Locus 2818

Sequence ID	X_DroMel_CAF1
Location	7,544,802 – 7,544,964
Length	162
Max. P	0.924955

overview

Window 5

Location	7,544,802 – 7,544,896
Length	94
Sequences	4
Columns	95
Reading direction	forward
Mean pairwise identity	95.77
Mean single sequence MFE	-18.33
Consensus MFE	-17.47
Energy contribution	-17.54
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.97
Structure conservation index	0.95
SVM decision value	1.17
SVM RNA-class probability	0.924955
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7544802 94 + 22224390
UUUCCUUCGACUGACAAUUUCGAUUUUAUUCAGCUCGAUUUUACUCGACUUC-UUGUGGUCGGCGAAAAAUUUCAAUUUCAAUUGAUUUCGUCGU
......((((((((...............)))).))))........((((..-....))))(((((((....(((((....)))))))))))).. ( -19.06)
>DroSec_CAF1 37890 94 + 1
UUUCCUUCGACUGACAAUUUCGAUUUUAUUCAGCUCGAUUUUACUCGACUUC-UUGUGGUCGGCGAAAAAUUUCAAUUUCAAUUAAUUUCGUCGU
......((((((((...............)))).))))........((((..-....))))(((((((((((........))))..))))))).. ( -16.06)
>DroSim_CAF1 38272 94 + 1
UUUCCUUCGACUGACAAUUUCGAUUUUAUUCAGCUCGAUUUUACUCGACUUC-UUGUGGUCGGCGAAAAAUUUCAAUUUCAAUUGAUUUCGUCGU
......((((((((...............)))).))))........((((..-....))))(((((((....(((((....)))))))))))).. ( -19.06)
>DroYak_CAF1 38612 92 + 1
UUU---UCGACUGACAAUUUCGAUUUUAUUCAGCUCGAUUUUACUCGACUUUUUUUUGGUCGACGAAAAAUUUCAAUUUCAAUUGAUUUCGUCGU
...---((((((((...............)))).))))........((((.......))))(((((((....(((((....)))))))))))).. ( -19.16)
>consensus
UUUCCUUCGACUGACAAUUUCGAUUUUAUUCAGCUCGAUUUUACUCGACUUC_UUGUGGUCGGCGAAAAAUUUCAAUUUCAAUUGAUUUCGUCGU
......((((((((...............)))).))))........((((.......))))(((((((....(((((....)))))))))))).. (-17.47 = -17.54 +   0.06)

alignment

secondary structure

dotplot

Window 6

Location	7,544,857 – 7,544,964
Length	107
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	95.50
Mean single sequence MFE	-25.94
Consensus MFE	-21.78
Energy contribution	-21.38
Covariance contribution	-0.40
Combinations/Pair	1.06
Mean z-score	-1.44
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.662373
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7544857 107 - 22224390
CGGUGAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAA--GAGCACAUGAUGGGUUUAUUUUGGUUGAAC---GACGACGAAAUCAAUUGAAAUUGAAAUUUUUCGCCGACCA
((((((((..((.((((((.(..((.....)).....--).))))))..))..((.((((..(((((.(---(....))...)))))..)))).))....)))))))).... ( -26.00)
>DroSec_CAF1 37945 107 - 1
CGGUGAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAA--GAGCACAUGAUGGGUUUAUUUUGGUUGAAC---GACGACGAAAUUAAUUGAAAUUGAAAUUUUUCGCCGACCA
((((((((((((....))))((......((((((((.--((((.(.....).)))).))))))))....---..))........................)))))))).... ( -24.50)
>DroSim_CAF1 38327 107 - 1
CGGUGAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAA--GAGCACAUGAUGGGUUUAUUUUGGUUGAAC---GACGACGAAAUCAAUUGAAAUUGAAAUUUUUCGCCGACCA
((((((((..((.((((((.(..((.....)).....--).))))))..))..((.((((..(((((.(---(....))...)))))..)))).))....)))))))).... ( -26.00)
>DroEre_CAF1 48854 109 - 1
CGGUAAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAGGGGAACACAUGAUGGGUUUAUUUUGGUUGAAC---GACGACGAAAUCAAUUGAAAUUGAAAUUUUUCGGCGACCA
.(((....((((....))))(((((((.((((((((...((((.(.....).)))).))))))))....---..........(((((....)))))..)))))))...))). ( -23.70)
>DroYak_CAF1 38665 110 - 1
CGGUGAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAA--GAACACAUGAUGGGUUUAUUUUGGUUGAGCGACGACGACGAAAUCAAUUGAAAUUGAAAUUUUUCGUCGACCA
.(((....((((....))))((..(...((((((((.--((((.(.....).)))).))))))))...)..)).(((((((((((((....)))))....))))))))))). ( -29.50)
>consensus
CGGUGAAAUGCAGAUGUGCACGAGGAAAAGCCAAAAA__GAGCACAUGAUGGGUUUAUUUUGGUUGAAC___GACGACGAAAUCAAUUGAAAUUGAAAUUUUUCGCCGACCA
.(((....((((....))))(((((((.((((((((...((((.(.....).)))).)))))))).................(((((....)))))..)))))))...))). (-21.78 = -21.38 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:44:18 2006