Locus 4832

Sequence ID	2R_DroMel_CAF1
Location	15,874,247 – 15,874,404
Length	157
Max. P	0.665596

overview

Window 3

Location	15,874,247 – 15,874,364
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.84
Mean single sequence MFE	-30.87
Consensus MFE	-15.72
Energy contribution	-17.19
Covariance contribution	1.48
Combinations/Pair	1.20
Mean z-score	-1.80
Structure conservation index	0.51
SVM decision value	0.28
SVM RNA-class probability	0.665596
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15874247 117 - 20766785
AUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUC-UAACGCCACAAGCUCAAACUACUACAGCGCAGUGCCCGAGCCGCAAAGCAUGCACAGUUC--U
..........((((.((((((....))))))((((.....(((.((((((......-....((.....))..........)))))).))))))))))).(((.....))).......--. ( -32.65)
>DroSec_CAF1 11521 117 - 1
AUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUC-UAUCGCCACAAGCUCGAACUACUACAGCGCAGUGCCCGGGCCGCAAAGCAUGCACAGUUC--U
........((((..(((((((....)))))))((((....(((.((((((......-....((.....))..........)))))).))).....))))))))..............--. ( -35.35)
>DroSim_CAF1 8966 117 - 1
AUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUC-UAACGCCACAAGCUCGAACUACUACAGCGCAGUGCCCGGGCCGCAAAGCAUGUACAGUUC--U
........((((..(((((((....)))))))((((....(((.((((((......-....((.....))..........)))))).))).....))))))))..............--. ( -35.35)
>DroEre_CAF1 9407 105 - 1
AUUUCAAAUUGCUCCUGGCCAUAACUGGGCAGGGCCAAAAGCUUGGCUGUUGACUC-UAACACCACAAGCUGGAACUACCACAGCGCAGUGC------------GCAUUCAAAGUCC--U
........(((..((((.(((....))).))))..))).(((((((.(((((....-))))).).))))))(((.((......((((...))------------))......)))))--. ( -31.90)
>DroYak_CAF1 11913 105 - 1
AUUUCCAAUUGCUCCUGGCCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUC-UAACGCCACAAGCUCGUACAACAACAGCGCAGUGC------------GCAUUCAAAGUCC--U
.........((((((((((((....)))))))))......(((.((((((((....-....((.....))........)))))))).)))..------------)))..........--. ( -33.59)
>DroAna_CAF1 5090 97 - 1
GUUUAUAAUUCA----ACCGAAAAUUUCCCAGGGCAAUACCUUUCACUGUUGACUUUUAACACCACAAACUCAAACUCCCAG---GCAG----------------GAUCUGGAGGCCCGA
............----...............((((............((((((...)))))).............((((.((---(...----------------..))))))))))).. ( -16.40)
>consensus
AUUUCAAAUUGCUCCUGGCCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUC_UAACGCCACAAGCUCGAACUACUACAGCGCAGUGC____________GCAUGCACAGUCC__U
.........(((.((((((((....)))))))).......(((.((((((..............................)))))).)))..............)))............. (-15.72 = -17.19 +   1.48)

alignment

secondary structure

dotplot

Window 4

Location	15,874,285 – 15,874,404
Length	119
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	91.34
Mean single sequence MFE	-29.28
Consensus MFE	-22.20
Energy contribution	-23.12
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-1.55
Structure conservation index	0.76
SVM decision value	-0.01
SVM RNA-class probability	0.526593
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15874285 119 - 20766785
CCGUUCUGGAACGUGGUAUUUCAUCCAUCAGCGUUAUCAAAUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUCUAACGCCACAAGCUCAAACUACU
..(((..((...((((..((.....((.(((((....................((((((((....))))))))((.....))..))))).)).....))..))))...))..))).... ( -31.30)
>DroSec_CAF1 11559 119 - 1
CCGUCCCGGAACGUGGUAUUUCAUCCAUCUGCGUUAUCAAAUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUCUAUCGCCACAAGCUCGAACUACU
(((...)))((((..(............)..)))).......(((...(((..((((((((....))))))))..))).(((((.(.((.(((.....))).)))))))).)))..... ( -27.40)
>DroSim_CAF1 9004 119 - 1
CCGUCCCGAAACGUGGUAUUUCAUCCAUCUGCGUUAUCAAAUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUCUAACGCCACAAGCUCGAACUACU
......(((...((((........))))..((((((..............((.((((((((....))))))))))(((.(((...))).)))....)))))).......)))....... ( -29.00)
>DroEre_CAF1 9433 119 - 1
CCGUCCCGCAACGUUAUAUUUCAAACAUCUCCGUUAUCAAAUUUCAAAUUGCUCCUGGCCAUAACUGGGCAGGGCCAAAAGCUUGGCUGUUGACUCUAACACCACAAGCUGGAACUACC
.(((......)))................(((................(((..((((.(((....))).))))..))).(((((((.(((((....))))).).)))))))))...... ( -27.90)
>DroYak_CAF1 11939 119 - 1
CCGUCCCGGAACGCAGUAUUUCAUACAGCUCCGUUAUCAAAUUUCCAAUUGCUCCUGGCCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUCUAACGCCACAAGCUCGUACAACA
......((((..((.((((...)))).))))))...............(((..((((((((....))))))))..))).(((((.((.((((....))))))...)))))......... ( -30.80)
>consensus
CCGUCCCGGAACGUGGUAUUUCAUCCAUCUGCGUUAUCAAAUUUCAAAUUGCUCCUGGUCAUAACUGGCCAGGGCCAAAAGCUUCGCUGUUGACUCUAACGCCACAAGCUCGAACUACU
.........(((((((............))))))).............(((..((((((((....))))))))..))).(((((...(((((....)))))....)))))......... (-22.20 = -23.12 +   0.92)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:21 2006