Locus 4668

Sequence ID	X_DroMel_CAF1
Location	12,189,007 – 12,189,248
Length	241
Max. P	0.854469

overview

Window 7

Location	12,189,007 – 12,189,116
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.14
Mean single sequence MFE	-32.33
Consensus MFE	-23.83
Energy contribution	-23.70
Covariance contribution	-0.13
Combinations/Pair	1.09
Mean z-score	-1.95
Structure conservation index	0.74
SVM decision value	0.80
SVM RNA-class probability	0.853817
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12189007 109 - 22224390
CUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGGGAAAUUGGGGGCAGGGAAAAGUGGGU----GGGAGC-------GAUG
.......(((..(((....)))..(((.(..(((((((.(.(((((....)))))..(((......(((((.....)))))..))).).)))))))..)----...)))-------))). ( -34.00)
>DroSec_CAF1 15339 107 - 1
CUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUUCAGACGGCCAGUGGGAAAUUGGGGGCAGGGAAAAGUGGGC----GG--GC-------GAUG
.......(((..(((....)))..(((....(((((((.(.(((((....)))))...........(((((.....)))))......).)))))))...----.)--))-------))). ( -32.60)
>DroEre_CAF1 15278 93 - 1
CUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGG--------------GGGAAAGUGGGU----GG--GU-------GAUG
......((((..(((....))).))))....(((((((((((((((....)))))..))))))((.(((.(..--------------.....).))).)----))--))-------)... ( -30.20)
>DroAna_CAF1 28050 117 - 1
CUUAAAAGUCGAUGUGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCACUGGGAAAAUG---UCCUGGAAAAGUGGGAAAGUGGGCGCCACUAGUGAUG
......((((..(((....))).))))....(((((((((((((((....)))))..))))))((.(((((.........---((((........)))).))))).)).....))))... ( -32.50)
>consensus
CUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGGGAAAUUG___GCAGGGAAAAGUGGGU____GG__GC_______GAUG
......((((..(((....))).))))....(((((((.(.(((((....)))))...........((....)).............).)))))))........................ (-23.83 = -23.70 +  -0.13)

alignment

secondary structure

dotplot

Window 8

Location	12,189,036 – 12,189,142
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	84.22
Mean single sequence MFE	-34.02
Consensus MFE	-22.83
Energy contribution	-22.70
Covariance contribution	-0.13
Combinations/Pair	1.09
Mean z-score	-1.54
Structure conservation index	0.67
SVM decision value	-0.01
SVM RNA-class probability	0.529805
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12189036 106 - 22224390
GGGUUUC-----------G--GCGGCGAUGGG-GCAACUACUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGGGAAAUUG
...((((-----------.--(((((....((-....)).......((((..(((....))).))))......(.(((((((((((....)))))..)))))).)))).)).)))).... ( -33.50)
>DroSec_CAF1 15366 106 - 1
GGGUUUC-----------G--GCGGGGAUGGG-GCAACUACUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUUCAGACGGCCAGUGGGAAAUUG
.((((((-----------(--((.(...((((-((((.........((((..(((....))).)))).........)))).(((((....)))))..))))..).))).....)))))). ( -29.97)
>DroEre_CAF1 15298 99 - 1
GGGUUGC-----------G--CCGGGAAUGGG-GCAACUACUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGG-------
.((((((-----------.--(((....))).-)))))).......((((..(((....))).))))....(((((((((((((((....)))))..)))))).....)))).------- ( -37.30)
>DroAna_CAF1 28087 120 - 1
AGGCGGCCAGGAAGGAGGGCUGGGGAGCUGGGGCCAACUACUUAAAAGUCGAUGUGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCACUGGGAAAAUG
.((.(((((((.((..((.((.((...)).)).))..)).)))....(((....((((.((((((.........)))))).(((((....)))))..))))))))))).))......... ( -35.30)
>consensus
GGGUUGC___________G__GCGGGGAUGGG_GCAACUACUUAAAAGUCGAUGCGCAAGCAAGGCUAAAACACUUUUGCAGUCACUCAAGUGACAAUGCAGACGGCCAGUGGGAAAUUG
.(((..........................................((((..(((....))).))))......(.(((((((((((....)))))..)))))).))))............ (-22.83 = -22.70 +  -0.13)

alignment

secondary structure

dotplot

Window 9

Location	12,189,142 – 12,189,248
Length	106
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	87.88
Mean single sequence MFE	-43.10
Consensus MFE	-33.42
Energy contribution	-34.87
Covariance contribution	1.45
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.78
SVM decision value	0.33
SVM RNA-class probability	0.691584
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12189142 106 + 22224390
GAGCACUUUCCCCGCCCACUUUCCAUUCCCCAUUUUCCAUUUCCCUUGCCAAAUGCUAGUGCAUCGGCGGU----GCAAGGUGGUGGGGGCAAAAGCGAGGGAGUUGCUC
(((((..((((((((....(((....((((((....((((((..((((((..((((....)))).))))).----)..))))))))))))..)))))).))))).))))) ( -38.10)
>DroSec_CAF1 15472 109 + 1
GAGCACUUUCCCCGCCCACUUUCCAUUCCCCAUUUUCCAUUUUCCCAGCCAAAUGCAAGUGCAUCGGCGGUGGGUGCGAGG-AGUGGGGGCAAAUGCGAGGGAGUUGCUC
(((((..((((((((....(..(((((((((((...(((.....((.(((..((((....)))).))))))))))).).))-)))))..).....))).))))).))))) ( -43.10)
>DroEre_CAF1 15397 107 + 1
GAGCACUUUCCCCGCCCACUUUCCAUUGCCCAUUUUCCAUUUC-CCAGCCAAAUGCAAGUGCAUCGGCGGAGGGAGC-A-GUGGUGGGGGAAAGUGCGAGGGAGCUGCUC
(((((..((((((((..(((((((....((((....(((((((-((.(((..((((....)))).)))...))))..-)-)))))))))))))))))).))))).))))) ( -48.10)
>consensus
GAGCACUUUCCCCGCCCACUUUCCAUUCCCCAUUUUCCAUUUCCCCAGCCAAAUGCAAGUGCAUCGGCGGUGGG_GC_AGGUGGUGGGGGCAAAUGCGAGGGAGUUGCUC
(((((..((((((((....(..((((..((.....((((.....((.(((..((((....)))).))))))))).....))..))))..).....))).))))).))))) (-33.42 = -34.87 +   1.45)

alignment

secondary structure

dotplot

Window 0

Location	12,189,142 – 12,189,248
Length	106
Sequences	3
Columns	110
Reading direction	reverse
Mean pairwise identity	87.88
Mean single sequence MFE	-45.53
Consensus MFE	-32.89
Energy contribution	-33.00
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-2.99
Structure conservation index	0.72
SVM decision value	0.80
SVM RNA-class probability	0.854469
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12189142 106 - 22224390
GAGCAACUCCCUCGCUUUUGCCCCCACCACCUUGC----ACCGCCGAUGCACUAGCAUUUGGCAAGGGAAAUGGAAAAUGGGGAAUGGAAAGUGGGCGGGGAAAGUGCUC
(((((.(((((((((((((..((((((((((((((----......(((((....)))))..))))))....)))....)))))....))))))))).))))....))))) ( -43.40)
>DroSec_CAF1 15472 109 - 1
GAGCAACUCCCUCGCAUUUGCCCCCACU-CCUCGCACCCACCGCCGAUGCACUUGCAUUUGGCUGGGAAAAUGGAAAAUGGGGAAUGGAAAGUGGGCGGGGAAAGUGCUC
(((((..((((.(((.(((.((((((.(-((.....((((..((((((((....))).))))))))).....)))...)))))...).)))....)))))))...))))) ( -45.10)
>DroEre_CAF1 15397 107 - 1
GAGCAGCUCCCUCGCACUUUCCCCCACCAC-U-GCUCCCUCCGCCGAUGCACUUGCAUUUGGCUGG-GAAAUGGAAAAUGGGCAAUGGAAAGUGGGCGGGGAAAGUGCUC
(((((..((((((.(((((((((((((((.-.-..((((...((((((((....))).))))).))-))..)))....))))....)))))))).).)))))...))))) ( -48.10)
>consensus
GAGCAACUCCCUCGCAUUUGCCCCCACCACCU_GC_CCCACCGCCGAUGCACUUGCAUUUGGCUGGGGAAAUGGAAAAUGGGGAAUGGAAAGUGGGCGGGGAAAGUGCUC
(((((..((((((.(((((.((((((................((((((((....))).)))))........(....).))))....)).))))).).)))))...))))) (-32.89 = -33.00 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:32 2006