Locus 1276

Sequence ID	3R_DroMel_CAF1
Location	3,790,611 – 3,790,770
Length	159
Max. P	0.998742

overview

Window 5

Location	3,790,611 – 3,790,730
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.32
Mean single sequence MFE	-27.58
Consensus MFE	-26.21
Energy contribution	-26.17
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.07
Structure conservation index	0.95
SVM decision value	0.13
SVM RNA-class probability	0.599912
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790611 119 + 27905053
CGUGCUAGCACCAGAUACCCGCCCCCU-UCUUCCACCGCCUCCCGCUGGCCACGGCAAAAUGUUGUUAUUUUGCCUGUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCAUGUCGCC
.((((.......((((((.(.......-.........(((.......)))...(((((((((....))))))))).).)))))).......))))..((((((.......))).)))... ( -28.54)
>DroSec_CAF1 20021 120 + 1
CGUGCUAGCACCAUAUACCCGCCCCCUUUCUUCCACCGCCUCCCGCUGGCCACGGCAAAAUGUUGUUAUUUUGCCUGUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCACGUCGCC
(((((..(((...........................(((.......)))((((((((((((....))))))))).)))...........)))..(((((.....))))))))))..... ( -29.20)
>DroSim_CAF1 24511 120 + 1
CGUGCUAGCACCAGAUACCCGCCCCCUUUCUUCCACCGCCUCCCGCUGGCCACGGCAAAAUGUUGUUAUUUUGCCUGUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCAUGUCGCC
.((((.......((((((.(.................(((.......)))...(((((((((....))))))))).).)))))).......))))..((((((.......))).)))... ( -28.54)
>DroEre_CAF1 10635 119 + 1
CGUGCUAGCACCAGAUACCCGCCCCU-UUCUUCCCCCGCCUCCCGCUAGCCACGGCAAAAUGUUGUUAUUUUGCCUCUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCAUGUCGCC
.((((((((....(.....)((....-..........)).....))))).)))(((((((((....)))))))))..(((((.........))))).((((((.......))).)))... ( -26.94)
>DroYak_CAF1 22141 117 + 1
CGUGCUAGCCCCAGAUAGCCGCCCCU---AUUCCCCCGCCUCCUGCUAGCCACGGCAAAAAGUUGUUAUUUUGCCUCUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCAUGUCGCC
.((((((((....(((((......))---)))............))))).)))(((((((........)))))))..(((((.........))))).((((((.......))).)))... ( -24.69)
>consensus
CGUGCUAGCACCAGAUACCCGCCCCCUUUCUUCCACCGCCUCCCGCUGGCCACGGCAAAAUGUUGUUAUUUUGCCUGUGUGUUUAAAAACUGCACAAGAUUGCUUAUCUUGCAUGUCGCC
.((((((((...................................))))).)))(((((((((....)))))))))..(((((.........))))).((((((.......))).)))... (-26.21 = -26.17 +  -0.04)

alignment

secondary structure

dotplot

Window 6

Location	3,790,650 – 3,790,770
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-33.28
Consensus MFE	-29.66
Energy contribution	-30.18
Covariance contribution	0.52
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.89
SVM decision value	3.21
SVM RNA-class probability	0.998742
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3790650 120 - 27905053
AAUUAUUUCUCUGCGGGUCUCUCAGCUCAUACAAAUUAGAGGCGACAUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACACAGGCAAAAUAACAACAUUUUGCCGUGGCCAGCGGGA
.........(((((((((......))))............(((.((..(((((((.....)))))))..................((((((((......)))))))))).))).))))). ( -34.00)
>DroSec_CAF1 20061 120 - 1
AAUUAUUUCUCUGCGGGUCUCUCAGCUCAUACAAAUUAGAGGCGACGUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACACAGGCAAAAUAACAACAUUUUGCCGUGGCCAGCGGGA
.........(((((((((......))))............(((.(((..((((((.....))))))..)................((((((((......)))))))))).))).))))). ( -38.00)
>DroSim_CAF1 24551 120 - 1
AAUUAUUUCUCUGCGGGUCUCUCAGCUCAUACAAAUUAGAGGCGACAUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACACAGGCAAAAUAACAACAUUUUGCCGUGGCCAGCGGGA
.........(((((((((......))))............(((.((..(((((((.....)))))))..................((((((((......)))))))))).))).))))). ( -34.00)
>DroEre_CAF1 10674 120 - 1
AAUUAUUUCUCUCCACGUCUCUCAGCACAUACAAAUUAGAGGCGACAUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACAGAGGCAAAAUAACAACAUUUUGCCGUGGCUAGCGGGA
...........(((.((.((...(((.(((.....((((((((..(..(((((((.....))))))))..)))))))).......((((((((......))))))))))))))))))))) ( -29.90)
>DroYak_CAF1 22178 119 - 1
AAUUAG-UCUCUCCAGGUCGCUCGGCACAUACAAAUUAGAGGCGACAUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACAGAGGCAAAAUAACAACUUUUUGCCGUGGCUAGCAGGA
......-............(((.(.(((.......((((((((..(..(((((((.....))))))))..)))))))).......(((((((........)))))))))).).))).... ( -30.50)
>consensus
AAUUAUUUCUCUGCGGGUCUCUCAGCUCAUACAAAUUAGAGGCGACAUGCAAGAUAAGCAAUCUUGUGCAGUUUUUAAACACACAGGCAAAAUAACAACAUUUUGCCGUGGCCAGCGGGA
.........(((((.((((.(..............((((((((..(..(((((((.....))))))))..)))))))).......((((((((......))))))))).)))).))))). (-29.66 = -30.18 +   0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:27 2006