Locus 513

Sequence ID	dm3.chr2L
Location	3,629,220 – 3,629,324
Length	104
Max. P	0.999795

overview

Window 8

Location	3,629,220 – 3,629,320
Length	100
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	62.63
Shannon entropy	0.60384
G+C content	0.48195
Mean single sequence MFE	-32.15
Consensus MFE	-16.27
Energy contribution	-19.15
Covariance contribution	2.88
Combinations/Pair	1.05
Mean z-score	-3.34
Structure conservation index	0.51
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	4.41
SVM RNA-class probability	0.999795
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 3629220 100 + 23011544
UUGAAAGAGAUUUUCUUGGCAUGAGCAC-ACUGCACUUAGCCCUCAUAAAGGGCCGAAUUUUCCUCAAAAUAAGUGUGGAAAGUUACGGCCCGCGGCCAAG
..............(((((((((((...-.(((....)))..)))))...((((((((((((((.((.......)).)))))))).))))))...)))))) ( -35.30, z-score =  -3.46, R)
>droSim1.chr2L 3588305 97 + 22036055
UCGAAAGAGAUUUUCUUGGCUUGAGCAC-ACUGCACUUAACCCUCAUGAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGUCGAG---
((....))......((((((....((..-...))................(((((((((((((((((.......))))))))))).))))))))))))--- ( -39.30, z-score =  -5.04, R)
>droSec1.super_5 1730259 98 + 5866729
UCGAAAGAGAUUUUCUUGGCAUGAGCUCCACUGCACUUAAUCCUCACAAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGUCGAG---
((....))......((((((....((......))................(((((((((((((((((.......))))))))))).))))))))))))--- ( -40.20, z-score =  -5.47, R)
>droVir3.scaffold_12963 5085772 79 - 20206255
-----------CUACAACAAGUUUGCAA-AUUGAAAGGCGCCGCCAAAGGGGGCAGAGUU--CAAAAGGUUUGGCAUAGAGAGCGAGAGAGAG--------
-----------..........(((((..-.(((((....(((.((...)).)))....))--)))...(.....).......)))))......-------- ( -13.80, z-score =   0.60, R)
>consensus
UCGAAAGAGAUUUUCUUGGCAUGAGCAC_ACUGCACUUAACCCUCAUAAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGUCGAG___
........................((......))................(((((((((((((((((.......))))))))))).))))))......... (-16.27 = -19.15 +   2.88)

alignment

secondary structure

dotplot

Window 9

Location	3,629,220 – 3,629,320
Length	100
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	62.63
Shannon entropy	0.60384
G+C content	0.48195
Mean single sequence MFE	-28.05
Consensus MFE	-13.70
Energy contribution	-15.08
Covariance contribution	1.38
Combinations/Pair	1.29
Mean z-score	-2.13
Structure conservation index	0.49
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.57
SVM RNA-class probability	0.992855
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 3629220 100 - 23011544
CUUGGCCGCGGGCCGUAACUUUCCACACUUAUUUUGAGGAAAAUUCGGCCCUUUAUGAGGGCUAAGUGCAGU-GUGCUCAUGCCAAGAAAAUCUCUUUCAA
((((((...((((((.((.(((((.((.......)).))))).))))))))...(((((.((..........-)).))))))))))).............. ( -34.70, z-score =  -2.83, R)
>droSim1.chr2L 3588305 97 - 22036055
---CUCGACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUCAUGAGGGUUAAGUGCAGU-GUGCUCAAGCCAAGAAAAUCUCUUUCGA
---(((((.((((((.((.((((((((.......)))))))).)))))))).))..)))((((.((..(...-)..))..))))..((((.....)))).. ( -34.60, z-score =  -3.21, R)
>droSec1.super_5 1730259 98 - 5866729
---CUCGACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUUGUGAGGAUUAAGUGCAGUGGAGCUCAUGCCAAGAAAAUCUCUUUCGA
---((((..((((((.((.((((((((.......)))))))).))))))))....))))......(.(((...(....).))))..((((.....)))).. ( -31.30, z-score =  -1.84, R)
>droVir3.scaffold_12963 5085772 79 + 20206255
--------CUCUCUCUCGCUCUCUAUGCCAAACCUUUUG--AACUCUGCCCCCUUUGGCGGCGCCUUUCAAU-UUGCAAACUUGUUGUAG-----------
--------.........((.......))........(((--((...((((((....)).))))...))))).-.(((((.....))))).----------- ( -11.60, z-score =  -0.62, R)
>consensus
___CUCGACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUUAUGAGGGCUAAGUGCAGU_GUGCUCAUGCCAAGAAAAUCUCUUUCGA
..........(((...(((((((((((.......))))))))(((.(((((((...))))))).)))........)))...)))................. (-13.70 = -15.08 +   1.38)

alignment

secondary structure

dotplot

Window 0

Location	3,629,224 – 3,629,324
Length	100
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	64.44
Shannon entropy	0.56971
G+C content	0.48445
Mean single sequence MFE	-32.38
Consensus MFE	-17.88
Energy contribution	-20.00
Covariance contribution	2.12
Combinations/Pair	1.18
Mean z-score	-3.15
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	4.14
SVM RNA-class probability	0.999652
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 3629224 100 + 23011544
AAGAGAUUUUCUUGGCAUGAGCAC--ACUGCACUUAGCCCUCAUAAAGGGCCGAAUUUUCCUCAAAAUAAGUGUGGAAAGUUACGGCCCGCGGCCAAGCUUG
..........(((((((((((...--.(((....)))..)))))...((((((((((((((.((.......)).)))))))).))))))...)))))).... ( -35.70, z-score =  -3.18, R)
>droSim1.chr2L 3588309 97 + 22036055
AAGAGAUUUUCUUGGCUUGAGCAC--ACUGCACUUAACCCUCAUGAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGU---CGAGCUUG
..(((.....)))(((((((((..--...))................(((((((((((((((((.......))))))))))).)))))).)---)))))).. ( -40.00, z-score =  -4.97, R)
>droSec1.super_5 1730263 98 + 5866729
AAGAGAUUUUCUUGGCAUGAGCUCC-ACUGCACUUAAUCCUCACAAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGU---CGAGCUUG
..........((((((....((...-...))................(((((((((((((((((.......))))))))))).))))))))---)))).... ( -38.30, z-score =  -4.59, R)
>droVir3.scaffold_12963 5085776 79 - 20206255
-------------AACAAGUUUGCAAAUUGAAAGGCGCCGCCAAAGGGGGCAGAGUU--CAAAAGGUUUGGCAUAGAGAGCGAGAGA--------GAGGUUG
-------------..(((.((..(...(((((....(((.((...)).)))....))--)))....(((.((.......)).)))).--------.)).))) ( -15.50, z-score =   0.12, R)
>consensus
AAGAGAUUUUCUUGGCAUGAGCAC__ACUGCACUUAACCCUCAUAAAGGGCCGAGUUUUCCACAAAAUAAGUGUGGAAAGCUACGGCCCGU___CGAGCUUG
.............(((....((.......))................(((((((((((((((((.......))))))))))).))))))........))).. (-17.88 = -20.00 +   2.12)

alignment

secondary structure

dotplot

Window 1

Location	3,629,224 – 3,629,324
Length	100
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	64.44
Shannon entropy	0.56971
G+C content	0.48445
Mean single sequence MFE	-28.52
Consensus MFE	-15.59
Energy contribution	-17.78
Covariance contribution	2.19
Combinations/Pair	1.32
Mean z-score	-2.21
Structure conservation index	0.55
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.83
SVM RNA-class probability	0.995673
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 3629224 100 - 23011544
CAAGCUUGGCCGCGGGCCGUAACUUUCCACACUUAUUUUGAGGAAAAUUCGGCCCUUUAUGAGGGCUAAGUGCAGU--GUGCUCAUGCCAAGAAAAUCUCUU
....((((((...((((((.((.(((((.((.......)).))))).))))))))...(((((.((..........--)).))))))))))).......... ( -34.90, z-score =  -2.47, R)
>droSim1.chr2L 3588309 97 - 22036055
CAAGCUCG---ACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUCAUGAGGGUUAAGUGCAGU--GUGCUCAAGCCAAGAAAAUCUCUU
....((((---(.((((((.((.((((((((.......)))))))).)))))))).))..)))((((.((..(...--)..))..))))((((.....)))) ( -33.90, z-score =  -2.93, R)
>droSec1.super_5 1730263 98 - 5866729
CAAGCUCG---ACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUUGUGAGGAUUAAGUGCAGU-GGAGCUCAUGCCAAGAAAAUCUCUU
..(((((.---((((((((.((.((((((((.......)))))))).))))))))..(((...........)))))-.)))))......((((.....)))) ( -34.70, z-score =  -2.85, R)
>droVir3.scaffold_12963 5085776 79 + 20206255
CAACCUC--------UCUCUCGCUCUCUAUGCCAAACCUUUUG--AACUCUGCCCCCUUUGGCGGCGCCUUUCAAUUUGCAAACUUGUU-------------
.......--------..............(((.(((....(((--((...((((((....)).))))...)))))))))))........------------- ( -10.60, z-score =  -0.60, R)
>consensus
CAAGCUCG___ACGGGCCGUAGCUUUCCACACUUAUUUUGUGGAAAACUCGGCCCUUUAUGAGGGCUAAGUGCAGU__GUGCUCAUGCCAAGAAAAUCUCUU
....((((.....((((((.((.((((((((.......)))))))).))))))))....))))(((..(((((.....)))))...)))............. (-15.59 = -17.78 +   2.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:14:16 2011