Locus 4434

Sequence ID	2L_DroMel_CAF1
Location	12,754,544 – 12,754,635
Length	91
Max. P	0.847194

overview

Window 5

Location	12,754,544 – 12,754,635
Length	91
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	74.22
Mean single sequence MFE	-18.79
Consensus MFE	-9.13
Energy contribution	-9.88
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.49
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12754544 91 + 22407834
-----CAGAAGCACACCAAAAAGGACCUCCGAUAGAGACACUCAUCCAUGCAAAUGGC-GCAAUAUGGCAUAGGACAUGCAAUAUGCCAUAUACGUA
-----.....(((.........((....))(((.(((...))))))..))).....((-(..((((((((((..........)))))))))).))). ( -20.50)
>DroPse_CAF1 40279 86 + 1
CG---CAGGGAUACAC-----AGGACCUC--AUAGAUACACUCAUCCAUGCAAAUGCC-GCAAUAUGGCAUAGAACAUGCAAUAUGCCACACACGGA
.(---((.((((....-----..(....)--...((.....)))))).))).....((-(.....(((((((..........)))))))....))). ( -17.60)
>DroSec_CAF1 31590 93 + 1
CU---CAGGAGCACACCAAAAAGGACCUCCGAUAGAGACACUCAUCCAUGCAAAUGGC-GCAAUAUGGCAUAGGACAUGCAAUAUGCCAUAUACGUA
((---(.((((....((.....))..))))....)))((......((((....)))).-...((((((((((..........))))))))))..)). ( -22.30)
>DroSim_CAF1 31833 93 + 1
CU---CAGGAGCACACCAAAAAGGACCUCCGAUAGAGACACUCAUCCAUGCAAAUGGC-GCAAUAUGGCAUAGGACAUGCAAUAUGCCAUAUACGUA
((---(.((((....((.....))..))))....)))((......((((....)))).-...((((((((((..........))))))))))..)). ( -22.30)
>DroEre_CAF1 32577 89 + 1
CACAG-------GCACCAAAAAGGACCUCCGAUAGAGACACUCAUCCAUGCAAAUGGC-GCAAUAUGGCAUAGGACAUGCAAUAUGCCAUAUACGUA
.((..-------((.(((....((....))(((.(((...))))))........))).-)).((((((((((..........))))))))))..)). ( -22.30)
>DroPer_CAF1 39781 87 + 1
CG---CAGGGAUACAC-----AGGACCUC--AUAGAUACACUCAUCCAUGCAAAUGCCCGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.(---(.(((.....(-----((((....--.............))).))......))))).................................... (  -7.73)
>consensus
CG___CAGGAGCACACCAAAAAGGACCUCCGAUAGAGACACUCAUCCAUGCAAAUGGC_GCAAUAUGGCAUAGGACAUGCAAUAUGCCAUAUACGUA
......................(((...................))).(((........)))((((((((((..........))))))))))..... ( -9.13 =  -9.88 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	12,754,544 – 12,754,635
Length	91
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	74.22
Mean single sequence MFE	-24.80
Consensus MFE	-15.68
Energy contribution	-17.07
Covariance contribution	1.39
Combinations/Pair	1.13
Mean z-score	-1.49
Structure conservation index	0.63
SVM decision value	0.77
SVM RNA-class probability	0.847194
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12754544 91 - 22407834
UACGUAUAUGGCAUAUUGCAUGUCCUAUGCCAUAUUGC-GCCAUUUGCAUGGAUGAGUGUCUCUAUCGGAGGUCCUUUUUGGUGUGCUUCUG-----
..(((((((((((((..........))))))))).)))-)......((((.((.(((..((((.....))))..))).)).)))).......----- ( -26.10)
>DroPse_CAF1 40279 86 - 1
UCCGUGUGUGGCAUAUUGCAUGUUCUAUGCCAUAUUGC-GGCAUUUGCAUGGAUGAGUGUAUCUAU--GAGGUCCU-----GUGUAUCCCUG---CG
.((((((((((((((..(....)..))))))))).)))-)).....(((.(((((...(.(((...--..))).).-----...))))).))---). ( -26.20)
>DroSec_CAF1 31590 93 - 1
UACGUAUAUGGCAUAUUGCAUGUCCUAUGCCAUAUUGC-GCCAUUUGCAUGGAUGAGUGUCUCUAUCGGAGGUCCUUUUUGGUGUGCUCCUG---AG
..(((((((((((((..........))))))))).)))-)......((((.((.(((..((((.....))))..))).)).)))).......---.. ( -26.10)
>DroSim_CAF1 31833 93 - 1
UACGUAUAUGGCAUAUUGCAUGUCCUAUGCCAUAUUGC-GCCAUUUGCAUGGAUGAGUGUCUCUAUCGGAGGUCCUUUUUGGUGUGCUCCUG---AG
..(((((((((((((..........))))))))).)))-)......((((.((.(((..((((.....))))..))).)).)))).......---.. ( -26.10)
>DroEre_CAF1 32577 89 - 1
UACGUAUAUGGCAUAUUGCAUGUCCUAUGCCAUAUUGC-GCCAUUUGCAUGGAUGAGUGUCUCUAUCGGAGGUCCUUUUUGGUGC-------CUGUG
..(((((((((((((..........))))))))).)))-).(((..((((.((.(((..((((.....))))..))).)).))))-------..))) ( -29.20)
>DroPer_CAF1 39781 87 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNUGCGGGCAUUUGCAUGGAUGAGUGUAUCUAU--GAGGUCCU-----GUGUAUCCCUG---CG
....................................(((((....(((((((((..(((....)))--...)))).-----)))))..))))---). ( -15.10)
>consensus
UACGUAUAUGGCAUAUUGCAUGUCCUAUGCCAUAUUGC_GCCAUUUGCAUGGAUGAGUGUCUCUAUCGGAGGUCCUUUUUGGUGUGCUCCUG___AG
.....((((((((((..........))))))))))...........((((.((.(((..((((.....))))..))).)).))))............ (-15.68 = -17.07 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:40 2006