Locus 5113

Sequence ID	dm3.chr2R
Location	17,829,782 – 17,829,879
Length	97
Max. P	0.816994

overview

Window 3

Location	17,829,782 – 17,829,879
Length	97
Sequences	7
Columns	111
Reading direction	forward
Mean pairwise identity	76.71
Shannon entropy	0.44730
G+C content	0.39289
Mean single sequence MFE	-26.69
Consensus MFE	-14.29
Energy contribution	-15.94
Covariance contribution	1.65
Combinations/Pair	1.32
Mean z-score	-1.67
Structure conservation index	0.54
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.63
SVM RNA-class probability	0.768365
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17829782 97 + 21146708
--------UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCU-GCAAGUAUUGAAAUGAAAU-----
--------.....(((((...(((....)))..(((((((((((.......(((((((((.....))).))))))...))))))))-))).)))))..........----- ( -30.30, z-score =  -2.26, R)
>droSim1.chr2R 16465500 97 + 19596830
--------UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGUGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCU-GCAAGUAUUGAAAUGAAAU-----
--------.....(((((...(((....)))..(((((((((((.......(((((((((.....))).))))))...))))))))-))).)))))..........----- ( -28.40, z-score =  -1.74, R)
>droSec1.super_177 13748 97 + 33666
--------UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGUGCAAGAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCU-GCAAGUAUUGAAAUGAAAU-----
--------.....(((((...(((....)))..((((((((((....((..(((((((((.....))).))))))..)))))))))-))).)))))..........----- ( -29.00, z-score =  -1.90, R)
>droYak2.chr2R 9785542 97 - 21139217
--------UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGUGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUUGCAAGCU-GCAAGUAUUGAAAUGAAAU-----
--------.....(((((...(((....)))..(((((((..((((((...(((((((((.....))).)))))).))))))))))-))).)))))..........----- ( -28.70, z-score =  -1.77, R)
>droEre2.scaffold_4845 11962142 97 + 22589142
--------UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCU-GCAAGUAUUGAAAUGAAAU-----
--------.....(((((...(((....)))..(((((((((((.......(((((((((.....))).))))))...))))))))-))).)))))..........----- ( -30.30, z-score =  -2.26, R)
>droAna3.scaffold_13266 8681429 95 - 19884421
AGACGCAGGAGCAGGGAUCCUUGAAACUGCAACUGCGACU---GCAAUAAAUGCGUUCAUUUAACAUGAAAUGCA-GCCG-------GCAAGUAUUGAAAUGAAAU-----
...(((((..((((............))))..)))))(((---((......(((((((((.....))).))))))-....-------)).))).............----- ( -25.30, z-score =  -1.64, R)
>droMoj3.scaffold_6496 10323423 87 - 26866924
----------------------AUCAACG-GAGCGCAGAGUUCGUA-UAAAUGCGUUCAUUUAACACGAAAUGCAACUUAAGAGCUUGCAUCAAAUCAAAUCAAACGCACU
----------------------.....((-(((((((.........-....)))))))............((((((((....)).))))))..............)).... ( -14.82, z-score =  -0.12, R)
>consensus
________UGGGAAAUGCAACUGCAAGUGCAAAUGCAGCUUGCGCAAUAAAUGCGUUCAUUUAACAUGAAAUGCAAGUCGCAAGCU_GCAAGUAUUGAAAUGAAAU_____
.............(((((...(((....)))..(((((((((((.......(((((((((.....))).))))))...)))))))).))).)))))............... (-14.29 = -15.94 +   1.65)

alignment

secondary structure

dotplot

Window 4

Location	17,829,782 – 17,829,879
Length	97
Sequences	7
Columns	111
Reading direction	reverse
Mean pairwise identity	76.71
Shannon entropy	0.44730
G+C content	0.39289
Mean single sequence MFE	-25.03
Consensus MFE	-12.89
Energy contribution	-13.74
Covariance contribution	0.86
Combinations/Pair	1.33
Mean z-score	-1.87
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.79
SVM RNA-class probability	0.816994
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2R 17829782 97 - 21146708
-----AUUUCAUUUCAAUACUUGC-AGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCGCAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA--------
-----.........((((...(((-((((((((...(((..(((((.....))))).))).......)))))))))))..(((....))))))).........-------- ( -28.70, z-score =  -2.79, R)
>droSim1.chr2R 16465500 97 - 19596830
-----AUUUCAUUUCAAUACUUGC-AGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA--------
-----.........((((...(((-(((((((((..(((..(((((.....))))).)))....)))))..)))))))..(((....))))))).........-------- ( -24.00, z-score =  -1.53, R)
>droSec1.super_177 13748 97 - 33666
-----AUUUCAUUUCAAUACUUGC-AGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUCUUGCACAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA--------
-----.........((((...(((-(((((((((..(((..(((((.....))))).)))....)))))..)))))))..(((....))))))).........-------- ( -24.00, z-score =  -1.57, R)
>droYak2.chr2R 9785542 97 + 21139217
-----AUUUCAUUUCAAUACUUGC-AGCUUGCAACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA--------
-----.........((((...(((-(((((((((..(((..(((((.....))))).)))....)))))..)))))))..(((....))))))).........-------- ( -24.30, z-score =  -1.76, R)
>droEre2.scaffold_4845 11962142 97 - 22589142
-----AUUUCAUUUCAAUACUUGC-AGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCGCAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA--------
-----.........((((...(((-((((((((...(((..(((((.....))))).))).......)))))))))))..(((....))))))).........-------- ( -28.70, z-score =  -2.79, R)
>droAna3.scaffold_13266 8681429 95 + 19884421
-----AUUUCAUUUCAAUACUUGC-------CGGC-UGCAUUUCAUGUUAAAUGAACGCAUUUAUUGC---AGUCGCAGUUGCAGUUUCAAGGAUCCCUGCUCCUGCGUCU
-----...................-------.(((-((((........((((((....)))))).)))---))))((((..((((.((....))...))))..)))).... ( -24.10, z-score =  -1.64, R)
>droMoj3.scaffold_6496 10323423 87 + 26866924
AGUGCGUUUGAUUUGAUUUGAUGCAAGCUCUUAAGUUGCAUUUCGUGUUAAAUGAACGCAUUUA-UACGAACUCUGCGCUC-CGUUGAU----------------------
(((((((((.(((((((..(((((((.((....)))))))))....))))))))))))))))..-.......((.(((...-))).)).---------------------- ( -21.40, z-score =  -0.99, R)
>consensus
_____AUUUCAUUUCAAUACUUGC_AGCUUGCGACUUGCAUUUCAUGUUAAAUGAACGCAUUUAUUGCACAAGCUGCAUUUGCACUUGCAGUUGCAUUUCCCA________
.....................(((.(((((((((..(((..(((((.....))))).)))....)))))..))))))).((((....)))).................... (-12.89 = -13.74 +   0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:42:03 2011