Locus 3539

Sequence ID	2R_DroMel_CAF1
Location	11,830,007 – 11,830,105
Length	98
Max. P	0.966188

overview

Window 5

Location	11,830,007 – 11,830,105
Length	98
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	85.58
Mean single sequence MFE	-24.32
Consensus MFE	-18.79
Energy contribution	-18.73
Covariance contribution	-0.05
Combinations/Pair	1.15
Mean z-score	-1.99
Structure conservation index	0.77
SVM decision value	0.07
SVM RNA-class probability	0.569289
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11830007 98 + 20766785
AACCAUUAAUUGCUCCAACCGAAGGACCAAACACAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACAUUCCUGCGCUCCCUGUCCGC
.........(((.(((.......))).))).....(((((((.(((...((((((......))))))(......)........))).)))).)))... ( -23.70)
>DroGri_CAF1 48818 91 + 1
AUACA----UUGUUC---UCCAAGGAUAAUGCACACACGGGCACGGGCAGCAGAAAGUCACGAUUGCGUCGUCCCACAUUUCUGCGCACGUUGUCCAC
...((----((((((---.....)))))))).......(((((((.((.(((((((((.(((((...)))))...)).))))))))).)).))))).. ( -30.50)
>DroSec_CAF1 20571 98 + 1
AACCAUUAAUUGCUCCAACCGAAGGACCAAACACAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACAUUCCUGCGCUCCCUGUCCGC
.........(((.(((.......))).))).....(((((((.(((...((((((......))))))(......)........))).)))).)))... ( -23.70)
>DroSim_CAF1 19414 98 + 1
AACCAUUAAUUGCUCCAACCGAAGGACCAAACCCAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACAUUCCUGCGCUCCCUGUCCGC
.........(((.(((.......))).))).....(((((((.(((...((((((......))))))(......)........))).)))).)))... ( -23.70)
>DroEre_CAF1 20432 98 + 1
AGCCACUAAUUCCUCCAACCGAAGGACCAAACACAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACAUUCCUGCGCUCCCUGUCCGC
.((.......((((.(....).)))).........(((((((.(((...((((((......))))))(......)........))).)))).))).)) ( -22.80)
>DroYak_CAF1 20779 98 + 1
AGCCACUAAUUCAUCCAACCGAAGGACCAAACACAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACUUUCCUGCGCUCCCUGUCCAC
.............(((.......))).........(((((((.(((...((((((......))))))(......)........))).)))).)))... ( -21.50)
>consensus
AACCAUUAAUUGCUCCAACCGAAGGACCAAACACAGACGGGAUCGCCUAGCAGAAAAUCUAUUCUGCGACGACCCACAUUCCUGCGCUCCCUGUCCGC
.......................((((....(.(((..(((.(((....((((((......))))))..))))))......))).)......)))).. (-18.79 = -18.73 +  -0.05)

alignment

secondary structure

dotplot

Window 6

Location	11,830,007 – 11,830,105
Length	98
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	85.58
Mean single sequence MFE	-35.95
Consensus MFE	-32.81
Energy contribution	-33.48
Covariance contribution	0.67
Combinations/Pair	1.14
Mean z-score	-2.18
Structure conservation index	0.91
SVM decision value	1.59
SVM RNA-class probability	0.966188
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11830007 98 - 20766785
GCGGACAGGGAGCGCAGGAAUGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGUGUUUGGUCCUUCGGUUGGAGCAAUUAAUGGUU
((((((...((((((((..(((.((((((((((((((......))))))..))))))))))))))))))).)))).((.....))))........... ( -38.70)
>DroGri_CAF1 48818 91 - 1
GUGGACAACGUGCGCAGAAAUGUGGGACGACGCAAUCGUGACUUUCUGCUGCCCGUGCCCGUGUGUGCAUUAUCCUUGGA---GAACAA----UGUAU
(.((...(((.(((((((((...(..((((.....))))..)))))))).)).))).)))....(((((((.((....))---....))----))))) ( -24.30)
>DroSec_CAF1 20571 98 - 1
GCGGACAGGGAGCGCAGGAAUGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGUGUUUGGUCCUUCGGUUGGAGCAAUUAAUGGUU
((((((...((((((((..(((.((((((((((((((......))))))..))))))))))))))))))).)))).((.....))))........... ( -38.70)
>DroSim_CAF1 19414 98 - 1
GCGGACAGGGAGCGCAGGAAUGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGGGUUUGGUCCUUCGGUUGGAGCAAUUAAUGGUU
((((((...((((.(((..(((.((((((((((((((......))))))..)))))))))))))).)))).)))).((.....))))........... ( -36.50)
>DroEre_CAF1 20432 98 - 1
GCGGACAGGGAGCGCAGGAAUGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGUGUUUGGUCCUUCGGUUGGAGGAAUUAGUGGCU
((.......((((((((..(((.((((((((((((((......))))))..)))))))))))))))))))..((((((....)))))).......)). ( -39.20)
>DroYak_CAF1 20779 98 - 1
GUGGACAGGGAGCGCAGGAAAGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGUGUUUGGUCCUUCGGUUGGAUGAAUUAGUGGCU
..((((...(((((((((...(.((((((((((((((......))))))..))))))))).))))))))).))))((((......))))......... ( -38.30)
>consensus
GCGGACAGGGAGCGCAGGAAUGUGGGUCGUCGCAGAAUAGAUUUUCUGCUAGGCGAUCCCGUCUGUGUUUGGUCCUUCGGUUGGAGCAAUUAAUGGUU
..((((...(((((((((...(.((((((((((((((......))))))..))))))))).))))))))).))))....................... (-32.81 = -33.48 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:01 2006