Locus 3505

Sequence ID	3L_DroMel_CAF1
Location	10,285,648 – 10,285,740
Length	92
Max. P	0.988051

overview

Window 3

Location	10,285,648 – 10,285,740
Length	92
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	75.58
Mean single sequence MFE	-14.45
Consensus MFE	-7.69
Energy contribution	-8.22
Covariance contribution	0.53
Combinations/Pair	1.08
Mean z-score	-1.89
Structure conservation index	0.53
SVM decision value	0.73
SVM RNA-class probability	0.835808
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10285648 92 + 23771897
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGAAAAGCCAGGCAAAACCAGUGGGUGGAGAAGAGCGAAG--GGG--
..........((........(((.((((((((........)))))))).((.....))..)))..(((....)))........))....--...-- ( -15.40)
>DroSec_CAF1 160643 93 + 1
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGAAAAGCCAGGAAAAACCAGUGUGUGGGGAAGGACGGGGA-GGG--
..........(((((...)))))..(((((..((..((.....(((.(......).))).......))..)).)))))............-...-- ( -15.10)
>DroSim_CAF1 167076 93 + 1
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGAAAAGCCAGGAAAAACCAGUGGGUGGGGAAGAACGGGGA-GGG--
..........(((((...)))))..((((((.((..((.....(((.(......).))).......))..))))))))............-...-- ( -15.30)
>DroEre_CAF1 171027 86 + 1
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGAAAAGCCCGGAAAA----CGGGAAGGAAAA---CUGG---GGGUU
..........(((((...))))).((((((((........))))))))........((((.....----))))........---....---..... ( -17.30)
>DroYak_CAF1 168805 74 + 1
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGA----------AAA----CUGGAUGGAAAA---CUGG---GGG--
..........(((((...))))).((((((((........))))))))....----------...----(..(.(....).---)..)---...-- ( -12.40)
>DroAna_CAF1 172374 75 + 1
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGAAAAGUA--------AA----GGAAGGAGCCGCGAGCUGUG-------AGGAGGGG--
..........(((((...)))))..(((.(((((.......(((.--------..----((......))....))).))-------))).))).-- ( -11.20)
>consensus
AAAAUAUUAAGCAUAAAAUAUGUAACCCAUUUCAAAGGGAAAAUGGGUAGGAAAAGCCAGGAAAAACCAGUGGGUGGAGAA___CGGGG__GGG__
..........(((((...))))).((((((((........))))))))................................................ ( -7.69 =  -8.22 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	10,285,648 – 10,285,740
Length	92
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	75.58
Mean single sequence MFE	-11.07
Consensus MFE	-7.07
Energy contribution	-7.60
Covariance contribution	0.53
Combinations/Pair	1.11
Mean z-score	-2.39
Structure conservation index	0.64
SVM decision value	2.10
SVM RNA-class probability	0.988051
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10285648 92 - 23771897
--CCC--CUUCGCUCUUCUCCACCCACUGGUUUUGCCUGGCUUUUCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
--...--....((..........(((..((.....)))))........(((((((((......)))))))))............)).......... ( -13.70)
>DroSec_CAF1 160643 93 - 1
--CCC-UCCCCGUCCUUCCCCACACACUGGUUUUUCCUGGCUUUUCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
--...-...(((.......(((.....))).......)))........(((((((((......)))))))))........................ ( -11.34)
>DroSim_CAF1 167076 93 - 1
--CCC-UCCCCGUUCUUCCCCACCCACUGGUUUUUCCUGGCUUUUCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
--...-.................(((..((.....)))))........(((((((((......)))))))))........................ ( -11.50)
>DroEre_CAF1 171027 86 - 1
AACCC---CCAG---UUUUCCUUCCCG----UUUUCCGGGCUUUUCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
.....---....---........((((----.....))))........(((((((((......)))))))))........................ ( -14.40)
>DroYak_CAF1 168805 74 - 1
--CCC---CCAG---UUUUCCAUCCAG----UUU----------UCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
--...---...(---((...(((..((----(..----------....(((((((((......))))))))).....)))..)))...)))..... ( -10.10)
>DroAna_CAF1 172374 75 - 1
--CCCCUCCU-------CACAGCUCGCGGCUCCUUCC----UU--------UACUUUUCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
--.(((....-------...(((.....)))......----..--------....((((....)))).)))......................... (  -5.40)
>consensus
__CCC__CCCCG___UUCUCCACCCACUGGUUUUUCCUGGCUUUUCCUACCCAUUUUCCCUUUGAAAUGGGUUACAUAUUUUAUGCUUAAUAUUUU
................................................(((((((((......)))))))))........................ ( -7.07 =  -7.60 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:46 2006