Locus 7439

Sequence ID	3R_DroMel_CAF1
Location	19,805,208 – 19,805,307
Length	99
Max. P	0.742529

overview

Window 6

Location	19,805,208 – 19,805,307
Length	99
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	81.87
Mean single sequence MFE	-28.92
Consensus MFE	-21.60
Energy contribution	-22.05
Covariance contribution	0.45
Combinations/Pair	1.10
Mean z-score	-1.56
Structure conservation index	0.75
SVM decision value	0.29
SVM RNA-class probability	0.672319
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19805208 99 + 27905053
ACCACAUCAUUAAUUUAUUAUCA-------------UCCAGGGUGGUCACAUCAAGAUACACUUGAAUACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUUCAGAG
......................(-------------(((((((((((....(((((.....)))))..))).......((((((....))))))...)))))))))...... ( -32.40)
>DroVir_CAF1 38778 100 + 1
AU-AUAUAUUUAAUA-----ACCG-CUCG-----CUUACAGGGUGGCCACAUCAAAAUACAUUUAAACACCGAUAUGCCGGUGCAGGUGGACGGCGAGCCAUGGAUUCAGAG
..-............-----.(((-((((-----((.....((((....))))......(((((...(((((......))))).)))))...)))))))...))........ ( -25.40)
>DroSec_CAF1 35632 104 + 1
ACCAUAUCAUUAAUUUAUGAACUUUAA--------CUCCAGGGUGGUCACAUCAAGAUACAUUUGAACACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUUCAGAG
......((((......)))).((((.(--------.(((((((((((....(((((.....)))))..))).......((((((....))))))...)))))))).).)))) ( -31.30)
>DroSim_CAF1 35688 112 + 1
ACCAUAUCAUUAAUUUAUGAACUUUAACUACUUAACUACAGGGUGGUCACAUCAAGAUACAUUUGAACACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUCCAGAG
......((((......))))..................(((((((((....(((((.....)))))..))).......((((((....))))))...))))))......... ( -26.30)
>DroEre_CAF1 36244 104 + 1
ACCUUAUUCUCAAUGUAUGUACUUUAA-------CUU-CAGGGUGGUCAUAUCAAGAUACACUUGAAUACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUCCAGAG
.....................((((..-------.((-(((((((((.((.(((((.....)))))))))).......((((((....))))))...))))))))...)))) ( -29.70)
>DroYak_CAF1 36270 105 + 1
ACCAUGUAAUUAAUGUAUGAAUUUUAA-------AUUGCAGGGUGGUCACAUCAAGAUACACUUGAAUACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUCCAGAG
.(((((((((((((......)))...)-------))))))(((((((....(((((.....)))))..))).......((((((....))))))...)))))))........ ( -28.40)
>consensus
ACCAUAUCAUUAAUUUAUGAACUUUAA________UUACAGGGUGGUCACAUCAAGAUACACUUGAACACCGAUAUGCCCGUCCAGGUGGACGGUGAGCCCUGGAUCCAGAG
......................................(((((((((....(((((.....)))))..))).......((((((....))))))...))))))......... (-21.60 = -22.05 +   0.45)

alignment

secondary structure

dotplot

Window 7

Location	19,805,208 – 19,805,307
Length	99
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	81.87
Mean single sequence MFE	-29.83
Consensus MFE	-22.79
Energy contribution	-22.90
Covariance contribution	0.11
Combinations/Pair	1.09
Mean z-score	-1.69
Structure conservation index	0.76
SVM decision value	0.45
SVM RNA-class probability	0.742529
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19805208 99 - 27905053
CUCUGAAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUAUUCAAGUGUAUCUUGAUGUGACCACCCUGGA-------------UGAUAAUAAAUUAAUGAUGUGGU
......((((((((....((((((....)))))).......(((..(((((.....)))))....))).)))))))-------------)...................... ( -34.30)
>DroVir_CAF1 38778 100 - 1
CUCUGAAUCCAUGGCUCGCCGUCCACCUGCACCGGCAUAUCGGUGUUUAAAUGUAUUUUGAUGUGGCCACCCUGUAAG-----CGAG-CGGU-----UAUUAAAUAUAU-AU
..........((.((((((.(.((((..(((((((....)))))))(((((.....))))).)))).)((...))..)-----))))-).))-----............-.. ( -23.00)
>DroSec_CAF1 35632 104 - 1
CUCUGAAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUGUUCAAAUGUAUCUUGAUGUGACCACCCUGGAG--------UUAAAGUUCAUAAAUUAAUGAUAUGGU
((.(((.(((((((....((((((....)))))).((((((((.((........)).))))))))....))))))).--------))).)).((((......))))...... ( -33.10)
>DroSim_CAF1 35688 112 - 1
CUCUGGAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUGUUCAAAUGUAUCUUGAUGUGACCACCCUGUAGUUAAGUAGUUAAAGUUCAUAAAUUAAUGAUAUGGU
(((((....)))))....((((((....)))))).((((((((((.(((.((........)).))).)))).....(((((....(((.......))).))))))))))).. ( -29.40)
>DroEre_CAF1 36244 104 - 1
CUCUGGAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUAUUCAAGUGUAUCUUGAUAUGACCACCCUG-AAG-------UUAAAGUACAUACAUUGAGAAUAAGGU
.(((.(((.(((((....((((((....)))))).......(((..(((((.....)))))....))).)))))-..(-------(......))....))).)))....... ( -30.90)
>DroYak_CAF1 36270 105 - 1
CUCUGGAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUAUUCAAGUGUAUCUUGAUGUGACCACCCUGCAAU-------UUAAAAUUCAUACAUUAAUUACAUGGU
...(((((.(((((....((((((....)))))).......(((..(((((.....)))))....))).)))))..))-------)))........................ ( -28.30)
>consensus
CUCUGAAUCCAGGGCUCACCGUCCACCUGGACGGGCAUAUCGGUAUUCAAAUGUAUCUUGAUGUGACCACCCUGGAA________UUAAAGUUCAUAAAUUAAUGAUAUGGU
.........(((((.....(((((....)))))((((((((((.((........)).)))))))).)).)))))...................................... (-22.79 = -22.90 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:02 2006