Locus 840

Sequence ID	3R_DroMel_CAF1
Location	2,874,183 – 2,874,301
Length	118
Max. P	0.849161

overview

Window 6

Location	2,874,183 – 2,874,301
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.60
Mean single sequence MFE	-41.45
Consensus MFE	-33.01
Energy contribution	-33.33
Covariance contribution	0.31
Combinations/Pair	1.14
Mean z-score	-1.77
Structure conservation index	0.80
SVM decision value	0.36
SVM RNA-class probability	0.706374
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2874183 118 + 27905053
UUUGGCUGCAUUUGCGGCGUGUUUGC--AGAUUGAAUGGAGCACUUCCGGCAUCCGGUUGCACUUUUUUGCCAUUGCUGCACUUUCGUCCUGUGAAAUGCAGCGACAUCGACGGCGAAUA
....(((((....))))).(((((((--...((((.((..(((...((((...)))).)))............((((((((.(((((.....)))))))))))))))))))..))))))) ( -38.90)
>DroSec_CAF1 5323 118 + 1
UUUCGCUGCAUUUGCAGCGUGUUUGC--AGAUUGAAUGGAGCACUUCCGGAAUCCGGUUGCACUUUUUUGCCAUUGCUGCACUUUCGUCCUGUGAGAUGCAGCGACAUCGACGGCGAAUA
...((((((....))))))(((((((--...((((.((..(((...((((...)))).)))............((((((((.(((((.....)))))))))))))))))))..))))))) ( -41.10)
>DroSim_CAF1 5676 120 + 1
UUUCGCUGCAUUUGCGGCGUGUUUGCUCGGAUUGAAUGGAGCACUUCCGGCAUCCGGUUGCACUUUUUUUCCAUUGGAGCACUUUCGUCCUGUGAGAUGCAGCGACAUGGACGGCGAAUA
..(((((((((((((((((....(((((.(((.(((.((.(((...((((...)))).))).))....))).))).)))))....)).)).)).)))))))))))............... ( -42.50)
>DroEre_CAF1 6276 117 + 1
UUUCGCUGCGUUUGCGGCGUGUUUGC--AGAUUGAAUGGAGCACUUCCGACAUCCGGUUGCACUUU-UUGCCAUUGCUGCACUUUCGUCCUGCGAGAUGCAGCGGCUUCGGCUGCGUAUA
...((((((....))))))..(((((--((..((((((.((((...(((.....)))..(((....-.)))...)))).))..))))..)))))))((((.(((((....))))))))). ( -43.30)
>consensus
UUUCGCUGCAUUUGCGGCGUGUUUGC__AGAUUGAAUGGAGCACUUCCGGCAUCCGGUUGCACUUUUUUGCCAUUGCUGCACUUUCGUCCUGUGAGAUGCAGCGACAUCGACGGCGAAUA
...((((((....))))))(((((((...(.((((.....(((...(((.....))).)))............((((((((.(((((.....)))))))))))))..))))).))))))) (-33.01 = -33.33 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	2,874,183 – 2,874,301
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.60
Mean single sequence MFE	-37.45
Consensus MFE	-28.96
Energy contribution	-29.77
Covariance contribution	0.81
Combinations/Pair	1.04
Mean z-score	-2.33
Structure conservation index	0.77
SVM decision value	0.78
SVM RNA-class probability	0.849161
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2874183 118 - 27905053
UAUUCGCCGUCGAUGUCGCUGCAUUUCACAGGACGAAAGUGCAGCAAUGGCAAAAAAGUGCAACCGGAUGCCGGAAGUGCUCCAUUCAAUCU--GCAAACACGCCGCAAAUGCAGCCAAA
.................(((((((((....((.((....(((((.(((((......((..(..((((...))))..)..)))))))....))--)))....))))..))))))))).... ( -35.90)
>DroSec_CAF1 5323 118 - 1
UAUUCGCCGUCGAUGUCGCUGCAUCUCACAGGACGAAAGUGCAGCAAUGGCAAAAAAGUGCAACCGGAUUCCGGAAGUGCUCCAUUCAAUCU--GCAAACACGCUGCAAAUGCAGCGAAA
..((((((((.(((((....)))))..)).)).))))..(((((.(((((......((..(..((((...))))..)..)))))))....))--)))....((((((....))))))... ( -39.50)
>DroSim_CAF1 5676 120 - 1
UAUUCGCCGUCCAUGUCGCUGCAUCUCACAGGACGAAAGUGCUCCAAUGGAAAAAAAGUGCAACCGGAUGCCGGAAGUGCUCCAUUCAAUCCGAGCAAACACGCCGCAAAUGCAGCGAAA
...............(((((((((......((.((....(((((.....(((....((..(..((((...))))..)..))...))).....)))))....))))....))))))))).. ( -37.40)
>DroEre_CAF1 6276 117 - 1
UAUACGCAGCCGAAGCCGCUGCAUCUCGCAGGACGAAAGUGCAGCAAUGGCAA-AAAGUGCAACCGGAUGUCGGAAGUGCUCCAUUCAAUCU--GCAAACACGCCGCAAACGCAGCGAAA
.....((((..(((((((((((((.(((.....)))..)))))))...)))..-..((..(..(((.....)))..)..))...)))...))--)).....(((.((....)).)))... ( -37.00)
>consensus
UAUUCGCCGUCGAUGUCGCUGCAUCUCACAGGACGAAAGUGCAGCAAUGGCAAAAAAGUGCAACCGGAUGCCGGAAGUGCUCCAUUCAAUCU__GCAAACACGCCGCAAAUGCAGCGAAA
...............(((((((((......(.((....)).).(((((((......((..(..((((...))))..)..)))))))........((......)).))..))))))))).. (-28.96 = -29.77 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:27 2006