Locus 1427

Sequence ID	2L_DroMel_CAF1
Location	3,807,724 – 3,807,993
Length	269
Max. P	0.999294

overview

Window 9

Location	3,807,724 – 3,807,833
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	93.15
Mean single sequence MFE	-45.30
Consensus MFE	-35.82
Energy contribution	-36.60
Covariance contribution	0.78
Combinations/Pair	1.04
Mean z-score	-3.81
Structure conservation index	0.79
SVM decision value	0.91
SVM RNA-class probability	0.879510
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3807724 109 + 22407834
CGGUGGCGCGGCCAAUAGCAGUAAGUGCGCCAAGAUUGGCGCACUGGCAGGGAAUGCCAGCGGAACUGUGGCCGCAACCGGAAACGGAAACGGCGGCAACGAGAAUGAG
..((.((((((((....(((((.(((((((((....)))))))))((((.....))))......)))))))))))..(((....))).....)).))............ ( -53.50)
>DroSec_CAF1 17032 103 + 1
CGGUGGCGUGGCCAAUAGCAGUAAGUGCGCCAAGAUUGGUG------CAGGUAAUGCCAGCGGAACUGGGACCGCAACCGGAAACGGAAACGGCGGCAACGAGAAUGAG
((.((((((.(((....((.....))((((((....)))))------).))).)))))).))...((.(..((((..(((....))).....))))...).))...... ( -41.20)
>DroSim_CAF1 17023 103 + 1
CGGUGGCGUGGCCAAUAGCAGUAAGUGCGCCAAGAUUGGUG------CAGGUAAUGCCAGCGGAACUGGGACCGCAACCGGAAACGGAAACGGCGGCAACGAGAAUGAG
((.((((((.(((....((.....))((((((....)))))------).))).)))))).))...((.(..((((..(((....))).....))))...).))...... ( -41.20)
>consensus
CGGUGGCGUGGCCAAUAGCAGUAAGUGCGCCAAGAUUGGUG______CAGGUAAUGCCAGCGGAACUGGGACCGCAACCGGAAACGGAAACGGCGGCAACGAGAAUGAG
((.((((((.(((....(((.....)))((((....)))).........))).)))))).))...((.(..((((..(((....))).....))))...).))...... (-35.82 = -36.60 +   0.78)

alignment

secondary structure

dotplot

Window 0

Location	3,807,724 – 3,807,833
Length	109
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	93.15
Mean single sequence MFE	-36.20
Consensus MFE	-27.53
Energy contribution	-27.03
Covariance contribution	-0.49
Combinations/Pair	1.11
Mean z-score	-2.64
Structure conservation index	0.76
SVM decision value	0.17
SVM RNA-class probability	0.619223
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3807724 109 - 22407834
CUCAUUCUCGUUGCCGCCGUUUCCGUUUCCGGUUGCGGCCACAGUUCCGCUGGCAUUCCCUGCCAGUGCGCCAAUCUUGGCGCACUUACUGCUAUUGGCCGCGCCACCG
........(((.((((((((..(((....)))..)))))..((((...(((((((.....)))))))((((((....))))))....)))).....))).)))...... ( -45.80)
>DroSec_CAF1 17032 103 - 1
CUCAUUCUCGUUGCCGCCGUUUCCGUUUCCGGUUGCGGUCCCAGUUCCGCUGGCAUUACCUG------CACCAAUCUUGGCGCACUUACUGCUAUUGGCCACGCCACCG
........(((.((((((((..(((....)))..)))))...........(((((.((..((------(.(((....))).)))..)).)))))..))).)))...... ( -31.40)
>DroSim_CAF1 17023 103 - 1
CUCAUUCUCGUUGCCGCCGUUUCCGUUUCCGGUUGCGGUCCCAGUUCCGCUGGCAUUACCUG------CACCAAUCUUGGCGCACUUACUGCUAUUGGCCACGCCACCG
........(((.((((((((..(((....)))..)))))...........(((((.((..((------(.(((....))).)))..)).)))))..))).)))...... ( -31.40)
>consensus
CUCAUUCUCGUUGCCGCCGUUUCCGUUUCCGGUUGCGGUCCCAGUUCCGCUGGCAUUACCUG______CACCAAUCUUGGCGCACUUACUGCUAUUGGCCACGCCACCG
........(((.((((((((..(((....)))..)))))..((((..(((..(.(((...(((....)))..))).)..))).....)))).....))).)))...... (-27.53 = -27.03 +  -0.49)

alignment

secondary structure

dotplot

Window 1

Location	3,807,759 – 3,807,873
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.27
Mean single sequence MFE	-38.07
Consensus MFE	-29.83
Energy contribution	-29.31
Covariance contribution	-0.52
Combinations/Pair	1.16
Mean z-score	-1.54
Structure conservation index	0.78
SVM decision value	0.20
SVM RNA-class probability	0.629858
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3807759 114 + 22407834
UUGGCGCACUGGCAGGGAAUGCCAGCGGAACUGUGGCCGCAACCG------GAAACGGAAACGGCGGCAACGAGAAUGAGCCGAGUGUGAUCAAGGCGUGCAGCAGCUCGCUAAAGAUGA
(((((((((((((.......(((.((((........))))..(((------....)))....)))(....)........))).)))))).))))((((.((....)).))))........ ( -45.00)
>DroSec_CAF1 17067 108 + 1
UUGGUG------CAGGUAAUGCCAGCGGAACUGGGACCGCAACCG------GAAACGGAAACGGCGGCAACGAGAAUGAGCCGAGUGUGAUCAAGGCGUGCAGCAGCUCGCUGAAGAUGA
(((((.------((......(((.((((........))))..(((------....)))....)))(....).....)).))))).....(((..((((.((....)).))))...))).. ( -36.20)
>DroSim_CAF1 17058 108 + 1
UUGGUG------CAGGUAAUGCCAGCGGAACUGGGACCGCAACCG------GAAACGGAAACGGCGGCAACGAGAAUGAGCCGAGUGUGAUCAAGGCGUGCAGCAGCUCGCUGAAGAUGA
(((((.------((......(((.((((........))))..(((------....)))....)))(....).....)).))))).....(((..((((.((....)).))))...))).. ( -36.20)
>DroEre_CAF1 18535 108 + 1
UUGGCG------CAGGGAUUGCCAGCGGAACCGGAGCCGCAACCG------GAAACGGAAACGGUGGCAACGAGAACGAGCCGAGUGUGAUCAAGGCGUGCAGCAGCUCGCUGAAGAUGA
...(((------(...(((..(...(((..(((..(((((..(((------....))).....)))))..)).)......)))...)..)))...)))).((((.....))))....... ( -38.60)
>DroYak_CAF1 18903 114 + 1
UUGGUG------AAGGGAAUGCCAGCGGAACGGGAGUGGCAACCGGCAACGGAAACGGAAACGGUGGCAACGAGAAUGAACCAAGUGUGAUCAAGGCGUGCAGCAGCUCGCUGAAGAUGA
(((((.------.......(((((((...((....)).))..(((....)))...((....)).)))))..........))))).....(((..((((.((....)).))))...))).. ( -34.37)
>consensus
UUGGUG______CAGGGAAUGCCAGCGGAACUGGGGCCGCAACCG______GAAACGGAAACGGCGGCAACGAGAAUGAGCCGAGUGUGAUCAAGGCGUGCAGCAGCUCGCUGAAGAUGA
(((((.........(....((((.((((........))))...............((....))..)))).)........))))).....(((..((((.((....)).))))...))).. (-29.83 = -29.31 +  -0.52)

alignment

secondary structure

dotplot

Window 2

Location	3,807,833 – 3,807,953
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.33
Mean single sequence MFE	-49.40
Consensus MFE	-49.14
Energy contribution	-49.14
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.79
Structure conservation index	0.99
SVM decision value	2.34
SVM RNA-class probability	0.992579
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3807833 120 - 22407834
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUAUUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGCUCAUCUUUAGCGAGCUGCUGCACGCCUUGAUCACACUCGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..))...((((((((((((.((.((((.........)))).)).))).)))...))))))..... ( -49.70)
>DroSec_CAF1 17135 120 - 1
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGCUCAUCUUCAGCGAGCUGCUGCACGCCUUGAUCACACUCGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..))...((((((((((((.((.((((.........)))).)).))).)))...))))))..... ( -49.00)
>DroSim_CAF1 17126 120 - 1
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGAAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGCUCAUCUUCAGCGAGCUGCUGCACGCCUUGAUCACACUCGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..))...((((((((((((.((.((((.........)))).)).))).)))...))))))..... ( -49.00)
>DroEre_CAF1 18603 120 - 1
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAGAUGUGGUGGCUGCUGUUGCUCAUCUUCAGCGAGCUGCUGCACGCCUUGAUCACACUCGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..)).((((((((((((((.((.((((.........)))).)).))).)))...)))))).)).. ( -50.30)
>DroYak_CAF1 18977 120 - 1
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGCUCAUCUUCAGCGAGCUGCUGCACGCCUUGAUCACACUUGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..))...((((((((((((.((.((((.........)))).)).))).)))...))))))..... ( -49.00)
>consensus
GCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGCUCAUCUUCAGCGAGCUGCUGCACGCCUUGAUCACACUCGG
((..((((((....)))((.(((((.((((((....))))))...))))))))))..))...((((((((((((.((.((((.........)))).)).))).)))...))))))..... (-49.14 = -49.14 +   0.00)

alignment

secondary structure

dotplot

Window 3

Location	3,807,873 – 3,807,993
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-53.80
Consensus MFE	-53.14
Energy contribution	-53.14
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.99
SVM decision value	3.49
SVM RNA-class probability	0.999294
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3807873 120 - 22407834
GCGGACUGACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUAUUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....))))))))).((((((((.(((((.((((((....))))))...)))))))))..))))..))))).)).))).))).. ( -53.70)
>DroSec_CAF1 17175 120 - 1
GCGGACUGACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....))))))))).((((((((.(((((.((((((....))))))...)))))))))..))))..))))).)).))).))).. ( -53.00)
>DroSim_CAF1 17166 120 - 1
GCGGACUGACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGAAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....))))))))).((((((((.(((((.((((((....))))))...)))))))))..))))..))))).)).))).))).. ( -53.00)
>DroEre_CAF1 18643 120 - 1
GCGGACUGACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAGAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....)))))))))(((((((((.(((((.((((((....))))))...)))))))))..))))).))))).)).))).))).. ( -56.30)
>DroYak_CAF1 19017 120 - 1
GCGGACUAACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....))))))))).((((((((.(((((.((((((....))))))...)))))))))..))))..))))).)).))).))).. ( -53.00)
>consensus
GCGGACUGACCGAACGCACCUCCAUAUCCAGGCCAGUGGUGCUGGCCGGACUGCUCCGCGAGCUGUUGUAGUGGAAACUAUACUUCGGCUGCGGCUGGUAAAUGUGGUGGCUGCUGUUGC
.(((.....)))((((((((.((((((((.((((((.....))))))))).((((((((.(((((.((((((....))))))...)))))))))..))))..))))).)).))).))).. (-53.14 = -53.14 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:20 2006