGCGCUGUGAAGCGCUCAACGAAAUGGUCCAAUUGCCGGGCAAGUGGACCAAAAGUGC-CGACGUCGCCUGUUGGA-UCUGUGUCUACUUUCUGUCUC
-------------((((.((((((((((....))))))).......(((((((.((((...)))).))))))).))))))-)((((...((....)).-....))))............. ( -40.40, z-score =  -2.93, R)
>droSec1.super_8 3130350 105 - 3762037
-------------GGCAACUUGAGCGCUGUGAAGCGCUCAACGAAAUGGCCCAAUUGCCGGGCAAGUGGACCAAAAGUGC-CGACGUCGCCUGUUGGA-UCUGUGUCUACUUUCUGUCUC
-------------((((..(((((((((....))))))))).((((..((((.......))))..((((((....((..(-(((((.....)))))).-.))..)))))))))))))).. ( -40.60, z-score =  -2.83, R)
>droYak2.chrX 20058716 105 - 21770863
-------------GGCAACUUGAGCGCCGUGAAGCGCUCAACGAAAUGGUCCAAUUGCCGGGCAAGUGGACCAAAAGUGC-CGACGUCGCCUGUUGGA-UCUGUGUCUACUUUCUGUCUC
-------------((((.(((((((((......)))))).......(((((((.((((...)))).))))))).))))))-)((((...((....)).-....))))............. ( -38.10, z-score =  -2.05, R)
>droEre2.scaffold_4690 17420945 105 - 18748788
-------------GGCAACUUGAGCGCUGUGAAGCGCUCAACGAAAUGGUCCAAUUGCCGGGCAAGUGGACCAAAAGUGC-CGACGUUGCCUGUUGGA-UCUGUGUCUACUUUCUGUCUC
-------------(((((((((((((((....))))))))).....(((((((.((((...)))).))))))).......-....))))))...((((-(....)))))........... ( -41.20, z-score =  -3.31, R)
>droAna3.scaffold_13334 1381587 101 - 1562580
-------------GACAACUUGAGCGCUGUGAAGCGCUCACCGAAAUGGUCCAAUUGCCGGCCAAGUGGACCAAAAGUGC-CGACGUCGCCUGUUGGA-U----GUCUACUUUCUGUCUC
-------------((((...((((((((....))))))))......(((((((.(((.....))).)))))))((((((.-.((((((........))-)----))))))))).)))).. ( -39.10, z-score =  -3.64, R)
>dp4.chrXL_group1e 9482001 105 - 12523060
-------------GGCAACUUGAAGGCUGUGAAGCGCUCACCAAAAUGGUCCAAUUGCCGGCCAAGUGGACCAAAAGUGC-CGACGUCGCCUGUUGGA-UCUACGUCUUCUCUAUAUAUC
-------------((((.(((((..(((....)))..)).......(((((((.(((.....))).))))))).))))))-)(((((..((....)).-...)))))............. ( -31.80, z-score =  -1.56, R)
>droPer1.super_22 962615 120 + 1688296
GGGGGGGGGGGGGUUUGACUUGAAAGGCUGGUAACGGCCUCCGCAAAGGGACAAAUGGCGGCCGAAUGGGGCAAAAGCGUGCGACACACGCUGUGGAAGUCAUCCCCUACACAAUCGAUA
((..(...(((((..((((((...((((((....))))))((((................(((......)))...((((((.....)))))))))))))))).)))))...)..)).... ( -45.90, z-score =  -1.72, R)
>consensus
_____________GGCAACUUGAGCGCUGUGAAGCGCUCAACGAAAUGGUCCAAUUGCCGGGCAAGUGGACCAAAAGUGC_CGACGUCGCCUGUUGGA_UCUGUGUCUACUUUCUGUCUC
.............(((((((((((((((....))))))).......(((((((.((((...)))).))))))).))))....((((...((....))......)))).......)))).. (-23.91 = -26.09 +   2.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 02:05:20 2011