Locus 3414

Sequence ID	2L_DroMel_CAF1
Location	9,882,770 – 9,882,930
Length	160
Max. P	0.985944

overview

Window 2

Location	9,882,770 – 9,882,864
Length	94
Sequences	3
Columns	94
Reading direction	forward
Mean pairwise identity	95.02
Mean single sequence MFE	-28.31
Consensus MFE	-24.16
Energy contribution	-24.83
Covariance contribution	0.67
Combinations/Pair	1.07
Mean z-score	-2.69
Structure conservation index	0.85
SVM decision value	0.83
SVM RNA-class probability	0.860667
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9882770 94 + 22407834
CACAAACCAGUGUUGUACACACGCAAAGUGGAGCAAUUCCGACAACUCCAUUUGCAUCGGUAUGUGUGCCAGUGGGUAUGUAUUUGUUUCCCAU
((((.(((.((((.....))))(((((.(((((............))))))))))...))).)))).....(((((.............))))) ( -26.62)
>DroSec_CAF1 90669 93 + 1
CACACACCAGUGU-AUACAUACGCAAAGUGGAGCAAUUCCGACAACUCCAUUUGCAUCGGUAUGUGCGCCACUGGGUAUGUAUUUGUUUCCCAU
.((((....))))-((((((((.((..((((.(((...(((((((......)))..))))....))).)))))).))))))))........... ( -28.70)
>DroSim_CAF1 97522 93 + 1
CACACACCAGUGU-AUACAUACGCAAAGUGGAGCAAUUCCGACAACUCCAUUUGUAUCGGUAUGUGUGCCACUGGGUAUGUAUUUGUUUCCCAU
.(((..(((((((-(((((((((((((.(((((............))))))))))....))))))))).))))))...)))............. ( -29.60)
>consensus
CACACACCAGUGU_AUACAUACGCAAAGUGGAGCAAUUCCGACAACUCCAUUUGCAUCGGUAUGUGUGCCACUGGGUAUGUAUUUGUUUCCCAU
.(((..((((((..(((((((((((((.(((((............))))))))))....))))))))..))))))...)))............. (-24.16 = -24.83 +   0.67)

alignment

secondary structure

dotplot

Window 3

Location	9,882,770 – 9,882,864
Length	94
Sequences	3
Columns	94
Reading direction	reverse
Mean pairwise identity	95.02
Mean single sequence MFE	-31.01
Consensus MFE	-29.59
Energy contribution	-30.37
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.95
Structure conservation index	0.95
SVM decision value	2.02
SVM RNA-class probability	0.985944
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9882770 94 - 22407834
AUGGGAAACAAAUACAUACCCACUGGCACACAUACCGAUGCAAAUGGAGUUGUCGGAAUUGCUCCACUUUGCGUGUGUACAACACUGGUUUGUG
.((((.............))))......((((.((((..(((((((((((..........)))))).)))))((((.....)))))))).)))) ( -28.22)
>DroSec_CAF1 90669 93 - 1
AUGGGAAACAAAUACAUACCCAGUGGCGCACAUACCGAUGCAAAUGGAGUUGUCGGAAUUGCUCCACUUUGCGUAUGUAU-ACACUGGUGUGUG
...(....).....(((((((((((....((((((....(((((((((((..........)))))).)))))))))))..-.)))))).))))) ( -34.30)
>DroSim_CAF1 97522 93 - 1
AUGGGAAACAAAUACAUACCCAGUGGCACACAUACCGAUACAAAUGGAGUUGUCGGAAUUGCUCCACUUUGCGUAUGUAU-ACACUGGUGUGUG
...(....).....(((((((((((....(((((((((......((((((..........))))))..))).))))))..-.)))))).))))) ( -30.50)
>consensus
AUGGGAAACAAAUACAUACCCAGUGGCACACAUACCGAUGCAAAUGGAGUUGUCGGAAUUGCUCCACUUUGCGUAUGUAU_ACACUGGUGUGUG
...(....)...((((((((.((((....((((((....(((((((((((..........)))))).)))))))))))....)))))))))))) (-29.59 = -30.37 +   0.78)

alignment

secondary structure

dotplot

Window 4

Location	9,882,833 – 9,882,930
Length	97
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	93.98
Mean single sequence MFE	-28.40
Consensus MFE	-24.88
Energy contribution	-25.08
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.70
Structure conservation index	0.88
SVM decision value	1.59
SVM RNA-class probability	0.966000
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9882833 97 + 22407834
GUGUGCCAGUGGGUAUGUAUUUGUUUCCCAUUUAUUCUGUGUCGGUGUGUCCUCACCGUUUAGAAUAAAGGUACUUCCACGCACACAAACGCACAGC
((((((..(((((...(((........((.(((((((((...(((((......)))))..)))))))))))))).)))))))))))........... ( -33.00)
>DroSec_CAF1 90731 96 + 1
GUGCGCCACUGGGUAUGUAUUUGUUUCCCAUUUAU-CUGUGCCGGUGUGUCCUCGCCGUUUAGAAUAAAGGUACCUCCACGCACACAAACGCACAGC
(((((....((((.............)))).....-.((((((((((......)))))...........((.....))..)))))....)))))... ( -25.82)
>DroSim_CAF1 97584 96 + 1
GUGUGCCACUGGGUAUGUAUUUGUUUCCCAUUUAU-CUGUGUCGGUGUGUCCUCGCCGUUUAGAAUAAAGGUACCUCCACGCACACAAACGCACAGC
((((((....((((((...(((((((..(((....-..))).(((((......)))))....))))))).))))))....))))))........... ( -25.90)
>DroEre_CAF1 95705 96 + 1
GUGUGCCAGUGGGUAUGUAUUUGUCUCGUAUUUAU-UUGUGUCGGUGUGUCCUCACCGUUUAGAAUAAAGGUACUUCCACGCACACAAAGGCACAGC
((((((..(((((...(((((.........(((((-((....(((((......)))))....)))))))))))).)))))))))))........... ( -28.90)
>DroYak_CAF1 95202 96 + 1
GUGUGCCAGUGGGUAUGUAUUUGUUUCCCAUUUAU-CUGUGUCGGUGUGCCCUCACCGUUUAGAAUAAAGGUACUUCCACGCACACAAACGCACAUC
((((((..(((((...((((((..(((.(((....-..))).(((((......)))))....)))...)))))).)))))))))))........... ( -28.40)
>consensus
GUGUGCCAGUGGGUAUGUAUUUGUUUCCCAUUUAU_CUGUGUCGGUGUGUCCUCACCGUUUAGAAUAAAGGUACUUCCACGCACACAAACGCACAGC
((((((..(((((...(((((.........(((((.(((...(((((......)))))..))).)))))))))).)))))))))))........... (-24.88 = -25.08 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:55 2006