Locus 2059

Sequence ID	2L_DroMel_CAF1
Location	5,567,130 – 5,567,264
Length	134
Max. P	0.992004

overview

Window 1

Location	5,567,130 – 5,567,228
Length	98
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	95.31
Mean single sequence MFE	-18.87
Consensus MFE	-17.52
Energy contribution	-17.12
Covariance contribution	-0.40
Combinations/Pair	1.09
Mean z-score	-1.29
Structure conservation index	0.93
SVM decision value	0.76
SVM RNA-class probability	0.843382
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5567130 98 + 22407834
CUUCACCUUUCACCUCUUUUGUUUUUCUUUUCCGCUCUUUUUCCAUUGAGCCGAAGACACACACUCAAAAAGCGUGAGUCGCACAAUGGGUCUUGUUG
...........((((.((.(((.......(((.((((..........)))).)))(((.(((.((.....)).))).)))))).)).))))....... ( -19.20)
>DroSec_CAF1 11807 98 + 1
CUUCACCUUUCAUCUCUUUUGUUUUUCUUUUCCGCUCUUUUUCCAUUGAGCCGAAGACACACACUCAAAAAGCGUGAGUCGCACAAUGGGACUCGUUG
............((((..((((.......(((.((((..........)))).)))(((.(((.((.....)).))).)))..)))).))))....... ( -19.10)
>DroSim_CAF1 11754 98 + 1
CUUCACCUUUCAUCUCUUUUGUUUUUCUUUUCCGCUCUUUUUCCAUUGAGCCGAAGACACACACUCAAAAAGCGUGAGUCGCACAAUGGGACUCGUUG
............((((..((((.......(((.((((..........)))).)))(((.(((.((.....)).))).)))..)))).))))....... ( -19.10)
>DroEre_CAF1 11798 97 + 1
CUUCACCUUUCACCUCCUUUGUUUUUCUUUUCCGCUCUUUUUCCAUCGAGCUGAAGACACACACUCAAAAAGCGUGAGUCGCACAAUGGGACUCG-UG
..........(((.((((((((.......(((.((((..........)))).)))(((.(((.((.....)).))).)))..)))).))))...)-)) ( -19.80)
>DroYak_CAF1 12003 98 + 1
CUUCACCUUUCACCUCCUUUGUUUUUCUUUUCCGCUCUUUUUCCAUUGAGUUGAAGACACACACUCAAAAAGCGUGAGUCCCACAAUGGGUCUUGUUG
.........((((((..((((......(((((.((((..........)))).)))))........)))).)).))))(.(((.....))).)...... ( -17.14)
>consensus
CUUCACCUUUCACCUCUUUUGUUUUUCUUUUCCGCUCUUUUUCCAUUGAGCCGAAGACACACACUCAAAAAGCGUGAGUCGCACAAUGGGACUCGUUG
..............(((.((((.......(((.((((..........)))).)))(((.(((.((.....)).))).)))..)))).)))........ (-17.52 = -17.12 +  -0.40)

alignment

secondary structure

dotplot

Window 2

Location	5,567,130 – 5,567,228
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	95.31
Mean single sequence MFE	-24.01
Consensus MFE	-20.42
Energy contribution	-20.46
Covariance contribution	0.04
Combinations/Pair	1.06
Mean z-score	-1.58
Structure conservation index	0.85
SVM decision value	0.81
SVM RNA-class probability	0.855457
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5567130 98 - 22407834
CAACAAGACCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAAGAAAAACAAAAGAGGUGAAAGGUGAAG
.......((((.((((..(((.(((((((...))))))).)))(((.((((..(....)..)))).))).......))))..).)))........... ( -23.60)
>DroSec_CAF1 11807 98 - 1
CAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAAGAAAAACAAAAGAGAUGAAAGGUGAAG
....(((((.(.....).))))).((((((((.....(((.(((((.((((..(....)..)))).))..)))...)))........))))))))... ( -23.62)
>DroSim_CAF1 11754 98 - 1
CAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAAGAAAAACAAAAGAGAUGAAAGGUGAAG
....(((((.(.....).))))).((((((((.....(((.(((((.((((..(....)..)))).))..)))...)))........))))))))... ( -23.62)
>DroEre_CAF1 11798 97 - 1
CA-CGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCAGCUCGAUGGAAAAAGAGCGGAAAAGAAAAACAAAGGAGGUGAAAGGUGAAG
((-((((((.(.....).))))).((((((((...(((...((((..((((..(....)..))))....))))...))).))))))))....)))... ( -28.10)
>DroYak_CAF1 12003 98 - 1
CAACAAGACCCAUUGUGGGACUCACGCUUUUUGAGUGUGUGUCUUCAACUCAAUGGAAAAAGAGCGGAAAAGAAAAACAAAGGAGGUGAAAGGUGAAG
...((...(((.((((.((((.(((((((...))))))).))))((..(((..(....)..)))..))........)))).)).).)).......... ( -21.10)
>consensus
CAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAAGAAAAACAAAAGAGGUGAAAGGUGAAG
.........((((((.(((((.(((((((...))))))).)))....)).)))))).......................................... (-20.42 = -20.46 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	5,567,157 – 5,567,264
Length	107
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	88.07
Mean single sequence MFE	-27.22
Consensus MFE	-24.42
Energy contribution	-24.54
Covariance contribution	0.12
Combinations/Pair	1.08
Mean z-score	-2.11
Structure conservation index	0.90
SVM decision value	2.30
SVM RNA-class probability	0.992004
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5567157 107 - 22407834
UCUA--AUAAUUUCAUAAUAUUUCUACAC--AAUAUUUGGCAACAAGACCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAA
....--..............((((..(..--....((((....))))..((((((.(((((.(((((((...))))))).)))....)).)))))).......)..)))). ( -28.50)
>DroSec_CAF1 11834 109 - 1
UUUAAAAACACUUUACAAUAUUUCAACAC--AAUAUUUCGCAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAA
.............................--....((((((........((((((.(((((.(((((((...))))))).)))....)).)))))).......)))))).. ( -26.56)
>DroSim_CAF1 11781 111 - 1
UUUACAAAAACUUCAUAAUAUUUUAAAACUAAAUAUUUCGCAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAA
...................................((((((........((((((.(((((.(((((((...))))))).)))....)).)))))).......)))))).. ( -26.56)
>DroEre_CAF1 11825 108 - 1
UUUACAGUAAUUUUACAAUAUGUGAACGC--AAUAUUUCGCA-CGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCAGCUCGAUGGAAAAAGAGCGGAAAA
......((...(((((.....))))).))--....((((((.-(.....((((((.(((((.(((((((...))))))).)))....)).)))))).....).)))))).. ( -29.80)
>DroYak_CAF1 12030 109 - 1
UGUACAAAAAUUUUGCAAUAUUUUAACAC--AACAUUUUGCAACAAGACCCAUUGUGGGACUCACGCUUUUUGAGUGUGUGUCUUCAACUCAAUGGAAAAAGAGCGGAAAA
..........((((((.............--....(((((...))))).((((((.(((((.(((((((...))))))).))))).....)))))).......)))))).. ( -24.70)
>consensus
UUUACAAAAAUUUUACAAUAUUUCAACAC__AAUAUUUCGCAACGAGUCCCAUUGUGCGACUCACGCUUUUUGAGUGUGUGUCUUCGGCUCAAUGGAAAAAGAGCGGAAAA
...................................((((((........((((((.(((((.(((((((...))))))).)))....)).)))))).......)))))).. (-24.42 = -24.54 +   0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:16 2006