Locus 10413

Sequence ID	dm3.chr3R
Location	13,654,709 – 13,654,835
Length	126
Max. P	0.999225

overview

Window 3

Location	13,654,709 – 13,654,803
Length	94
Sequences	7
Columns	114
Reading direction	forward
Mean pairwise identity	70.08
Shannon entropy	0.55613
G+C content	0.47894
Mean single sequence MFE	-28.66
Consensus MFE	-12.88
Energy contribution	-14.84
Covariance contribution	1.96
Combinations/Pair	1.18
Mean z-score	-1.94
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.46
SVM RNA-class probability	0.939844
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13654709 94 + 27905053
-----------AGCACUUUGUGACUAU--GUUUAAUGAUGAAGUCGGGGGCU---UCUGGCUUUAUCUCUGCUUACUUUGCCACCUUG---UGGGUGGGACACUCUCACAUUC-
-----------.......(((((...(--(((....((((((((((((....---)))))))))))).............(((((...---..)))))))))...)))))...- ( -28.70, z-score =  -2.37, R)
>droPer1.super_6 3961018 114 + 6141320
GUGACUGGUGUGGGUUUUUCCGACUCUCGACUUGAUGACGAAGUCAGGUCGGAAAAGUGUCUUUAUCUCUGCUUACUUUUCCACCUAGCAGGGGGUUCCUCCCCUCCCCGCACC
......((((((((((((((((((.((.(((((.......)))))))))))))))))...........(((((.............)))))((((.....))))..)))))))) ( -44.72, z-score =  -3.29, R)
>droAna3.scaffold_13340 11639311 88 - 23697760
---------CAACGAUGUUCUGGCUCU--GCCUCAUGACGAAGUCGGGGGAAAAGUAUUUCUUUAUCUCUGCUUACUUUGCCACCUUU------------CUCUCUCCACU---
---------.....(((....(((...--))).)))(.((((((((((((.((((.....)))).))))))...)))))).)......------------...........--- ( -15.10, z-score =   0.36, R)
>droEre2.scaffold_4770 9775734 93 - 17746568
-----------AGCUCUUUGUGACUAU--GUUUAAUGAUGAAGUCGGGGGCC---GCUGGUUUUAUCUCUGCUUACUUUGCCACCUUG---UGGGUGGGAACCUCACG-AUUC-
-----------......((((((....--((((...((((((..(((.....---.)))..)))))).............(((((...---..))))))))).)))))-)...- ( -24.20, z-score =  -0.36, R)
>droYak2.chr3R 2236743 93 + 28832112
-----------AGCACUUUGUGACUAU--GUUUAAUGAUGAAGUCGGGGGUC---ACUGGCUUUAUCUCUGCUUACUUUGCCACCUUA---UGGGUGGGA-ACUACCAGAUUU-
-----------(((((...))).))..--.......(((((((((((.....---.)))))))))))((((......((.(((((...---..))))).)-)....))))...- ( -26.60, z-score =  -1.61, R)
>droSim1.chr3R 19681663 97 - 27517382
-----------AACACUUUGUGACUAU--GUUUAAUGAUGAAGUCGGGGGCU---UCCGGCUUUAUCUCUGCUUACUUUGCCACCUCGUCGUGGGUGGCACACUCUCACAUUC-
-----------.......(((((...(--((.....((((((((((((....---))))))))))))............(((((((......))))))))))...)))))...- ( -33.60, z-score =  -4.22, R)
>droSec1.super_12 1623481 97 - 2123299
-----------AACACUUUGUGACUAU--GUUUAAUGAUGAAGUCGGGGGCU---UCAGGCUUUAUCUCUGCUUACUUUGCCACCUCGUCGUGGGUGGCACACUCUCACAUUC-
-----------.......(((((...(--((.....(((((((((.......---...)))))))))............(((((((......))))))))))...)))))...- ( -27.70, z-score =  -2.11, R)
>consensus
___________AGCACUUUGUGACUAU__GUUUAAUGAUGAAGUCGGGGGCU___UCUGGCUUUAUCUCUGCUUACUUUGCCACCUUG___UGGGUGGCACACUCUCACAUUC_
....................................(((((((((((.........))))))))))).............((((((......))))))................ (-12.88 = -14.84 +   1.96)

alignment

secondary structure

dotplot

Window 4

Location	13,654,733 – 13,654,835
Length	102
Sequences	7
Columns	113
Reading direction	forward
Mean pairwise identity	67.14
Shannon entropy	0.64173
G+C content	0.50832
Mean single sequence MFE	-29.71
Consensus MFE	-17.50
Energy contribution	-19.39
Covariance contribution	1.88
Combinations/Pair	1.30
Mean z-score	-2.31
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.72
SVM RNA-class probability	0.999225
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 13654733 102 + 27905053
AUGAAGUCGGGGGCU---UCUGGCUUUAUCUCUGCUUACUUUGCCACCUUGU---GGGUGGG-ACACUCUCACAUUCACCGUUUCA----UCCUCCGACUUCUCCUCGGAGUU
..(((((((((((..---..((((..................))))....((---(.(((((-.....)))))...))).......----.)))))))))))((....))... ( -31.47, z-score =  -1.82, R)
>droPer1.super_6 3961055 106 + 6141320
ACGAAGUCAGGUCGGAAAAGUGUCUUUAUCUCUGCUUACUUUUCCACCUAGCAGGGGGUUCCUCCCCUCCCCGCACCGCCCAUGCCCCUACCCUCUUUUCUCCCUC-------
..((((..((((.(((((((((..............))))))))))))).((.(((((........))))).))......................))))......------- ( -25.94, z-score =  -1.72, R)
>droAna3.scaffold_13340 11639337 92 - 23697760
ACGAAGUCGGGGGAAAAGUAUUUCUUUAUCUCUGCUUACUUUGCCACCUUUC-----UCUCU-CCACUGGCAGUUCCAUUUGCCUAC---UCCCCUGACUU------------
...(((((((((((((((((................))))))..........-----.....-.....(((((......)))))...---)))))))))))------------ ( -27.39, z-score =  -4.19, R)
>droEre2.scaffold_4770 9775758 100 - 17746568
AUGAAGUCGGGGGCC---GCUGGUUUUAUCUCUGCUUACUUUGCCACCUUGU---GGGUGGG-AACCUCACG-AUUCUCUCUUUC-----UCCUCUGACUUCUCUACGGAGUU
..(((((((((((..---(.((((..................)))).)((((---(((.(..-..)))))))-)...........-----.)))))))))))((....))... ( -29.57, z-score =  -1.28, R)
>droYak2.chr3R 2236767 105 + 28832112
AUGAAGUCGGGGGUC---ACUGGCUUUAUCUCUGCUUACUUUGCCACCUUAU---GGGUGGG-A-ACUACCAGAUUUUCCUAUUCUCCUUUUCUCUGAAUUCUCUCUGGAGUU
((((((((((.....---.))))))))))..............(((((....---.))))).-(-(((.(((((.......((((...........))))....))))))))) ( -27.70, z-score =  -0.94, R)
>droSim1.chr3R 19681687 105 - 27517382
AUGAAGUCGGGGGCU---UCCGGCUUUAUCUCUGCUUACUUUGCCACCUCGUCGUGGGUGGC-ACACUCUCACAUUCUCCGCUUCA----UCCUCUGACUUCUCCUCGAAGUU
((((((.((((((..---...(((.........))).....((((((((......)))))))-)...........)))))))))))----).....((((((.....)))))) ( -32.90, z-score =  -3.08, R)
>droSec1.super_12 1623505 105 - 2123299
AUGAAGUCGGGGGCU---UCAGGCUUUAUCUCUGCUUACUUUGCCACCUCGUCGUGGGUGGC-ACACUCUCACAUUCUCCGUUUCA----UCCUCUGACUUCUCCUCGAAGUU
..(((((((((((..---..((((.........))))....((((((((......)))))))-)......................----.)))))))))))........... ( -33.00, z-score =  -3.11, R)
>consensus
AUGAAGUCGGGGGCU___UCUGGCUUUAUCUCUGCUUACUUUGCCACCUUGU___GGGUGGC_ACACUCUCACAUUCUCCGUUUCA____UCCUCUGACUUCUCCUCGGAGUU
..(((((((((((........(((.........))).......((((((......))))))..............................)))))))))))........... (-17.50 = -19.39 +   1.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:23:32 2011