Locus 3392

Sequence ID	2R_DroMel_CAF1
Location	11,457,433 – 11,457,530
Length	97
Max. P	0.962072

overview

Window 4

Location	11,457,433 – 11,457,530
Length	97
Sequences	4
Columns	118
Reading direction	forward
Mean pairwise identity	86.40
Mean single sequence MFE	-29.60
Consensus MFE	-22.29
Energy contribution	-22.85
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-2.60
Structure conservation index	0.75
SVM decision value	1.53
SVM RNA-class probability	0.962072
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11457433 97 + 20766785
AAUUGAUUGCCAUGCCACUUGGCAGG--------------------GGCAUCCAGCAUCCAGCACCAUAUCCACUUCU-AGCUACUUAGCACUUCGAGUGCCGACUAGUUGGCAAUUA
...((((((((.((((....))))((--------------------(((.....)).)))..................-(((((.(..((((.....))))..).))))))))))))) ( -29.30)
>DroSec_CAF1 7485 98 + 1
AAUUGAUUGCCAUGCCACUUGACAGGG-------------------GGCAUCCAGCAUCCAGCACCAUCUCCACUUCU-AGCUACUUAGCACUUCGAGUGCCGACUAGUUGGCAAUUA
...(((((((((((((.(((....)))-------------------)))))...((.....))...............-(((((.(..((((.....))))..).))))))))))))) ( -27.70)
>DroSim_CAF1 7536 97 + 1
AAUUGAUUGCCAUGCCACUUGGCAGG--------------------GGCAUCCAGCAUCCAGCACCAUCUCCACUUCU-AGCUACUUAGCACUUCGAGUGCCGACUAGUUGGCAAUUA
...((((((((.((((....))))((--------------------((.((...((.....))...))))))......-(((((.(..((((.....))))..).))))))))))))) ( -30.10)
>DroYak_CAF1 7555 118 + 1
AAUUGAUUGCCAUGCCACUUGCCAUGCCACUUGGCUUCUAGCAUCUAGCAUCUAGCAUCCAGCAUCACCUCCACUUCUCAGCUACUUAGCACUUCGAGUGCCGACUAGUUGGCAAUUA
...((((((((((((....(((...(((....))).....((.....)).....)))....))))..............(((((.(..((((.....))))..).))))))))))))) ( -31.30)
>consensus
AAUUGAUUGCCAUGCCACUUGGCAGG____________________GGCAUCCAGCAUCCAGCACCAUCUCCACUUCU_AGCUACUUAGCACUUCGAGUGCCGACUAGUUGGCAAUUA
...(((((((((((((....))))......................((((..(.((.....)).................(((....))).....)..)))).......))))))))) (-22.29 = -22.85 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	11,457,433 – 11,457,530
Length	97
Sequences	4
Columns	118
Reading direction	reverse
Mean pairwise identity	86.40
Mean single sequence MFE	-32.17
Consensus MFE	-24.67
Energy contribution	-24.61
Covariance contribution	-0.06
Combinations/Pair	1.08
Mean z-score	-1.43
Structure conservation index	0.77
SVM decision value	0.02
SVM RNA-class probability	0.542152
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11457433 97 - 20766785
UAAUUGCCAACUAGUCGGCACUCGAAGUGCUAAGUAGCU-AGAAGUGGAUAUGGUGCUGGAUGCUGGAUGCC--------------------CCUGCCAAGUGGCAUGGCAAUCAAUU
..((((((......((((((.((..((..(((.((.((.-....))..)).)))..)).))))))))(((((--------------------.((....)).)))))))))))..... ( -31.30)
>DroSec_CAF1 7485 98 - 1
UAAUUGCCAACUAGUCGGCACUCGAAGUGCUAAGUAGCU-AGAAGUGGAGAUGGUGCUGGAUGCUGGAUGCC-------------------CCCUGUCAAGUGGCAUGGCAAUCAAUU
..((((((......((((((.((..((..(((....((.-....)).....)))..)).))))))))(((((-------------------..((....)).)))))))))))..... ( -28.60)
>DroSim_CAF1 7536 97 - 1
UAAUUGCCAACUAGUCGGCACUCGAAGUGCUAAGUAGCU-AGAAGUGGAGAUGGUGCUGGAUGCUGGAUGCC--------------------CCUGCCAAGUGGCAUGGCAAUCAAUU
..((((((......((((((.((..((..(((....((.-....)).....)))..)).))))))))(((((--------------------.((....)).)))))))))))..... ( -30.30)
>DroYak_CAF1 7555 118 - 1
UAAUUGCCAACUAGUCGGCACUCGAAGUGCUAAGUAGCUGAGAAGUGGAGGUGAUGCUGGAUGCUAGAUGCUAGAUGCUAGAAGCCAAGUGGCAUGGCAAGUGGCAUGGCAAUCAAUU
..((((((..(((((((((((((.(...(((....))).......).)))....)))))...)))))((((((..(((((...(((....))).)))))..))))))))))))..... ( -38.50)
>consensus
UAAUUGCCAACUAGUCGGCACUCGAAGUGCUAAGUAGCU_AGAAGUGGAGAUGGUGCUGGAUGCUGGAUGCC____________________CCUGCCAAGUGGCAUGGCAAUCAAUU
..(((((((.(((((.(((((.....)))))...((((.................))))...)))))...........................((((....)))))))))))..... (-24.67 = -24.61 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:27 2006