Locus 2369

Sequence ID	X_DroMel_CAF1
Location	6,327,592 – 6,327,693
Length	101
Max. P	0.981170

overview

Window 4

Location	6,327,592 – 6,327,693
Length	101
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.87
Mean single sequence MFE	-24.33
Consensus MFE	-12.78
Energy contribution	-13.50
Covariance contribution	0.72
Combinations/Pair	1.05
Mean z-score	-2.50
Structure conservation index	0.53
SVM decision value	1.88
SVM RNA-class probability	0.981170
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6327592 101 + 22224390
UCCUUCAACCUUUCCCCACCCU---UUGCGCUGUUUCCCUUUU--------CCCUCCGGCGGCUGUCCGAAAUUGAGUUUUGAUUUCAAAACUCAAUU-CACAUUAAGCGGGG
.............((((.....---...(((((..........--------.....)))))(((......((((((((((((....))))))))))))-.......))))))) ( -28.88)
>DroSec_CAF1 12304 103 + 1
UCCUUCAACAUUUCCGUACCCUCCUUUCCGAUGUUUCCCUUUU--------CCCUCCGGCGGCUGUCCGAAAUUGAGUUUUGAUUUCA-AACUCAAUU-CACAUUAAGCGGGG
..................((((.(((...(((((.........--------.....((((....).))).((((((((((.(....))-)))))))))-.)))))))).)))) ( -19.30)
>DroSim_CAF1 5705 103 + 1
UCCUUCAACCUUUCCCCACCCUCCAUUCCGCUGUUUCCCUUUU--------CCCUCAGGCGGCUGUCCGAAAUUGAGUUUUGAUUUCA-AACUCAAUU-CACAUUAAGCGGGG
.............((((...........((((...........--------......))))(((......((((((((((.(....))-)))))))))-.......))))))) ( -22.55)
>DroEre_CAF1 9873 89 + 1
UCCUUCAACCUUUCCCU-----CGCUCUC---------GCUUU--------CCCUCCGGCGGCUGUCCGAAAUUGAGUUUUGAUUUCA-AACUCAAUU-CACAUUAAGCGGGG
..............(((-----((((.((---------(((..--------......)))))......(((.((((((((.(....))-)))))))))-)......))))))) ( -23.30)
>DroYak_CAF1 8366 98 + 1
UCCCUCAACCUUCCCCU-----CGCUUUCCCCCCCUCCGUUUU--------CCCUCCGGCGGCUGGCCGAAAUUGAGUUUUGAUUUCA-AACUCAAUU-CACAUUAAGCGGGG
..............(((-----(((((..((..((.(((....--------.....))).))..))..(((.((((((((.(....))-)))))))))-).....)))))))) ( -26.50)
>DroMoj_CAF1 15466 105 + 1
GGCCUCAGCCUCAGCCU-----CGCUGCCCCACU-GCCCCAUUGCCCCACCGCCA-CGGCGCGUGUCCAAAAUUGAGUUUUGAUUUGA-AACCCAAUUUCCCAUAAUGCGAUG
(((........((((..-----.)))).......-))).((((((..((((((..-..))).)))....((((((.(((((.....))-))).))))))........)))))) ( -25.46)
>consensus
UCCUUCAACCUUUCCCU_____CGCUUCCGCUGUUUCCCUUUU________CCCUCCGGCGGCUGUCCGAAAUUGAGUUUUGAUUUCA_AACUCAAUU_CACAUUAAGCGGGG
.....................................................(((((.(((....))).(((((((((.((....)).)))))))))..........))))) (-12.78 = -13.50 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	6,327,592 – 6,327,693
Length	101
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.87
Mean single sequence MFE	-30.87
Consensus MFE	-13.52
Energy contribution	-13.97
Covariance contribution	0.45
Combinations/Pair	1.17
Mean z-score	-2.37
Structure conservation index	0.44
SVM decision value	1.10
SVM RNA-class probability	0.915879
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6327592 101 - 22224390
CCCCGCUUAAUGUG-AAUUGAGUUUUGAAAUCAAAACUCAAUUUCGGACAGCCGCCGGAGGG--------AAAAGGGAAACAGCGCAA---AGGGUGGGGAAAGGUUGAAGGA
((((((((..((((-..((((((((((....))))))))))((((((.(....)))))))..--------.....(....)..)))).---.))))))))............. ( -35.10)
>DroSec_CAF1 12304 103 - 1
CCCCGCUUAAUGUG-AAUUGAGUU-UGAAAUCAAAACUCAAUUUCGGACAGCCGCCGGAGGG--------AAAAGGGAAACAUCGGAAAGGAGGGUACGGAAAUGUUGAAGGA
..((..(((((((.-..(((((((-(.......))))))))(((((.((..((.((((....--------.....(....).))))...))...)).)))))))))))).)). ( -24.70)
>DroSim_CAF1 5705 103 - 1
CCCCGCUUAAUGUG-AAUUGAGUU-UGAAAUCAAAACUCAAUUUCGGACAGCCGCCUGAGGG--------AAAAGGGAAACAGCGGAAUGGAGGGUGGGGAAAGGUUGAAGGA
((((((((..((((-(((((((((-(.......)))))))))))...))).((((((.....--------...))(....).))))......))))))))............. ( -32.20)
>DroEre_CAF1 9873 89 - 1
CCCCGCUUAAUGUG-AAUUGAGUU-UGAAAUCAAAACUCAAUUUCGGACAGCCGCCGGAGGG--------AAAGC---------GAGAGCG-----AGGGAAAGGUUGAAGGA
((((((((..((((-(((((((((-(.......)))))))))))...)))((..((....))--------...))---------..)))))-----.)))............. ( -26.70)
>DroYak_CAF1 8366 98 - 1
CCCCGCUUAAUGUG-AAUUGAGUU-UGAAAUCAAAACUCAAUUUCGGCCAGCCGCCGGAGGG--------AAAACGGAGGGGGGGAAAGCG-----AGGGGAAGGUUGAGGGA
((((((((.....(-(((((((((-(.......)))))))))))...((..((.(((.....--------....))).))..))..)))))-----.)))............. ( -32.10)
>DroMoj_CAF1 15466 105 - 1
CAUCGCAUUAUGGGAAAUUGGGUU-UCAAAUCAAAACUCAAUUUUGGACACGCGCCG-UGGCGGUGGGGCAAUGGGGC-AGUGGGGCAGCG-----AGGCUGAGGCUGAGGCC
..((((.......(((((((((((-(.......))))))))))))...(((((.(((-(.((......)).)))).))-.))).....)))-----)((((........)))) ( -34.40)
>consensus
CCCCGCUUAAUGUG_AAUUGAGUU_UGAAAUCAAAACUCAAUUUCGGACAGCCGCCGGAGGG________AAAAGGGAAACAGCGGAAGCG_____AGGGAAAGGUUGAAGGA
.(((............((((((((.((....)).))))))))(((((.......))))))))................................................... (-13.52 = -13.97 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:52 2006