Locus 4109

Sequence ID	X_DroMel_CAF1
Location	10,843,064 – 10,843,184
Length	120
Max. P	0.770819

overview

Window 4

Location	10,843,064 – 10,843,184
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.03
Mean single sequence MFE	-23.08
Consensus MFE	-17.24
Energy contribution	-17.30
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.78
Structure conservation index	0.75
SVM decision value	0.45
SVM RNA-class probability	0.740169
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10843064 120 + 22224390
UUUUCUUUGGCGUUUUUGCCACCGAUUGUAAUGACUGCAAACAUUUCAAUUUUAAUUCAAGUUUUAAUUGCUUGUAAAAAUGCGUUAUUGUAUUUUUUGUUGUGUUUUUAUUCAUUAUUU
...((..(((((....)))))..))..(((((((.((.((((((..((.........(((((.......))))).(((((((((....)))))))))))..)))))).)).))))))).. ( -26.50)
>DroSec_CAF1 21849 119 + 1
UUUUCUUUGGCGUUUUUGCCACCGAUUGUAAUGACUGCAAACAUUUCAAUUUUAAUUUAAGUUUUAAUUGCUUGUAAAAUUGCGUUAUUGUAUUU-UUGUUGGGUUUUUAUUCAUUAUUU
...((..(((((....)))))..))..(((((((.((.((((....(((((..(((....)))..)))))((..(((((.((((....)))).))-)))..)))))).)).))))))).. ( -21.20)
>DroSim_CAF1 2735 119 + 1
UUUUCUUUGGCGUUUUUGCCACCGAUUGUAAUGACUGCAAACAUUUCAAUUUUAAUUCAAGUUUUAAUUGCUUGUAAAAUUGCGUUAUUGUAUUU-UUGUUGUGUUUUUAUUCAUUAUUU
...((..(((((....)))))..))..(((((((.((.((((((..(((........(((((.......)))))......((((....))))...-)))..)))))).)).))))))).. ( -23.00)
>DroYak_CAF1 10897 114 + 1
UUUCCUUUGGCAUUUUUGCCACCGAUUGUAAUGACUGCAAACAUUUCAAUUUGAAUUCAAGUUUUAAUUGCUUGUAAAAUUGCGUUAUUGUAUUU-UC-----GUUUUUACACUCUAUUU
.......(((((....)))))..((.(((((.((((((((.((....((((((....)))))).....)).)))))(((.((((....)))).))-).-----))).))))).))..... ( -21.60)
>consensus
UUUUCUUUGGCGUUUUUGCCACCGAUUGUAAUGACUGCAAACAUUUCAAUUUUAAUUCAAGUUUUAAUUGCUUGUAAAAUUGCGUUAUUGUAUUU_UUGUUGUGUUUUUAUUCAUUAUUU
.......(((((....))))).......(((((((.(((((((...(((((..(((....)))..)))))..)))....))))))))))).............................. (-17.24 = -17.30 +   0.06)

alignment

secondary structure

dotplot

Window 5

Location	10,843,064 – 10,843,184
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.03
Mean single sequence MFE	-17.25
Consensus MFE	-13.12
Energy contribution	-14.00
Covariance contribution	0.88
Combinations/Pair	1.07
Mean z-score	-2.55
Structure conservation index	0.76
SVM decision value	0.53
SVM RNA-class probability	0.770819
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10843064 120 - 22224390
AAAUAAUGAAUAAAAACACAACAAAAAAUACAAUAACGCAUUUUUACAAGCAAUUAAAACUUGAAUUAAAAUUGAAAUGUUUGCAGUCAUUACAAUCGGUGGCAAAAACGCCAAAGAAAA
...((((((....(((((.....((((((.(......).)))))).((((.........))))..............)))))....))))))...((..((((......))))..))... ( -18.10)
>DroSec_CAF1 21849 119 - 1
AAAUAAUGAAUAAAAACCCAACAA-AAAUACAAUAACGCAAUUUUACAAGCAAUUAAAACUUAAAUUAAAAUUGAAAUGUUUGCAGUCAUUACAAUCGGUGGCAAAAACGCCAAAGAAAA
...((((((....((((.......-.............((((((((.(((.........)))....))))))))....))))....))))))...((..((((......))))..))... ( -14.45)
>DroSim_CAF1 2735 119 - 1
AAAUAAUGAAUAAAAACACAACAA-AAAUACAAUAACGCAAUUUUACAAGCAAUUAAAACUUGAAUUAAAAUUGAAAUGUUUGCAGUCAUUACAAUCGGUGGCAAAAACGCCAAAGAAAA
...((((((....(((((......-.............((((((((((((.........))))...))))))))...)))))....))))))...((..((((......))))..))... ( -19.05)
>DroYak_CAF1 10897 114 - 1
AAAUAGAGUGUAAAAAC-----GA-AAAUACAAUAACGCAAUUUUACAAGCAAUUAAAACUUGAAUUCAAAUUGAAAUGUUUGCAGUCAUUACAAUCGGUGGCAAAAAUGCCAAAGGAAA
.....((.((((((...-----..-.....................((((.........))))..(((.....)))...)))))).)).......((..(((((....)))))..))... ( -17.40)
>consensus
AAAUAAUGAAUAAAAACACAACAA_AAAUACAAUAACGCAAUUUUACAAGCAAUUAAAACUUGAAUUAAAAUUGAAAUGUUUGCAGUCAUUACAAUCGGUGGCAAAAACGCCAAAGAAAA
...((((((....((((.............(......)((((((((((((.........))))...))))))))....))))....))))))...((..((((......))))..))... (-13.12 = -14.00 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:36 2006