Locus 12197

Sequence ID	dm3.chr3R
Location	26,395,082 – 26,395,223
Length	141
Max. P	0.999249

overview

Window 5

Location	26,395,082 – 26,395,193
Length	111
Sequences	7
Columns	119
Reading direction	forward
Mean pairwise identity	74.92
Shannon entropy	0.45575
G+C content	0.49350
Mean single sequence MFE	-36.57
Consensus MFE	-21.47
Energy contribution	-23.43
Covariance contribution	1.96
Combinations/Pair	1.18
Mean z-score	-1.93
Structure conservation index	0.59
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.58
SVM RNA-class probability	0.951810
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26395082 111 + 27905053
AAUGUGUCGACGACGAGUAUCUGACAGAUACAU-------UUCGG-UUCCCGUCUAGUUUACCGUGCGGAUCUGCAUGGUGGGCUGGAUUUCGGUAUCGAGAACAGGUAGCGUUUGAGG
......((((((.(..(((((.....))))).(-------(((((-(.((.(((((((((((((((((....)))))))))))))))))...)).))))))).......))).)))).. ( -41.50, z-score =  -2.67, R)
>droSim1.chr3R 26040472 111 + 27517382
AAUGUGUCGACGACGAGUAUCUGACAGAUACAU-------UUCGG-UUCCCGUCUAGUUUACCGUGCAGAUCUGCAUGGUGGGCUGGAUUUUGGUAUCGAGAACAGGUAGCGUUUGAGC
......((((((.(..(((((.....))))).(-------(((((-(.((.(((((((((((((((((....)))))))))))))))))...)).))))))).......))).)))).. ( -42.30, z-score =  -3.48, R)
>droSec1.super_4 5221809 111 + 6179234
AAUGUGUCGACGACGAGUAUCUGACAGAUACAU-------UUCGG-UUCCCGUCUAGUUUACCGUGCGGAUCUGCAUGGUGGGCUGGAUUUCGGUAUCGAGAACAGGUAGCGUUUUAGC
...((...((((.(..(((((.....))))).(-------(((((-(.((.(((((((((((((((((....)))))))))))))))))...)).))))))).......)))))...)) ( -41.20, z-score =  -2.91, R)
>droYak2.chr3R 27314636 111 + 28832112
GAUGUGUCGACGACGAGUAUCUGACAGAUACAU-------UUCGG-UGGCCGUCUGGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUUUGGGUAUUGAGAACAGGUAUCUUUUCAGG
....((((...)))).....((((.((((((.(-------(((((-((.(((((..((((((((((((....))))))))))))..)))..)).))))))))....))))))..)))). ( -43.00, z-score =  -3.81, R)
>droEre2.scaffold_4820 8860086 112 - 10470090
AAUGUGUCGACGACGAGUAUCUGGCAGAUACAU-------UUCGGCUUGCCGUCUAGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUAUUGGUAUCGAGAACAGGUAUCUUUUGAGG
..........(((.(((((((((...(((((..-------...((....))(((((((((((((((((....)))))))))))))))))....))))).....)))))).))))))... ( -40.00, z-score =  -2.89, R)
>dp4.chr2 29657408 104 - 30794189
AACGUGUUGACGACUCGCAUCUGACAGAUACGUACAUCGCCUCACGUUCGCGUCUUGUUAACAGUG--GAUUUGCAUGGUCCGAUGG-UUCUAAUGCCAACUGCUGC------------
.((.(((((((((..((((((.....)))((((..........))))..)))..)))))))))))(--((((.....)))))..(((-(......))))........------------ ( -24.70, z-score =   1.04, R)
>droPer1.super_7 515439 104 - 4445127
AACGUGUUGACGACUCGCAUCUGACAGAUACGUACAUCGCCUCACGUUCACGUCUUGUUAACAGUG--GAUUUGCAUGGUCCGAUGG-UUCUAAUGCCAACUGCUGC------------
((((((..(.(((..((.(((.....))).))....))))..)))))).............(((((--((((.....)))))..(((-(......))))...)))).------------ ( -23.30, z-score =   1.19, R)
>consensus
AAUGUGUCGACGACGAGUAUCUGACAGAUACAU_______UUCGG_UUCCCGUCUAGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUUUUGGUAUCGAGAACAGGUAGCGUUUGAGG
...((.((((......(((((.....)))))....................(((((((((((((((((....))))))))))))))))).......))))..))............... (-21.47 = -23.43 +   1.96)

alignment

secondary structure

dotplot

Window 6

Location	26,395,115 – 26,395,223
Length	108
Sequences	7
Columns	110
Reading direction	forward
Mean pairwise identity	68.82
Shannon entropy	0.59172
G+C content	0.48382
Mean single sequence MFE	-38.04
Consensus MFE	-16.36
Energy contribution	-19.81
Covariance contribution	3.45
Combinations/Pair	1.17
Mean z-score	-3.25
Structure conservation index	0.43
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.74
SVM RNA-class probability	0.999249
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26395115 108 + 27905053
UUCGG-UUCCCGUCUAGUUUACCGUGCGGAUCUGCAUGGUGGGCUGGAUUUCGGUAUCGAGAACAGGUAGCGUUUGAGGUACUCUAUUUUAACAGGAAGCAUUACCCCA-
...(.-((((.(((((((((((((((((....)))))))))))))))))...((((((..((((.......))))..))))))...........)))).).........- ( -38.50, z-score =  -2.48, R)
>droSim1.chr3R 26040505 108 + 27517382
UUCGG-UUCCCGUCUAGUUUACCGUGCAGAUCUGCAUGGUGGGCUGGAUUUUGGUAUCGAGAACAGGUAGCGUUUGAGCUACUCUACUUGAACGGGGAACAUUAUACCA-
....(-((((((((((((((((((((((....)))))))))))))))))....((.(((((....((((((......))))))...))))))).)))))).........- ( -48.50, z-score =  -5.72, R)
>droSec1.super_4 5221842 108 + 6179234
UUCGG-UUCCCGUCUAGUUUACCGUGCGGAUCUGCAUGGUGGGCUGGAUUUCGGUAUCGAGAACAGGUAGCGUUUUAGCUACUCUACUUGAACAGGGAACAUUAUACCA-
....(-((((((((((((((((((((((....)))))))))))))))))....((.(((((....((((((......))))))...))))))).)))))).........- ( -47.90, z-score =  -5.70, R)
>droYak2.chr3R 27314669 109 + 28832112
UUCGG-UGGCCGUCUGGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUUUGGGUAUUGAGAACAGGUAUCUUUUCAGGUGCUCUAUUUGAACGGGUAAUUUGAUAGCUG
(((((-((.(((((..((((((((((((....))))))))))))..)))..)).)))))))..(((((((((.((((((((...)))))))).)))).)))))....... ( -40.40, z-score =  -3.93, R)
>droEre2.scaffold_4820 8860119 110 - 10470090
UUCGGCUUGCCGUCUAGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUAUUGGUAUCGAGAACAGGUAUCUUUUGAGGUACUCUAUUUUAACGGGAAACAUUAUACCAG
...((....))(((((((((((((((((....)))))))))))))))))..((((((..((((.((((((((....)))))).)).))))....(....)...)))))). ( -39.60, z-score =  -4.03, R)
>dp4.chr2 29657448 95 - 30794189
CUCACGUUCGCGUCUUGUUAACAGUG--GAUUUGCAUGGUCCGAUGG-UUCUAAUGCCAACUGCUGCUGCCCUC-------CUUUGGGGGAACGAACGAUUUCGA-----
....((((((......((...(((((--((((.....)))))..(((-(......))))))))..))..(((((-------....)))))..)))))).......----- ( -27.00, z-score =  -0.51, R)
>droPer1.super_7 515479 95 - 4445127
CUCACGUUCACGUCUUGUUAACAGUG--GAUUUGCAUGGUCCGAUGG-UUCUAAUGCCAACUGCUGCUGCCCUC-------CUUUGGGAGAACGAACGAUUUCGA-----
....(((((.......((...(((((--((((.....)))))..(((-(......))))))))..))....(((-------(....))))...))))).......----- ( -24.40, z-score =  -0.35, R)
>consensus
UUCGG_UUCCCGUCUAGUUUACCGUGCGGAUUUGCAUGGUGGGCUGGAUUUUGGUAUCGAGAACAGGUAGCGUUUGAGGUACUCUAUUUGAACGGGAAACAUUAUACCA_
...........(((((((((((((((((....)))))))))))))))))................((((((......))))))........................... (-16.36 = -19.81 +   3.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:38 2011