Locus 4918

Sequence ID	3R_DroMel_CAF1
Location	12,909,935 – 12,910,025
Length	90
Max. P	0.999432

overview

Window 0

Location	12,909,935 – 12,910,025
Length	90
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	73.33
Mean single sequence MFE	-36.90
Consensus MFE	-24.05
Energy contribution	-24.83
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-1.31
Structure conservation index	0.65
SVM decision value	0.08
SVM RNA-class probability	0.575256
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12909935 90 + 27905053
GGCCGAAGACGUGACCGUUGGUCAGGAGGCCGGAGCGGA------------------------------GGAAAUCCCCGCCAAGAAGGAUGUCGAGGAUAAGAACGUCAAUGGCCAGGA
(((((..(((((..((.((((((....)))))).((((.------------------------------((....))))))......)).((((...))))...)))))..))))).... ( -33.10)
>DroEre_CAF1 27067 120 + 1
AGCCGAGGACGUAACCGUUGGCCAGGAGGCCGGUGCGGAGACACCGAAGAAGGGCGGCUCACCCAUUAAGGAAAUCCCCACAGAGAAGGAUGUCAAGGAUAAGAACGUCGAUGGCCAGAA
.((((..(((((..(((((((((....)))))..)))).((((((......(((.......))).....((......))........)).))))..........)))))..))))..... ( -38.30)
>DroYak_CAF1 28120 120 + 1
AGCCCAGGACGUGACCGUUGGCCAGGAAGCCGGUGCGGAGACACCGAAGAAAGGCGGCUCGCCCAUUAAGGAGAUCCCCGCCGAGAAGGAUGUCGAGAGUAAGAACGUCGAUGGACAGAA
.(.(((.(((((..((((((((......))))..)))).((((((.......(((((.((.((......)).))...))))).....)).))))..........)))))..))).).... ( -39.30)
>consensus
AGCCGAGGACGUGACCGUUGGCCAGGAGGCCGGUGCGGAGACACCGAAGAA_GGCGGCUC_CCCAUUAAGGAAAUCCCCGCCGAGAAGGAUGUCGAGGAUAAGAACGUCGAUGGCCAGAA
.((((..(((((..(((((((((....)))))..))))................................((.((((..........)))).))..........)))))..))))..... (-24.05 = -24.83 +   0.78)

alignment

secondary structure

dotplot

Window 1

Location	12,909,935 – 12,910,025
Length	90
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	73.33
Mean single sequence MFE	-36.73
Consensus MFE	-28.34
Energy contribution	-29.24
Covariance contribution	0.90
Combinations/Pair	1.21
Mean z-score	-2.12
Structure conservation index	0.77
SVM decision value	3.60
SVM RNA-class probability	0.999432
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12909935 90 - 27905053
UCCUGGCCAUUGACGUUCUUAUCCUCGACAUCCUUCUUGGCGGGGAUUUCC------------------------------UCCGCUCCGGCCUCCUGACCAACGGUCACGUCUUCGGCC
....((((...(((((......................(((((((.....)------------------------------))))))..((((...........)))))))))...)))) ( -27.80)
>DroEre_CAF1 27067 120 - 1
UUCUGGCCAUCGACGUUCUUAUCCUUGACAUCCUUCUCUGUGGGGAUUUCCUUAAUGGGUGAGCCGCCCUUCUUCGGUGUCUCCGCACCGGCCUCCUGGCCAACGGUUACGUCCUCGGCU
....((((...(((((......((..............(((((((((..((.....(((((...)))))......)).)))))))))..((((....))))...))..)))))...)))) ( -41.20)
>DroYak_CAF1 28120 120 - 1
UUCUGUCCAUCGACGUUCUUACUCUCGACAUCCUUCUCGGCGGGGAUCUCCUUAAUGGGCGAGCCGCCUUUCUUCGGUGUCUCCGCACCGGCUUCCUGGCCAACGGUCACGUCCUGGGCU
....(((((..(((((..........(((..........((((((((..((.....(((((...)))))......)).))))))))...((((....))))....)))))))).))))). ( -41.20)
>consensus
UUCUGGCCAUCGACGUUCUUAUCCUCGACAUCCUUCUCGGCGGGGAUUUCCUUAAUGGG_GAGCCGCC_UUCUUCGGUGUCUCCGCACCGGCCUCCUGGCCAACGGUCACGUCCUCGGCU
....((((...(((((..........(((..........((((((((.........((((.....)))).........))))))))...((((....))))....))))))))...)))) (-28.34 = -29.24 +   0.90)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:01 2006