Locus 6702

Sequence ID	3R_DroMel_CAF1
Location	17,635,394 – 17,635,552
Length	158
Max. P	0.995226

overview

Window 2

Location	17,635,394 – 17,635,512
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.70
Mean single sequence MFE	-22.42
Consensus MFE	-21.39
Energy contribution	-21.47
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.81
Structure conservation index	0.95
SVM decision value	2.55
SVM RNA-class probability	0.995226
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17635394 118 + 27905053
AUAAAAACAGCACUUUUGGUGUAAGUAAGUCAUAAAAAACUCAUAACAGCACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCU-UUUUUUGUAUGUAAA-AACCUGACUUAU
.........((((.....))))..((((((((.............((((((((.((......(((.....))).....))))))))))...-.((((((....))))-))..)))))))) ( -21.30)
>DroSec_CAF1 30283 117 + 1
AUAAAAACAGCACUUUUGGUGUAAGUAAGUCAUAAAAAACUCAUAACAGCACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCU-UU-UUUGUAUGUAAA-AACCUGACUUAC
.........((((.....))))..((((((((.........((((((((((((.((......(((.....))).....))))))))))...-..-....))))....-....)))))))) ( -22.53)
>DroSim_CAF1 30092 117 + 1
AUAAAAACAGCACUUUUGGUGUAAGUAAGUCAUAAAAAACUCAUAACAGCACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCU-UU-UUCGUAUGUAAA-AACCUGACUUAC
.........((((.....))))..((((((((.........((((((((((((.((......(((.....))).....))))))))))...-..-....))))....-....)))))))) ( -22.53)
>DroEre_CAF1 32190 117 + 1
AUAAAAACAGCACUUUUGGUGUAAGUAAGUCAUAAAAAACUCAUAACAGCACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCU-UU-UUGGUAUGUAAA-AACCUGACUUAC
.........((((.....))))..((((((((.........((((((((((((.((......(((.....))).....))))))))))((.-..-..))))))....-....)))))))) ( -24.53)
>DroYak_CAF1 34801 119 + 1
AUAAAAACAGCACUUUCGGUGUAAGUAAGUCAUAAAAAACUCAUAACAACACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCUGUU-UUUGUAUGUAAAAAACCCGACAUAC
..(((((((((((.....)))........................((((((((.((......(((.....))).....)))))))))).)))))-)))((((((..........)))))) ( -21.20)
>consensus
AUAAAAACAGCACUUUUGGUGUAAGUAAGUCAUAAAAAACUCAUAACAGCACUUGCUUUCAAAGUUUAUCACUCAUACGCAGUGUUGUCCU_UU_UUUGUAUGUAAA_AACCUGACUUAC
.........((((.....))))..((((((((.........((((((((((((.((......(((.....))).....))))))))))...........)))).........)))))))) (-21.39 = -21.47 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	17,635,434 – 17,635,552
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.69
Mean single sequence MFE	-24.32
Consensus MFE	-19.44
Energy contribution	-20.08
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.80
SVM decision value	0.77
SVM RNA-class probability	0.846861
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17635434 118 - 27905053
AAAUCAAUUUGAACCUGAAAAAAUAUUACGAAUACGACACAUAAGUCAGGUU-UUUACAUACAAAAAA-AGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGCUGUUAUGA
...(((....((((((((..........((....)).........)))))))-)..............-..((((.((((((....((((.....)))).....)).)))).)))).))) ( -21.81)
>DroSec_CAF1 30323 117 - 1
AAAUCAAUUUGAACCUGAAAAAAUAUUACGCAUACGACACGUAAGUCAGGUU-UUUACAUACAAA-AA-AGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGCUGUUAUGA
...(((....((((((((.......(((((.........))))).)))))))-)...........-..-..((((.((((((....((((.....)))).....)).)))).)))).))) ( -24.20)
>DroSim_CAF1 30132 117 - 1
AAAUCAAUUUGAACCUGAAAAAAUAUUACGCAUACGACACGUAAGUCAGGUU-UUUACAUACGAA-AA-AGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGCUGUUAUGA
...(((....((((((((.......(((((.........))))).)))))))-)...........-..-..((((.((((((....((((.....)))).....)).)))).)))).))) ( -24.20)
>DroEre_CAF1 32230 117 - 1
AAAUCAAUUUGAACCUAAAAGAAUAUUACGCAUACGACACGUAAGUCAGGUU-UUUACAUACCAA-AA-AGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGCUGUUAUGA
......(((((......((((..((((((.((((((.((.((..(((.(((.-.......)))..-..-..)))...)))))))))).))))))..)))).....))))).......... ( -22.70)
>DroYak_CAF1 34841 119 - 1
AAAUCAAUUUGAACCUAAAAGAAUAUUACGCAUACGACACGUAUGUCGGGUUUUUUACAUACAAA-AACAGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGUUGUUAUGA
.......((((......(((((((....((((((((...)))))).)).))))))).....))))-..((.(((((((((((....((((.....)))).....)).))))))))).)). ( -28.70)
>consensus
AAAUCAAUUUGAACCUGAAAAAAUAUUACGCAUACGACACGUAAGUCAGGUU_UUUACAUACAAA_AA_AGGACAACACUGCGUAUGAGUGAUAAACUUUGAAAGCAAGUGCUGUUAUGA
...(((.....(((((((.......(((((.........))))).)))))))...................((((.((((((....((((.....)))).....)).)))).)))).))) (-19.44 = -20.08 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:27:56 2006