Locus 6840

Sequence ID	3L_DroMel_CAF1
Location	18,355,918 – 18,356,040
Length	122
Max. P	0.880608

overview

Window 4

Location	18,355,918 – 18,356,020
Length	102
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	80.19
Mean single sequence MFE	-24.35
Consensus MFE	-17.65
Energy contribution	-17.18
Covariance contribution	-0.47
Combinations/Pair	1.22
Mean z-score	-1.86
Structure conservation index	0.72
SVM decision value	0.86
SVM RNA-class probability	0.868006
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18355918 102 - 23771897
-GCUUACGAGUGGAC-UGUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAUCCUCACUGAAGCCCACACUCC--UUUA----CAGUAC
-......(((((.((-.(((((((((((....))))))))))).))................((((..(.........)..))))...))))).--....----...... ( -24.40)
>DroPse_CAF1 165514 92 - 1
CGCUUAGGAGUGGAC-UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAAUUGGAGCCACACACACACAGGCACACACGC-----------------
.((((..(.((((.(-((((((((((((....))))))))).((((......)))).........)))))))).)......))))........----------------- ( -22.30)
>DroSec_CAF1 140067 102 - 1
-GCUUACGAGUGGAC-UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGUCCAACCUCACUGAAUCCCAUACUCC--UUCA----CAGCCC
-(((...((((((((-..((((((((((....))))))))))((((......))))...........)))))..)))..((((...........--))))----.))).. ( -22.90)
>DroEre_CAF1 135388 102 - 1
-GCUUACGAGUGGAC-CUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAACCUCACUGAUUCCCACACUCC--UUCG----CAGCAC
-((..(.(((((.((-..((((((((((....))))))))))..))........(((....(((...((....))..)))..)))...))))).--)..)----)..... ( -23.10)
>DroYak_CAF1 146236 96 - 1
-GCUUACGAGUGGAC-CUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGACGAAAUUAAGUUUUGGCCAACA------CUUCCCACACUCC--UCUA----CAGCAC
-(((...(((((.((-..((((((((((....))))))))))..))..((((((........)))))).......------.......))))).--....----.))).. ( -24.50)
>DroAna_CAF1 136508 109 - 1
-GCUUAGGAAUGGACCUUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAACAUCACACAUUCCCGUACACACGUACGAACUCAAAGC
-((((.((((((......((((((((((....))))))))))((((......))))......((..((.....))..)).))))))(((((....)))))......)))) ( -28.90)
>consensus
_GCUUACGAGUGGAC_UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAACCUCACUGAUUCCCACACUCC__UUCA____CAGCAC
.........((((.....((((((((((....))))))))))((((......)))).............................))))..................... (-17.65 = -17.18 +  -0.47)

alignment

secondary structure

dotplot

Window 5

Location	18,355,942 – 18,356,040
Length	98
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.57
Mean single sequence MFE	-29.48
Consensus MFE	-15.99
Energy contribution	-16.80
Covariance contribution	0.81
Combinations/Pair	1.16
Mean z-score	-2.44
Structure conservation index	0.54
SVM decision value	0.91
SVM RNA-class probability	0.880608
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18355942 98 - 23771897
GCCGAAACG--------------------CAAUUGACCAG-GCUUACGAGUGGAC-UGUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAUCCUCACU
((((((((.--------------------.((((..(((.-.(....)..)))((-.(((((((((((....))))))))))).))..........))))..)))))))).......... ( -28.90)
>DroPse_CAF1 165527 119 - 1
UCCAAGACGCAGUUCAAGGAAGGGAAGUCCAAUUGACCGGCGCUUAGGAGUGGAC-UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAAUUGGAGCCACACACACA
((((((.(((.(.((((.....((....))..)))).).)))))).)))((((.(-((((((((((((....))))))))).((((......)))).........))))))))....... ( -34.60)
>DroSec_CAF1 140091 98 - 1
GCCGAAACG--------------------CAAUUGACCAG-GCUUACGAGUGGAC-UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGUCCAACCUCACU
(((......--------------------..........)-))....((((((((-..((((((((((....))))))))))((((......))))...........)))))..)))... ( -25.19)
>DroYak_CAF1 146259 93 - 1
GCCGAAACG--------------------CAAUUGACCAG-GCUUACGAGUGGAC-CUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGACGAAAUUAAGUUUUGGCCAACA-----
((((((((.--------------------.((((..(((.-.(....)..)))..-..((((((((((....))))))))))((((......))))))))..)))))))).....----- ( -28.50)
>DroAna_CAF1 136538 99 - 1
ACCAAGACG--------------------CAAUUGACCAG-GCUUAGGAAUGGACCUUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAACAUCACA
.((((((((--------------------(((((..((..-((..(((......)))..)))).))))))..........((((.......)))).......)))))))........... ( -25.10)
>DroPer_CAF1 166544 119 - 1
UCCAAGACGCAGUUCAAGGAAGGGAAGUCCAAUUGACCGGCGCUUAGGAGUGGAC-UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAAUUGGAGCCACACACACA
((((((.(((.(.((((.....((....))..)))).).)))))).)))((((.(-((((((((((((....))))))))).((((......)))).........))))))))....... ( -34.60)
>consensus
GCCAAAACG____________________CAAUUGACCAG_GCUUACGAGUGGAC_UUUGCGGAAAUUGCAAAAUUUCUGCAUCGUAAUAAGAUGAAAUUAAGUUUUGGCCAACCUCACA
.(((((((............................(((...(....)..))).....((((((((((....))))))))))((((......))))......)))))))........... (-15.99 = -16.80 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:03 2006