Locus 4354

Sequence ID	2R_DroMel_CAF1
Location	14,322,954 – 14,323,108
Length	154
Max. P	0.871325

overview

Window 0

Location	14,322,954 – 14,323,069
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.76
Mean single sequence MFE	-20.19
Consensus MFE	-3.10
Energy contribution	-3.82
Covariance contribution	0.72
Combinations/Pair	1.25
Mean z-score	-1.84
Structure conservation index	0.15
SVM decision value	0.87
SVM RNA-class probability	0.871325
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14322954 115 + 20766785
AAGACCGUUUCCAAAAACAA--UAAAAUAUCAUAGUUAA-AAAACUUCAGAGAAUGCAAAACGAAAGUGUUGGAAACAUUUCUAAGAUUAUGAUUG--AUCUUGAGCACUUUACUCAAAA
......((((((((......--.......((..((((..-..))))...)).........((....)).))))))))......(((((((....))--)))))(((.......))).... ( -19.80)
>DroSec_CAF1 51968 115 + 1
AAGACCGUUUCCAAAAAUAA--AAAAAUGUCAUAGUCAA-AGAACUUCAGAGAAUGCAAAACGAUAGUGUUGGAAAUAUUUCUAAGAUUAUGAUUG--AUCUUGAGCACUGAACUCAAAA
.(((..((((((((......--.....((.(((..((..-.........))..)))))...........))))))))...)))(((((((....))--)))))(((.......))).... ( -15.75)
>DroSim_CAF1 53990 115 + 1
AAGACAGUUUCCAAAAAUAA--UAAAAUGUCAUAGUUAA-AAAACUUCAGAAAAUGCAACACGAAAGUGUUGUAAACAUUUCUAAGCUUAUGAUUG--AUCUUGAGCACUGAACUUAAAA
..((((..............--.....))))........-.....(((((....((((((((....))))))))...........(((((.((...--.)).))))).)))))....... ( -26.01)
>DroEre_CAF1 52764 115 + 1
AACAACGUGUUUAAAAAUGAUAUAAAAUAUCAUAGGUAA-AUAAGAUCAGUAAAUGUAUAACUAAAACGGUGAAAGAA----UAAGAUUAUGCUUGUUACUUUGAGCACUGACAACCAAA
.......((((((...(((((((...)))))))...)))-)))...(((((....((.........))(.(.((((((----((((......)))))).)))).).))))))........ ( -17.70)
>DroYak_CAF1 53639 112 + 1
--------AUUUAGAAAUGAUCUAGAAUAUCAUAGUUCAAAAAGGAUCAGUAAAUGUAUAACUAGUUCGCUGCUUGAACUUCUAAGAUUAUGAUUCUUAAUUUGAGCACUGAACACAAAA
--------(((((....((((((.((((......)))).....)))))).))))).........(((((.((((..((....(((((.......))))).))..)))).)))))...... ( -21.70)
>consensus
AAGACCGUUUCCAAAAAUAA__UAAAAUAUCAUAGUUAA_AAAACUUCAGAAAAUGCAAAACGAAAGUGUUGGAAAAAUUUCUAAGAUUAUGAUUG__AUCUUGAGCACUGAACUCAAAA
............................(((((((((..........((.....))(((.((....)).))).............))))))))).......................... ( -3.10 =  -3.82 +   0.72)

alignment

secondary structure

dotplot

Window 1

Location	14,322,991 – 14,323,108
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.67
Mean single sequence MFE	-21.04
Consensus MFE	-1.34
Energy contribution	-2.70
Covariance contribution	1.36
Combinations/Pair	1.21
Mean z-score	-1.72
Structure conservation index	0.06
SVM decision value	0.79
SVM RNA-class probability	0.851709
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 14322991 117 + 20766785
AAAACUUCAGAGAAUGCAAAACGAAAGUGUUGGAAACAUUUCUAAGAUUAUGAUUG--AUCUUGAGCACUUUACUCAAAAUAGAUGAACGAAUAAU-UUUAAUUUACCUGACCUUCAAAA
......((((.(((......((....))..((....)).)))(((((((((..((.--((((((((.......))))....)))).))...)))))-))))......))))......... ( -18.90)
>DroSec_CAF1 52005 117 + 1
AGAACUUCAGAGAAUGCAAAACGAUAGUGUUGGAAAUAUUUCUAAGAUUAUGAUUG--AUCUUGAGCACUGAACUCAAAAUAGAUGAACAAAUAAU-UUUAAUUUACCUGACCUUCAAAA
.(((..((((....(.(((.((....)).))).)........(((((((((..((.--((((((((.......))))....)))).))...)))))-))))......))))..))).... ( -18.50)
>DroSim_CAF1 54027 117 + 1
AAAACUUCAGAAAAUGCAACACGAAAGUGUUGUAAACAUUUCUAAGCUUAUGAUUG--AUCUUGAGCACUGAACUUAAAAUAAAUGAACGAGUAAU-UUUAAUUUACCUGACCUUCAAAA
.....(((((....((((((((....))))))))...........(((((.((...--.)).))))).)))))...........((((((.((((.-......)))).))...))))... ( -25.70)
>DroEre_CAF1 52803 115 + 1
AUAAGAUCAGUAAAUGUAUAACUAAAACGGUGAAAGAA----UAAGAUUAUGCUUGUUACUUUGAGCACUGACAACCAAAUAAAAGAUGGAAAUAU-UUGAAUUUUUAUGACCUUCAAAA
((((((....(((((((..........(((((((((((----((((......)))))).))))...)))))....(((.........)))..))))-)))...))))))........... ( -16.60)
>DroYak_CAF1 53671 120 + 1
AAAGGAUCAGUAAAUGUAUAACUAGUUCGCUGCUUGAACUUCUAAGAUUAUGAUUCUUAAUUUGAGCACUGAACACAAAAUAAACCAACCACAUAUAUUAUAUUUAUCUGACCUUCAGAA
.((((.((((((((((((......(((((.((((..((....(((((.......))))).))..)))).))))).....(((...........)))..)))))))).))))))))..... ( -25.50)
>consensus
AAAACUUCAGAAAAUGCAAAACGAAAGUGUUGGAAAAAUUUCUAAGAUUAUGAUUG__AUCUUGAGCACUGAACUCAAAAUAAAUGAACGAAUAAU_UUUAAUUUACCUGACCUUCAAAA
......((((......(((.((....)).))).............................(((((.......))))).............................))))......... ( -1.34 =  -2.70 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:40 2006