Locus 4104

Sequence ID	3L_DroMel_CAF1
Location	11,985,616 – 11,985,718
Length	102
Max. P	0.690953

overview

Window 4

Location	11,985,616 – 11,985,718
Length	102
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	81.79
Mean single sequence MFE	-41.69
Consensus MFE	-25.11
Energy contribution	-26.53
Covariance contribution	1.42
Combinations/Pair	1.19
Mean z-score	-2.20
Structure conservation index	0.60
SVM decision value	0.33
SVM RNA-class probability	0.690953
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11985616 102 + 23771897
ACAUAUGGUGGAUCCGGUUCCUGCAGCGGCACCUCAAAGAACAGUGGCUUCAGGGCCAACUGCACAGCCGCCAAACUGGAGGCUGUCA---CCCUGGAUC---CCACU
......((((((((((((.((((.(((.((.............)).))).)))))))...((.((((((.((.....)).))))))))---....)))).---))))) ( -41.02)
>DroSim_CAF1 3173 102 + 1
ACAUAUGGUGGAUCCGGUUCCUGCAGCGGCACCUCGAAGAACAGUGGCUUCAGGGCCAACUGCACAGCCGCCAAACUGGAGGCUGUCA---CCCGGGAUC---CCACU
......(((((((((((.....((((.(((.(((.((((........))))))))))..))))((((((.((.....)).))))))..---.)).)))).---))))) ( -43.60)
>DroEre_CAF1 4002 102 + 1
ACGUAUGGAGGAUCCGGCUCCUGCAGCGGCACCUCAAAAAACAAUGGCUUCAGGGCCAGCUGAACAGCCGCCAGGCUGGAGGCUGUCA---CCCUGGAUC---CCACU
......(..((((((((((.....)))((((((((......((.(((((....)))))..))..(((((....))))))))).)))).---...))))))---)..). ( -41.50)
>DroWil_CAF1 4424 99 + 1
ACAUACGGUGGGUCGGGUUCCUGCAGCGGCACCUCAAAGAACAAGGGUUUCAGAGCCAGCUGAACGGCUGCGUGAGCAGCUGCUGCCG---CUCUG---C---CCCCA
......((.(((.(((((....))((((((((((.........)))..(((((......)))))(((((((....))))))).)))))---)))))---)---)))). ( -42.00)
>DroYak_CAF1 3174 102 + 1
ACGUACGGAGGAUCUGGCUCCUGCAGCGGCACCUCAAAGAACAACGGCUUCAGGGCCAACUGAACAGCCGCCAAGGUGGAGGCUGUCA---CCCUGGAAC---CCACU
..((.(.((((..(((((....))..)))..))))...).))...((.(((((((.....(((.(((((.((.....)).))))))))---))))))).)---).... ( -34.80)
>DroAna_CAF1 3988 108 + 1
AAGUACGGAGGAUCCGGCUCCUGCAGGGGCACCUCAAAGAAGAGUGGCUUGAGGGCCAACUGGACAGCCGCCAGAGUAGAGGCUGUAAGUCCCCUGGAUCCUCCCGCU
.(((..(((((((((.((....))(((((...(((......)))(((((....)))))(((..((((((...........)))))).))))))))))))))))).))) ( -47.20)
>consensus
ACAUACGGAGGAUCCGGCUCCUGCAGCGGCACCUCAAAGAACAAUGGCUUCAGGGCCAACUGAACAGCCGCCAAACUGGAGGCUGUCA___CCCUGGAUC___CCACU
......((..((((((((.((((.(((.(...............).))).)))))))......((((((.((.....)).)))))).........)))))...))... (-25.11 = -26.53 +   1.42)

alignment

secondary structure

dotplot

Window 5

Location	11,985,616 – 11,985,718
Length	102
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-43.27
Consensus MFE	-28.25
Energy contribution	-29.53
Covariance contribution	1.28
Combinations/Pair	1.24
Mean z-score	-1.74
Structure conservation index	0.65
SVM decision value	0.19
SVM RNA-class probability	0.625009
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11985616 102 - 23771897
AGUGG---GAUCCAGGG---UGACAGCCUCCAGUUUGGCGGCUGUGCAGUUGGCCCUGAAGCCACUGUUCUUUGAGGUGCCGCUGCAGGAACCGGAUCCACCAUAUGU
....(---(((((.((.---..((((((.((.....)).))))))(((((.((((((((((........)))).))).)))))))).....))))))))......... ( -43.90)
>DroSim_CAF1 3173 102 - 1
AGUGG---GAUCCCGGG---UGACAGCCUCCAGUUUGGCGGCUGUGCAGUUGGCCCUGAAGCCACUGUUCUUCGAGGUGCCGCUGCAGGAACCGGAUCCACCAUAUGU
....(---(((((.((.---..((((((.((.....)).))))))(((((.((((((((((........)))).))).)))))))).....))))))))......... ( -46.10)
>DroEre_CAF1 4002 102 - 1
AGUGG---GAUCCAGGG---UGACAGCCUCCAGCCUGGCGGCUGUUCAGCUGGCCCUGAAGCCAUUGUUUUUUGAGGUGCCGCUGCAGGAGCCGGAUCCUCCAUACGU
.(..(---(((((.((.---((((((((.((.....)).))))).))).))(((((((.(((((((.........))))..))).)))).)))))))))..)...... ( -45.70)
>DroWil_CAF1 4424 99 - 1
UGGGG---G---CAGAG---CGGCAGCAGCUGCUCACGCAGCCGUUCAGCUGGCUCUGAAACCCUUGUUCUUUGAGGUGCCGCUGCAGGAACCCGACCCACCGUAUGU
.((((---(---(((((---(((((((.(((((....))))).)))..))).)))))).............(((.(((.((......)).))))))))).))...... ( -37.00)
>DroYak_CAF1 3174 102 - 1
AGUGG---GUUCCAGGG---UGACAGCCUCCACCUUGGCGGCUGUUCAGUUGGCCCUGAAGCCGUUGUUCUUUGAGGUGCCGCUGCAGGAGCCAGAUCCUCCGUACGU
.((((---(....((((---((((((((.((.....)).)))))))...(((((((((.(((.((..(((...)))..)).))).)))).)))))))))))).))).. ( -39.10)
>DroAna_CAF1 3988 108 - 1
AGCGGGAGGAUCCAGGGGACUUACAGCCUCUACUCUGGCGGCUGUCCAGUUGGCCCUCAAGCCACUCUUCUUUGAGGUGCCCCUGCAGGAGCCGGAUCCUCCGUACUU
....((((((((((((((........))))).....(((..(((..(((..((((((((((.........))))))).))).))))))..))))))))))))...... ( -47.80)
>consensus
AGUGG___GAUCCAGGG___UGACAGCCUCCACUCUGGCGGCUGUUCAGUUGGCCCUGAAGCCACUGUUCUUUGAGGUGCCGCUGCAGGAACCGGAUCCACCAUACGU
.((((...(((((.((......((((((.((.....)).)))))).((((.((((((((((........)))).))).)))))))......)))))))..)))).... (-28.25 = -29.53 +   1.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:35 2006