Locus 4164

Sequence ID	3R_DroMel_CAF1
Location	11,327,646 – 11,327,805
Length	159
Max. P	0.892519

overview

Window 8

Location	11,327,646 – 11,327,766
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.33
Mean single sequence MFE	-32.96
Consensus MFE	-30.92
Energy contribution	-30.88
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.13
Structure conservation index	0.94
SVM decision value	0.13
SVM RNA-class probability	0.595760
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11327646 120 + 27905053
UCGCCCUUUCAUGUCAAGGUAGCAUAAUUUUCGGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
..((((((.......))))..))((((...(((((((((((....((((((..(....)...)))))))))))))))))....)))).....(((.(((((((....)).)))))))).. ( -33.00)
>DroSec_CAF1 66806 115 + 1
-----CUUUCAUGUUAAGGUAGCAUAAUUUUCGGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
-----......((((......(((.(((..(((((((((((....((((((..(....)...)))))))))))))))))..)))))).........(((((((....)).))))))))). ( -31.40)
>DroSim_CAF1 64971 120 + 1
UCGCCCUUUCAUGUUAAGGUAUCAUAAUUUUCGGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
....((((.......))))....((((...(((((((((((....((((((..(....)...)))))))))))))))))....)))).....(((.(((((((....)).)))))))).. ( -32.00)
>DroEre_CAF1 62256 120 + 1
UCGCCCCUGCAUGUUAAGGUAGCAUAAUUUUCAGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
..((.(((........)))..))((((...(((((((((((....((((((..(....)...)))))))))))))))))....)))).....(((.(((((((....)).)))))))).. ( -34.70)
>DroYak_CAF1 64069 120 + 1
UCGCCCUUUCAUGUCAAGGUAGCAUAAUUUUCAGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
..((((((.......))))..))((((...(((((((((((....((((((..(....)...)))))))))))))))))....)))).....(((.(((((((....)).)))))))).. ( -33.70)
>consensus
UCGCCCUUUCAUGUUAAGGUAGCAUAAUUUUCGGGCAUUUAACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACAC
.....................(((.(((..(((((((((((....((((((..(....)...)))))))))))))))))..)))))).....(((.(((((((....)).)))))))).. (-30.92 = -30.88 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	11,327,686 – 11,327,805
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.83
Mean single sequence MFE	-37.08
Consensus MFE	-36.42
Energy contribution	-36.62
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.44
Structure conservation index	0.98
SVM decision value	0.97
SVM RNA-class probability	0.892519
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11327686 119 + 27905053
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCC-CCGUUUGCCAA
....((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..)))))).-..))).)))). ( -36.80)
>DroSec_CAF1 66841 120 + 1
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCCCCCGUUUGCCAA
....((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..))))))....))).)))). ( -36.80)
>DroSim_CAF1 65011 120 + 1
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCCCCCGUUUGCCAA
....((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..))))))....))).)))). ( -36.80)
>DroEre_CAF1 62296 118 + 1
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCC-CCGU-UGCCAA
....((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..)))))).-..))-))))). ( -36.20)
>DroYak_CAF1 64109 119 + 1
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCC-CCGUUUGCCAG
...(((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..)))))).-..))).))))) ( -38.80)
>consensus
AACCUGGCCAACCCGGAAGCAUUUGGCUUAAAUGUCUGGUCAUUUGUAAAUAGUUCGUGUCGCAGCCGCAGACGCAACACUUGACGGAAAUGGCCAAGAAAUGAGCCC_CCGUUUGCCAA
....((((.(((.(....).....((((((....(((((((((((.(....(((..(((((((....)).)))))...)))....).)))))))).)))..))))))....))).)))). (-36.42 = -36.62 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:58 2006