Locus 3542

Sequence ID	3L_DroMel_CAF1
Location	10,378,033 – 10,378,133
Length	100
Max. P	0.990730

overview

Window 0

Location	10,378,033 – 10,378,133
Length	100
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	90.76
Mean single sequence MFE	-28.97
Consensus MFE	-26.27
Energy contribution	-26.11
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.91
SVM decision value	2.23
SVM RNA-class probability	0.990730
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10378033 100 + 23771897
AGGAAGAUAUGCCAUCGUCUGGCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAA-AAGAAAAGAUGGGGAG-----GCCGAGGCCACAUGACUUGGCCAAGCCCA
.........(((((((((((((.(........).))..)))))))....))))..-...........(((.(-----((((((.........)))))))...))). ( -29.90)
>DroSec_CAF1 251686 100 + 1
ACGAAGAUAUGCCAUCGUCUGCCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAAAAAGAAAAGAUG-GGAG-----GCCGAGGCCACAUGACUUGGCCAAGCCCA
.........((((((((((.......................)))))).))))............((-((.(-----((((((.........)))))))...)))) ( -28.70)
>DroSim_CAF1 262469 100 + 1
ACGAAGAUAUGCCAUCGUCUGCCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAAAAAGAAAAGAUG-GGAG-----GCCGAGGCCACAUGACUUGGCCAAGCCCA
.........((((((((((.......................)))))).))))............((-((.(-----((((((.........)))))))...)))) ( -28.70)
>DroEre_CAF1 266939 100 + 1
ACCAAGAUACGCCAUCGUCUGCCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAAAA-----AGAUG-GGAGGCCGGGCCGAGGCCACAUGACUUGGCCAAGCCCA
............((((((((..................)))))))).(((((.....-----...((-(....)))(((((((.........)))))))..))))) ( -31.37)
>DroYak_CAF1 264206 98 + 1
ACUAAGAUACGCCAUCGUCUGCCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAAAA-----AGAUG-GGAGGU--AGCUUAGGCCACAUGACUUGGCCAAGCCCA
............((((((((..................)))))))).(((((.....-----...((-((....--..))))(((((.......)))))..))))) ( -26.17)
>consensus
ACGAAGAUAUGCCAUCGUCUGCCGAAAAACUCCACCCAAGAUGAUGAUGGGCAAAAAAGAAAAGAUG_GGAG_____GCCGAGGCCACAUGACUUGGCCAAGCCCA
............((((((((..................)))))))).(((((................((........))..(((((.......)))))..))))) (-26.27 = -26.11 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	10,378,033 – 10,378,133
Length	100
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	90.76
Mean single sequence MFE	-31.70
Consensus MFE	-23.22
Energy contribution	-23.06
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-1.72
Structure conservation index	0.73
SVM decision value	0.02
SVM RNA-class probability	0.541551
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10378033 100 - 23771897
UGGGCUUGGCCAAGUCAUGUGGCCUCGGC-----CUCCCCAUCUUUUCUU-UUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGCCAGACGAUGGCAUAUCUUCCU
.(((((.(((((.......)))))..)))-----))..(((((.......-((..((((.........))))..))((((......)))))))))........... ( -31.00)
>DroSec_CAF1 251686 100 - 1
UGGGCUUGGCCAAGUCAUGUGGCCUCGGC-----CUCC-CAUCUUUUCUUUUUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGGCAGACGAUGGCAUAUCUUCGU
.(((((.(((((.......)))))..)))-----)).(-((((........((..((((.........))))..))((((......)))))))))........... ( -31.00)
>DroSim_CAF1 262469 100 - 1
UGGGCUUGGCCAAGUCAUGUGGCCUCGGC-----CUCC-CAUCUUUUCUUUUUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGGCAGACGAUGGCAUAUCUUCGU
.(((((.(((((.......)))))..)))-----)).(-((((........((..((((.........))))..))((((......)))))))))........... ( -31.00)
>DroEre_CAF1 266939 100 - 1
UGGGCUUGGCCAAGUCAUGUGGCCUCGGCCCGGCCUCC-CAUCU-----UUUUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGGCAGACGAUGGCGUAUCUUGGU
.(((((.(((((.......)))))..))))).(((.((-((((.-----..((..((((.........))))..))((((......))))))))).)......))) ( -35.30)
>DroYak_CAF1 264206 98 - 1
UGGGCUUGGCCAAGUCAUGUGGCCUAAGCU--ACCUCC-CAUCU-----UUUUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGGCAGACGAUGGCGUAUCUUAGU
..((((((((((.......))))).)))))--.....(-((((.-----..((..((((.........))))..))((((......)))))))))........... ( -30.20)
>consensus
UGGGCUUGGCCAAGUCAUGUGGCCUCGGC_____CUCC_CAUCUUUUCUUUUUUGCCCAUCAUCAUCUUGGGUGGAGUUUUUCGGCAGACGAUGGCAUAUCUUCGU
...(((.(((((.......)))))..)))..........((((........((..((((.........))))..))((((......))))))))............ (-23.22 = -23.06 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:40 2006