Locus 6064

Sequence ID	3L_DroMel_CAF1
Location	16,142,714 – 16,142,887
Length	173
Max. P	0.862437

overview

Window 9

Location	16,142,714 – 16,142,826
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-36.76
Consensus MFE	-22.36
Energy contribution	-23.08
Covariance contribution	0.72
Combinations/Pair	1.16
Mean z-score	-1.72
Structure conservation index	0.61
SVM decision value	0.03
SVM RNA-class probability	0.547740
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142714 112 - 23771897
--CGGCUCUCCCCUCAUCACCACGAAUGCUCUCCACAUCGUCAGUGGCCGCCGUCUGGCGGGGAGAGCUGUAAUCGUGGGCACACCGAAAGAAU------AUAUUCCCCAAUGAUCUGAA
--(((((((((((......((((..(((..........)))..))))..(((....))))))))))))))..((((((((.....(....)...------......))).)))))..... ( -38.04)
>DroSec_CAF1 4905 104 - 1
--CGGCUCUCCCCUC--------GAAUGCUCUUCACAUCGUCAGUGGCCGCCGUCUGGCGGGGAGAGCUGUAAUCGUGGGCACACCGAAAGAAU------AUAUUCCCCAAUGAUCUGAA
--(((((((((((..--------(((.....))).....((((((((...))).))))))))))))))))..((((((((.....(....)...------......))).)))))..... ( -37.04)
>DroSim_CAF1 5689 112 - 1
--CGGCUCUCCCCUCGCCACCACGAAUGCUCUCCACAUCGUCAGUGGCCGCCGUCUGGCGGGGAGAGCUGUAAUCGUGGGCACACCGAAAGAAU------AUAUUCCCCAAUGAUCUGAA
--(((((((((((..(((((.((((.((.......))))))..))))).(((....))))))))))))))..((((((((.....(....)...------......))).)))))..... ( -44.04)
>DroEre_CAF1 4268 111 - 1
CCCGAUUCUCCCCUCUUC-CCACGGAUGCUCCACACAUUGG--AGUGCCGCCGUCUGGCG--GAGAGCUGUAAUCGUGGGCACACCGAAAGAAUACUUGUAUAUUCCCCACUGAUC----
...((((..(..((((((-((((((.(((((((.....)))--))))...))))..)).)--)))))..).))))(((((.....(....).(((....)))....))))).....---- ( -32.60)
>DroYak_CAF1 4957 108 - 1
CCAG-CGCUCCCCUCUUU-CCGUGGAUGCUCCACUCAUUGG--GGAGCCGUCGUCUGGCA--GAGAGCUUUAAUCGUGGGCACACCAAAAGAAU------AUAUUCCCCAUUGAUCUGGU
((((-.............-..((((.....))))(((.(((--(((((((.....)))).--...........((.(((.....)))...))..------....)))))).))).)))). ( -32.10)
>consensus
__CGGCUCUCCCCUCUUC_CCACGAAUGCUCUACACAUCGUCAGUGGCCGCCGUCUGGCGGGGAGAGCUGUAAUCGUGGGCACACCGAAAGAAU______AUAUUCCCCAAUGAUCUGAA
..(((((((((((.........(((.((.......)))))......((((.....)))))))))))))))..((((((((..........((((........)))))))).))))..... (-22.36 = -23.08 +   0.72)

alignment

secondary structure

dotplot

Window 0

Location	16,142,748 – 16,142,850
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-43.20
Consensus MFE	-27.49
Energy contribution	-28.55
Covariance contribution	1.06
Combinations/Pair	1.05
Mean z-score	-2.06
Structure conservation index	0.64
SVM decision value	0.83
SVM RNA-class probability	0.862437
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142748 102 + 23771897
CCCACGAUUACAGCUCUCCCCGCCAGACGGCGGCCACUGACGAUGUGGAGAGCAUUCGUGGUGAUGAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA----
............((((((((((((....)))...((((.(((((((.....))).))))))))....)))))))))((--------------(....)))....(((....)))..---- ( -44.10)
>DroSec_CAF1 4939 94 + 1
CCCACGAUUACAGCUCUCCCCGCCAGACGGCGGCCACUGACGAUGUGAAGAGCAUUC--------GAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA----
............((((((((((((....))).........((((((.....))).))--------).)))))))))((--------------(....)))....(((....)))..---- ( -38.50)
>DroSim_CAF1 5723 102 + 1
CCCACGAUUACAGCUCUCCCCGCCAGACGGCGGCCACUGACGAUGUGGAGAGCAUUCGUGGUGGCGAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA----
............((((((((((((....))).((((((.(((((((.....))).))))))))))..)))))))))((--------------(....)))....(((....)))..---- ( -51.10)
>DroEre_CAF1 4304 115 + 1
CCCACGAUUACAGCUCUC--CGCCAGACGGCGGCACU--CCAAUGUGUGGAGCAUCCGUGG-GAAGAGGGGAGAAUCGGGUGAUUGGAGACAGGAGACUGGAGACAGGAGACAGGAGACC
.((.(((((((..(((((--(......(.((((..((--(((.....)))))...)))).)-.....))))))......)))))))....(((....)))......(....).))..... ( -39.10)
>consensus
CCCACGAUUACAGCUCUCCCCGCCAGACGGCGGCCACUGACGAUGUGGAGAGCAUUCGUGG_GA_GAGGGGAGAGCCG______________GGAGACUGCAGACAGGAGACUGGA____
............((((((((((((....)))..........(((((.....)))))...........)))))))))................(....)......(((....)))...... (-27.49 = -28.55 +   1.06)

alignment

secondary structure

dotplot

Window 1

Location	16,142,788 – 16,142,887
Length	99
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.03
Mean single sequence MFE	-31.85
Consensus MFE	-20.41
Energy contribution	-21.47
Covariance contribution	1.06
Combinations/Pair	1.05
Mean z-score	-1.92
Structure conservation index	0.64
SVM decision value	0.55
SVM RNA-class probability	0.779830
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16142788 99 + 23771897
CGAUGUGGAGAGCAUUCGUGGUGAUGAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA-------GACAGGAGACAGGCGACCGGUCGCAAAGUGGCUCAAU
.........((((...(...(((((..((.....((((--------------(....)).....(((....)))..-------....(....).)))..)).)))))...)..))))... ( -30.90)
>DroSec_CAF1 4979 87 + 1
CGAUGUGAAGAGCAUUC--------GAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA-------GACAGGAGACAGGC----GGUCGCAAAGUGGCUCAAU
((((((.....))).))--------)......((((((--------------.(.((((((...(((....)))..-------....(....)..))----)))).)....))))))... ( -30.80)
>DroSim_CAF1 5763 99 + 1
CGAUGUGGAGAGCAUUCGUGGUGGCGAGGGGAGAGCCG--------------GGAGACUGCAGACAGGAGACUGGA-------GACAGGAGACAGGCGACCGGUCGCAAAGUGGCUCAAU
.........((((...(...(((((..((.....((((--------------(....)).....(((....)))..-------....(....).)))..)).)))))...)..))))... ( -31.90)
>DroEre_CAF1 4340 119 + 1
CAAUGUGUGGAGCAUCCGUGG-GAAGAGGGGAGAAUCGGGUGAUUGGAGACAGGAGACUGGAGACAGGAGACAGGAGACCGGAGACAGGAGACAGGCGACCGGUCGCAAAGUGGCUCAAU
.........((((.(((....-..........(..((.(((..(((....)))...))).))..).(....).)))((((((.(...(....)...)..))))))........))))... ( -33.80)
>consensus
CGAUGUGGAGAGCAUUCGUGG_GA_GAGGGGAGAGCCG______________GGAGACUGCAGACAGGAGACUGGA_______GACAGGAGACAGGCGACCGGUCGCAAAGUGGCUCAAU
.(((((.....)))))................(((((...............(....)......(((....)))..........((.(....)..((((....))))...)))))))... (-20.41 = -21.47 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:08:55 2006