Locus 5979

Sequence ID	3R_DroMel_CAF1
Location	15,768,681 – 15,768,839
Length	158
Max. P	0.998616

overview

Window 4

Location	15,768,681 – 15,768,799
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.34
Mean single sequence MFE	-29.23
Consensus MFE	-25.71
Energy contribution	-25.90
Covariance contribution	0.19
Combinations/Pair	1.09
Mean z-score	-1.67
Structure conservation index	0.88
SVM decision value	0.66
SVM RNA-class probability	0.814560
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15768681 118 + 27905053
CCUAUGCCUGAAACAUUCGGAUU-UCGGAAAACGGAAAAGUUAAAAAAUAUUACCCAAACUGGCCA-ACCAAACCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUUGAA
(((((.(((.(..(((((((.((-(((.....))))).......................(((...-.)))..))))))).....).))))))))......((..((.....))..)).. ( -23.90)
>DroSec_CAF1 25839 114 + 1
CCUAUGCCUCGGACAUUCGGAUUUUCGGAAAACGGAAAAGGUAAAAAAUAUUACCCAAACUGGCCA-A-----CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAA
(((((.(((((..(((((((.((((((.....)))))).(((((......)))))...........-.-----))))))).....))))))))))........(((((.......))))) ( -31.20)
>DroSim_CAF1 25819 114 + 1
CCUAUGCCUCGGACAUUCGGAUUUUCGGAAAACGGAAAAGGUAAAAAAUAUUACCCAAACUGGCCA-A-----CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAA
(((((.(((((..(((((((.((((((.....)))))).(((((......)))))...........-.-----))))))).....))))))))))........(((((.......))))) ( -31.20)
>DroEre_CAF1 28405 115 + 1
CCUAUGCCU-GGACA---GGGAUUUCGGAAAACGGAAUGGG-GAAAAAUAUUACCCAAACUGGCCCGAACUGACCGAAUGAUAAAUGAUGGUAGGGCCCUGCAUUUGAUUAUCAUUUGAA
...((.(((-....)---)).))(((((....(((..((((-...........))))..)))..))))).....((((((((((..((((.(((....)))))))...)))))))))).. ( -30.60)
>consensus
CCUAUGCCUCGGACAUUCGGAUUUUCGGAAAACGGAAAAGGUAAAAAAUAUUACCCAAACUGGCCA_A_____CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAA
.....(((.............((((((.....)))))).(((((......)))))......)))..........((((((((((.((((.((((....)))).)))).)))))))))).. (-25.71 = -25.90 +   0.19)

alignment

secondary structure

dotplot

Window 5

Location	15,768,720 – 15,768,839
Length	119
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.99
Mean single sequence MFE	-33.65
Consensus MFE	-33.45
Energy contribution	-33.08
Covariance contribution	-0.38
Combinations/Pair	1.09
Mean z-score	-2.93
Structure conservation index	0.99
SVM decision value	3.16
SVM RNA-class probability	0.998616
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15768720 119 + 27905053
UUAAAAAAUAUUACCCAAACUGGCCA-ACCAAACCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUUGAACAAAUAUGCAGCCGAAAUUGCGGUGGCGGGUAAAAUUUAC
.....((((.((((((....(((...-.)))...((((((((((.((((.((((....)))).)))).)))))))))).........((.((((......)))).)))))))).)))).. ( -34.70)
>DroSec_CAF1 25879 114 + 1
GUAAAAAAUAUUACCCAAACUGGCCA-A-----CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAACAAAUAUGCAGCUGAAAUUGCGGUGGCGGGUAAAAUUUAC
.....((((.((((((......((((-.-----(((((((((((.((((.((((....)))).)))).)))))))))..........((((......)))))))))))))))).)))).. ( -34.60)
>DroSim_CAF1 25859 114 + 1
GUAAAAAAUAUUACCCAAACUGGCCA-A-----CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAACAAAUAUGCAGCUGAAAUUGCGGUGGCGGGUAAAAUUUAC
.....((((.((((((......((((-.-----(((((((((((.((((.((((....)))).)))).)))))))))..........((((......)))))))))))))))).)))).. ( -34.60)
>DroEre_CAF1 28441 119 + 1
G-GAAAAAUAUUACCCAAACUGGCCCGAACUGACCGAAUGAUAAAUGAUGGUAGGGCCCUGCAUUUGAUUAUCAUUUGAACAAAUAUGCAGCUGAAAUUGCGGUGGCGGGUGAAAUUUGC
.-...((((.((((((..((((((((......((((.((.....))..)))).)))))(((((((((.(((.....))).)))..))))))..........)))...)))))).)))).. ( -30.70)
>consensus
GUAAAAAAUAUUACCCAAACUGGCCA_A_____CCGAAUGAUAAAUGAGGGUAGGGUCCUGCAUUUGAUUAUCAUUCGAACAAAUAUGCAGCUGAAAUUGCGGUGGCGGGUAAAAUUUAC
.....((((.((((((..................((((((((((.((((.((((....)))).)))).)))))))))).........((.((((......)))).)))))))).)))).. (-33.45 = -33.08 +  -0.38)

alignment

secondary structure

dotplot

Window 6

Location	15,768,720 – 15,768,839
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.99
Mean single sequence MFE	-28.09
Consensus MFE	-23.87
Energy contribution	-24.68
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-2.17
Structure conservation index	0.85
SVM decision value	1.22
SVM RNA-class probability	0.932207
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15768720 119 - 27905053
GUAAAUUUUACCCGCCACCGCAAUUUCGGCUGCAUAUUUGUUCAAAUGAUAAUCAAAUGCAGGACCCUACCCUCAUUUAUCAUUCGGUUUGGU-UGGCCAGUUUGGGUAAUAUUUUUUAA
..((((.(((((((((((((((........)))........((.((((((((....(((.(((.......)))))))))))))).))...)).-))))......)))))).))))..... ( -26.50)
>DroSec_CAF1 25879 114 - 1
GUAAAUUUUACCCGCCACCGCAAUUUCAGCUGCAUAUUUGUUCGAAUGAUAAUCAAAUGCAGGACCCUACCCUCAUUUAUCAUUCGG-----U-UGGCCAGUUUGGGUAAUAUUUUUUAC
(((((..(((((((((((((((........)))..........(((((((((....(((.(((.......)))))))))))))))))-----.-))))......)))))).....))))) ( -30.90)
>DroSim_CAF1 25859 114 - 1
GUAAAUUUUACCCGCCACCGCAAUUUCAGCUGCAUAUUUGUUCGAAUGAUAAUCAAAUGCAGGACCCUACCCUCAUUUAUCAUUCGG-----U-UGGCCAGUUUGGGUAAUAUUUUUUAC
(((((..(((((((((((((((........)))..........(((((((((....(((.(((.......)))))))))))))))))-----.-))))......)))))).....))))) ( -30.90)
>DroEre_CAF1 28441 119 - 1
GCAAAUUUCACCCGCCACCGCAAUUUCAGCUGCAUAUUUGUUCAAAUGAUAAUCAAAUGCAGGGCCCUACCAUCAUUUAUCAUUCGGUCAGUUCGGGCCAGUUUGGGUAAUAUUUUUC-C
.........((((((....))........((((((..(((((.....)))))....))))))(((((.(((..............)))......))))).....))))..........-. ( -24.04)
>consensus
GUAAAUUUUACCCGCCACCGCAAUUUCAGCUGCAUAUUUGUUCAAAUGAUAAUCAAAUGCAGGACCCUACCCUCAUUUAUCAUUCGG_____U_UGGCCAGUUUGGGUAAUAUUUUUUAC
..((((.((((((((....))......((((((........(((((((((((....(((.(((.......))))))))))))))))).........).))))).)))))).))))..... (-23.87 = -24.68 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:41 2006