Locus 6767

Sequence ID	X_DroMel_CAF1
Location	16,822,481 – 16,822,606
Length	125
Max. P	0.861834

overview

Window 4

Location	16,822,481 – 16,822,585
Length	104
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	88.74
Mean single sequence MFE	-25.06
Consensus MFE	-19.54
Energy contribution	-19.38
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.80
Structure conservation index	0.78
SVM decision value	0.63
SVM RNA-class probability	0.804416
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16822481 104 + 22224390
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAAAAAAUGGGAGCUACAACAAGUG
((..(((((((.......)))))))((((.((((.((((....))))).(((((.((((......)))))))))--------....))).....)))).))........... ( -23.70)
>DroSec_CAF1 20187 89 + 1
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAGAA---------------AAGUG
...((((((((.......))))))))....((((.((((....))))).(((((.((((......)))))))))--------....)))...---------------..... ( -20.90)
>DroSim_CAF1 4935 103 + 1
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------AGAGGCAGAA-AUGGGAGCUACAACAAGUG
((..(((((((.......)))))))((((.((((.((((....))))).(((((.((((......)))))))))--------....)))...-.)))).))........... ( -25.50)
>DroEre_CAF1 4907 103 + 1
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAGCA-AUGGGAGCUACAACAAGUG
((..(((((((.......)))))))((((.((((.((((....))))).(((((.((((......)))))))))--------.......)))-.)))).))........... ( -27.60)
>DroYak_CAF1 5015 111 + 1
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUAUCCAGUUGUGCUGUUGUGCUGGCUGAA-AUGGGAGCUACAACAAGUG
(((((((((((.......))))))))....)))(.((((....))))).(((((.((((......)))))))))(((((((((((..(....-..)..))).))))).))). ( -27.60)
>consensus
GCAAUGUUGCAAAAUUAAUGCGAUAUCCAAUGCGAUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU________ACAGGCAGAA_AUGGGAGCUACAACAAGUG
((..(((..((....(((((((........))).))))....))..)))(((((.((((......)))))))))............))........................ (-19.54 = -19.38 +  -0.16)

alignment

secondary structure

dotplot

Window 5

Location	16,822,515 – 16,822,606
Length	91
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	87.18
Mean single sequence MFE	-22.48
Consensus MFE	-17.76
Energy contribution	-18.20
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.90
Structure conservation index	0.79
SVM decision value	0.83
SVM RNA-class probability	0.861834
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16822515 91 + 22224390
AUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAAAAAAUGGGAGCUACAACAAGUGUUACAACCACUUGAAGUUGGU
........((((((((((((.((((......)))))))))--------...(((...........)))........)))))))((((........)))) ( -20.90)
>DroSec_CAF1 20221 76 + 1
AUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAGAA---------------AAGUGUUACAACCACUUGAAGUUGGU
........((((((.(((((.((((......)))))))))--------....((....---------------..))))))))((((........)))) ( -18.30)
>DroSim_CAF1 4969 90 + 1
AUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------AGAGGCAGAA-AUGGGAGCUACAACAAGUGUUACAACCACUUGAAGUUGGU
........(((((((......((((......))))(((((--------((...((...-.))....)))))))...)))))))((((........)))) ( -25.10)
>DroEre_CAF1 4941 90 + 1
AUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU--------ACAGGCAGCA-AUGGGAGCUACAACAAGUGUUACAACCACUUGAAGUUGGU
........((((((((((((.((((......)))))))))--------....(.(((.-......))).)......)))))))((((........)))) ( -21.70)
>DroYak_CAF1 5049 98 + 1
AUUACAGAUGUGACAACAACAUGGGCAAAUAUCCAGUUGUGCUGUUGUGCUGGCUGAA-AUGGGAGCUACAACAAGUGUUACAACCACUUGAAGUUGGU
........((((((((((((.((((......)))))))))..(((((((((..(....-..)..))).))))))..)))))))((((........)))) ( -26.40)
>consensus
AUUACAGAUGUGACAACAACAUGGGCAAAUACCCAGUUGU________ACAGGCAGAA_AUGGGAGCUACAACAAGUGUUACAACCACUUGAAGUUGGU
........((((((((((((.((((......)))))))))...........(((...........)))........)))))))((((........)))) (-17.76 = -18.20 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	16,822,515 – 16,822,606
Length	91
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	87.18
Mean single sequence MFE	-20.36
Consensus MFE	-15.88
Energy contribution	-16.68
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.78
SVM decision value	0.25
SVM RNA-class probability	0.652728
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16822515 91 - 22224390
ACCAACUUCAAGUGGUUGUAACACUUGUUGUAGCUCCCAUUUUUUGCCUGU--------ACAACUGGGUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
....((..((((((.......))))))..))............((((.(((--------((((((((((....))))).)))))....)))...)))). ( -20.80)
>DroSec_CAF1 20221 76 - 1
ACCAACUUCAAGUGGUUGUAACACUU---------------UUCUGCCUGU--------ACAACUGGGUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
.........(((((.......)))))---------------.......((.--------((((((((((....))))).)))))...)).......... ( -15.70)
>DroSim_CAF1 4969 90 - 1
ACCAACUUCAAGUGGUUGUAACACUUGUUGUAGCUCCCAU-UUCUGCCUCU--------ACAACUGGGUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
....((..((((((.......))))))..)).........-...((...(.--------((((((((((....))))).))))).)...))........ ( -19.70)
>DroEre_CAF1 4941 90 - 1
ACCAACUUCAAGUGGUUGUAACACUUGUUGUAGCUCCCAU-UGCUGCCUGU--------ACAACUGGGUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
........((((((.......))))))..(((((......-.))))).((.--------((((((((((....))))).)))))...)).......... ( -24.50)
>DroYak_CAF1 5049 98 - 1
ACCAACUUCAAGUGGUUGUAACACUUGUUGUAGCUCCCAU-UUCAGCCAGCACAACAGCACAACUGGAUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
....((..((((((.......))))))..)).........-..(((.....(((((((((....(((........)))))))))))).....))).... ( -21.10)
>consensus
ACCAACUUCAAGUGGUUGUAACACUUGUUGUAGCUCCCAU_UUCUGCCUGU________ACAACUGGGUAUUUGCCCAUGUUGUUGUCACAUCUGUAAU
....((..((((((.......))))))..))............................((((((((((....))))).)))))............... (-15.88 = -16.68 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:22:30 2006