Locus 9975

Sequence ID	3R_DroMel_CAF1
Location	26,692,132 – 26,692,270
Length	138
Max. P	0.980730

overview

Window 0

Location	26,692,132 – 26,692,230
Length	98
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.75
Mean single sequence MFE	-40.30
Consensus MFE	-30.02
Energy contribution	-30.55
Covariance contribution	0.53
Combinations/Pair	1.03
Mean z-score	-1.78
Structure conservation index	0.74
SVM decision value	0.35
SVM RNA-class probability	0.698591
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26692132 98 + 27905053
ACAUUACGCAAAGUGGGGG--------GCGUGGGAGUGGGCGUGUG-------GC-------AUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
...((((((..........--------))))))........((.((-------((-------((.((..(((((((((((.....))))))........)))))..)))))))).))... ( -36.90)
>DroSec_CAF1 282827 104 + 1
ACAUUACGCAAAGUGG-GG--------GCGUGGGAGUGGGCGUGUG-------GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
...........((((.-.(--------((((.(...(((((.((((-------((....((((.((.(((.....))).))))))...)))))).....)))))..).)))))...)))) ( -38.10)
>DroSim_CAF1 279596 105 + 1
ACAUUACGCAAAGUGGGGG--------GCGUGGGAGUGGGCGUGUG-------GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
...........((((...(--------((((.(...(((((.((((-------((....((((.((.(((.....))).))))))...)))))).....)))))..).)))))...)))) ( -38.40)
>DroEre_CAF1 298860 120 + 1
ACAUUACGCAAAGUGUGGGGCGGUGAGGCGUGGGAGUGGGCGUGUGGCAUGUGGCAUGUGGCAUGUGGGUGGGCGGCCAAGUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
.(((..(.(........).)..))).(((((.(...(((((.((((((....(((((.((((.(((......))))))).)))))...)))))).....)))))..).)))))....... ( -45.40)
>DroYak_CAF1 287960 118 + 1
ACAUUACGCAAAGUGUGGGGCGGUGAGGCGUGGGAGUGGGCGU--GGAAGUGGGCGUGUGGCAUGUGGGUGGGCGGCCAAGUGCUGUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
...((((((..(.(.(.(.((......)).).).).)..))))--))........((.((((((.((..((((((((((.......)))))........)))))..)))))))).))... ( -42.70)
>consensus
ACAUUACGCAAAGUGGGGG________GCGUGGGAGUGGGCGUGUG_______GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUU
...((((((..................))))))..((.(((((..........(((((...)))))(..(((((((((((.....))))))........)))))..).)))))..))... (-30.02 = -30.55 +   0.53)

alignment

secondary structure

dotplot

Window 1

Location	26,692,132 – 26,692,230
Length	98
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.75
Mean single sequence MFE	-30.10
Consensus MFE	-23.99
Energy contribution	-24.99
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.80
SVM decision value	0.41
SVM RNA-class probability	0.725090
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26692132 98 - 27905053
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAU-------GC-------CACACGCCCACUCCCACGC--------CCCCCACUUUGCGUAAUGU
...((.((((((((..(((((........((((((.....)))))))))))..)).))-------))-------)).))..........((((--------..........))))..... ( -30.70)
>DroSec_CAF1 282827 104 - 1
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC-------CACACGCCCACUCCCACGC--------CC-CCACUUUGCGUAAUGU
.((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))..-------...............((((--------..-.......))))..... ( -29.10)
>DroSim_CAF1 279596 105 - 1
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC-------CACACGCCCACUCCCACGC--------CCCCCACUUUGCGUAAUGU
.((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))..-------...............((((--------..........))))..... ( -29.00)
>DroEre_CAF1 298860 120 - 1
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCACUUGGCCGCCCACCCACAUGCCACAUGCCACAUGCCACACGCCCACUCCCACGCCUCACCGCCCCACACUUUGCGUAAUGU
.((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))...((((.....((((..........((......))..........)))).)))) ( -30.95)
>DroYak_CAF1 287960 118 - 1
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCACAGCACUUGGCCGCCCACCCACAUGCCACACGCCCACUUCC--ACGCCCACUCCCACGCCUCACCGCCCCACACUUUGCGUAAUGU
...((.((((((((..(((((........(((((.......))))))))))..)).)))))).))..........--((((..........((......))..........))))..... ( -30.75)
>consensus
AAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC_______CACACGCCCACUCCCACGC________CCCCCACUUUGCGUAAUGU
......((((((((..(((((........((((((.....)))))))))))..)).))))))...........................((((..................))))..... (-23.99 = -24.99 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	26,692,164 – 26,692,270
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-38.26
Consensus MFE	-29.12
Energy contribution	-30.12
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.76
SVM decision value	1.87
SVM RNA-class probability	0.980730
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26692164 106 + 27905053
CGUGUG-------GC-------AUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
.((.((-------((-------((.((..(((((((((((.....))))))........)))))..)))))))).))..(((.....((((.....))))..((....)).)))...... ( -33.70)
>DroSec_CAF1 282858 113 + 1
CGUGUG-------GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
.(((((-------((.(.((((((.((..(((((((((((.....))))))........)))))..)))))))).)...........((((.....))))..)))).))).......... ( -39.00)
>DroSim_CAF1 279628 113 + 1
CGUGUG-------GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
.(((((-------((.(.((((((.((..(((((((((((.....))))))........)))))..)))))))).)...........((((.....))))..)))).))).......... ( -39.00)
>DroEre_CAF1 298900 120 + 1
CGUGUGGCAUGUGGCAUGUGGCAUGUGGGUGGGCGGCCAAGUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
.(((((((...(((.(((((((((.((..((((((((((((...)))))))........)))))..)))))))..)))).)))....((((.....))))..)))).))).......... ( -40.50)
>DroYak_CAF1 288000 118 + 1
CGU--GGAAGUGGGCGUGUGGCAUGUGGGUGGGCGGCCAAGUGCUGUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
.((--.((.((((((((.((((((.((..((((((((((.......)))))........)))))..)))))))).))..........((((.....))))..)))..)))....)).)). ( -39.10)
>consensus
CGUGUG_______GCAUGUGGCAUGUGGGUGGGCGGCCAACUGCUUUGGCCAUAAACAAGCCCAAACAAUGCCAGACAUUUCAAACACAAUAAAUAAUUGAAGCCAGCGCAGAGUCAACA
..................((((((.((..(((((((((((.....))))))........)))))..))))))))(((..........((((.....))))..((....))...))).... (-29.12 = -30.12 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	26,692,164 – 26,692,270
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-34.14
Consensus MFE	-27.90
Energy contribution	-28.90
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.51
Structure conservation index	0.82
SVM decision value	0.44
SVM RNA-class probability	0.736328
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26692164 106 - 27905053
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAU-------GC-------CACACG
....(((...((....))(((((.(((.....))).)))))..)))((((((((..(((((........((((((.....)))))))))))..)).))-------))-------)).... ( -31.40)
>DroSec_CAF1 282858 113 - 1
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC-------CACACG
..........(.(.(((((((((.(((.....))).)))))((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))))-------))).). ( -34.70)
>DroSim_CAF1 279628 113 - 1
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC-------CACACG
..........(.(.(((((((((.(((.....))).)))))((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))))-------))).). ( -34.70)
>DroEre_CAF1 298900 120 - 1
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCACUUGGCCGCCCACCCACAUGCCACAUGCCACAUGCCACACG
..........(((.(((((((((.(((.....))).)))))((((..(((((((..(((((........((((((.....)))))))))))..)).)))))))))))))..)))...... ( -36.30)
>DroYak_CAF1 288000 118 - 1
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCACAGCACUUGGCCGCCCACCCACAUGCCACACGCCCACUUCC--ACG
...............((((((((.(((.....))).)))))..((.((((((((..(((((........(((((.......))))))))))..)).)))))).))))).......--... ( -33.60)
>consensus
UGUUGACUCUGCGCUGGCUUCAAUUAUUUAUUGUGUUUGAAAUGUCUGGCAUUGUUUGGGCUUGUUUAUGGCCAAAGCAGUUGGCCGCCCACCCACAUGCCACAUGC_______CACACG
....(((...((....))(((((.(((.....))).)))))..)))((((((((..(((((........((((((.....)))))))))))..)).)))))).................. (-27.90 = -28.90 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:12 2006