Locus 2910

Sequence ID	3R_DroMel_CAF1
Location	7,793,367 – 7,793,459
Length	92
Max. P	0.962862

overview

Window 9

Location	7,793,367 – 7,793,459
Length	92
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	79.56
Mean single sequence MFE	-34.04
Consensus MFE	-20.63
Energy contribution	-21.18
Covariance contribution	0.55
Combinations/Pair	1.08
Mean z-score	-2.39
Structure conservation index	0.61
SVM decision value	1.55
SVM RNA-class probability	0.962862
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7793367 92 + 27905053
UCAAGGUGC----CGGUGUGACCAG-----------CUUGGCAC---CAGGCGAUAGCCAAUUUGAGCCGUAGAUAUAUUUCAAAGGUGUCGAAACGGUCACUCCGCUGA
.......((----.((.((((((..-----------.(((((((---(.(((....)))..((((((..(((....)))))))))))))))))...)))))).))))... ( -35.00)
>DroSec_CAF1 3793 95 + 1
UCAAGGUGC----CAGUGUGACCAG-----------CUUGGCACCACCAAGCGAUAGCCAAUUUGAGCCGAAGAUAUAUUUCAAAGGUGUCGAAACGGUCACUCCGCUGA
.........----((((((((((.(-----------(((((.....)))))).........((((((((...((......))...))).)))))..))))))...)))). ( -29.60)
>DroSim_CAF1 3849 95 + 1
UCAAGGUGC----CAGUGUGACCAG-----------CUUGGCACCACCAGGCGAUAGCCAAUUUGAGCCGAAGAUAUAUUUCAAAGGUGUCGAAACGGUCACUUCGCUGA
.........----((((((((((..-----------.((((((((....(((....)))..((((((............))))))))))))))...))))))...)))). ( -31.70)
>DroEre_CAF1 3885 95 + 1
------------UAAGUGUGACCAGCGGACAUGGGGCUUGGCAA---UUGGCGAUAGCCGAUUUGAGCCGAAGAUAUAUUUCAAAGGUGCCGAAACGGUCACUCCGCUGA
------------..........(((((((.....((((..(..(---(((((....)))))))..)))).................((((((...))).)))))))))). ( -34.40)
>DroYak_CAF1 3931 107 + 1
GUAAAUUGCUGAUAAGUGUGACCAGCGGACAUUCGGCUUGGCGA---UUGGCGAUAGCCGAUUUGAGCCGAACAUAUAUUUCAAAGGUGCCGAAACGGUCACUCCGCUGA
.......(((....))).....(((((((..(((((((..(..(---(((((....)))))))..)))))))..............((((((...))).)))))))))). ( -39.50)
>consensus
UCAAGGUGC____CAGUGUGACCAG___________CUUGGCAC___CAGGCGAUAGCCAAUUUGAGCCGAAGAUAUAUUUCAAAGGUGUCGAAACGGUCACUCCGCUGA
.............((((((((((.((.........))(((((.......(((....))).......(((...((......))...))))))))...))))))...)))). (-20.63 = -21.18 +   0.55)

alignment

secondary structure

dotplot

Window 0

Location	7,793,367 – 7,793,459
Length	92
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	79.56
Mean single sequence MFE	-29.31
Consensus MFE	-23.62
Energy contribution	-23.22
Covariance contribution	-0.40
Combinations/Pair	1.11
Mean z-score	-1.63
Structure conservation index	0.81
SVM decision value	0.68
SVM RNA-class probability	0.821586
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7793367 92 - 27905053
UCAGCGGAGUGACCGUUUCGACACCUUUGAAAUAUAUCUACGGCUCAAAUUGGCUAUCGCCUG---GUGCCAAG-----------CUGGUCACACCG----GCACCUUGA
....(((.(((((((((((((.....)))))))........(((.(.....(((....)))..---).)))...-----------..)))))).)))----......... ( -29.10)
>DroSec_CAF1 3793 95 - 1
UCAGCGGAGUGACCGUUUCGACACCUUUGAAAUAUAUCUUCGGCUCAAAUUGGCUAUCGCUUGGUGGUGCCAAG-----------CUGGUCACACUG----GCACCUUGA
....(((.(((((((((((((.....)))))))........((((......))))...((((((.....)))))-----------).)))))).)))----......... ( -29.50)
>DroSim_CAF1 3849 95 - 1
UCAGCGAAGUGACCGUUUCGACACCUUUGAAAUAUAUCUUCGGCUCAAAUUGGCUAUCGCCUGGUGGUGCCAAG-----------CUGGUCACACUG----GCACCUUGA
...((.(.(((((((((((((.....)))))))........((((((....(((....)))...))).)))...-----------..))))))..).----))....... ( -27.50)
>DroEre_CAF1 3885 95 - 1
UCAGCGGAGUGACCGUUUCGGCACCUUUGAAAUAUAUCUUCGGCUCAAAUCGGCUAUCGCCAA---UUGCCAAGCCCCAUGUCCGCUGGUCACACUUA------------
(((((((((((.(((...)))))).................((((..(((.(((....))).)---))....)))).....)))))))).........------------ ( -28.10)
>DroYak_CAF1 3931 107 - 1
UCAGCGGAGUGACCGUUUCGGCACCUUUGAAAUAUAUGUUCGGCUCAAAUCGGCUAUCGCCAA---UCGCCAAGCCGAAUGUCCGCUGGUCACACUUAUCAGCAAUUUAC
(((((((((((.(((...)))))).............((((((((......(((....)))..---......)))))))).))))))))..................... ( -32.34)
>consensus
UCAGCGGAGUGACCGUUUCGACACCUUUGAAAUAUAUCUUCGGCUCAAAUUGGCUAUCGCCUG___GUGCCAAG___________CUGGUCACACUG____GCACCUUGA
........(((((((((((((.....)))))))........(((.......(((....))).......)))................))))))................. (-23.62 = -23.22 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:37 2006