Locus 5566

Sequence ID	2L_DroMel_CAF1
Location	15,832,093 – 15,832,293
Length	200
Max. P	0.831290

overview

Window 7

Location	15,832,093 – 15,832,213
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-36.83
Consensus MFE	-33.52
Energy contribution	-34.30
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.19
Structure conservation index	0.91
SVM decision value	0.72
SVM RNA-class probability	0.831290
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15832093 120 + 22407834
AAACUUUGCCAGCUGUAUUGCAUUACGCCUUUAAUUUCAUUACACGUCCAGACGGAACGGGAAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAGUCGAGGGAAACACUUGUAAAGUC
..(((((((((((((((.((.((((......))))..)).))).........((((((((((....))))......))))))))))))).........(((((....).)))).))))). ( -33.30)
>DroSec_CAF1 4687 120 + 1
AAACUUUGCCAGCUGUAUUGCAUUACGCCCUUAAUUUCAUUACACGGCCAGUGGGAACGGGGAAAGUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUC
..(((((((.((..(((......))).((((..((((.((.....(((((((.(((((.(((.........)))..)))))..))))))).)).))))..)))).....)).))))))). ( -39.50)
>DroSim_CAF1 4876 120 + 1
AAACUUUGCCAGCUGUAUUGCAUUACGCCUUUAAUUUCAUUACACGGCCAGUGGGAACGGGGAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUC
..(((((((((((((((.((.((((......))))..)).))).(((....((((..(((((....)))))))))....)))))))))).........(((((....).)))).))))). ( -37.70)
>consensus
AAACUUUGCCAGCUGUAUUGCAUUACGCCUUUAAUUUCAUUACACGGCCAGUGGGAACGGGGAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUC
..(((((((((((((((.((.((((......))))..)).))).(((....((((..(((((....)))))))))....)))))))))).........(((((....).)))).))))). (-33.52 = -34.30 +   0.78)

alignment

secondary structure

dotplot

Window 8

Location	15,832,133 – 15,832,253
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.56
Mean single sequence MFE	-44.81
Consensus MFE	-39.59
Energy contribution	-40.37
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.30
Structure conservation index	0.88
SVM decision value	0.66
SVM RNA-class probability	0.813993
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15832133 120 + 22407834
UACACGUCCAGACGGAACGGGAAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAGUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCA
.....((((...((((((((((....))))......))))))....(((.........(((((....).))))........)))))))(((((((((((....))))))...)))))... ( -43.33)
>DroSec_CAF1 4727 120 + 1
UACACGGCCAGUGGGAACGGGGAAAGUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCA
.....(((((((.(((((.(((.........)))..)))))..)))))))........(((((....).))))....(((.....)))(((((((((((....))))))...)))))... ( -46.40)
>DroSim_CAF1 4916 120 + 1
UACACGGCCAGUGGGAACGGGGAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCAAAGGUCUCA
.....(((((((.(((((.(((.........)))..)))))..)))))))........(((((....).))))....(((.....)))((((.((((((....))))))....))))... ( -44.70)
>consensus
UACACGGCCAGUGGGAACGGGGAAACUCCCGCCCAAGUUCCGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCA
.....(((((((.(((((((((....))))......)))))..)))))))........(((((....).))))....(((.....)))(((((((((((....))))))...)))))... (-39.59 = -40.37 +   0.78)

alignment

secondary structure

dotplot

Window 9

Location	15,832,173 – 15,832,293
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-41.51
Consensus MFE	-38.80
Energy contribution	-39.47
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.93
SVM decision value	0.44
SVM RNA-class probability	0.736056
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15832173 120 + 22407834
CGAGCUGGCCCAUAAAGUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCAUAUUGCAUGGCGCCUCAUCUCGACCAACACUGCAGCUCAG
.((((((.(.......(((((((((..(.(((((((.(((.....)))(((((((((((....))))))...))))).....))))).)).)..)).))))))).......))))))).. ( -41.44)
>DroSec_CAF1 4767 120 + 1
CGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCAUAUUGCAUGGCGCCUCACCUCGAGCAACACUGCAGCUCAG
.((((((.(........((((((((..(.(((((((.(((.....)))(((((((((((....))))))...))))).....))))).)).)..)).))))))........))))))).. ( -42.49)
>DroSim_CAF1 4956 120 + 1
CGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCAAAGGUCUCAUAUUGCAUGGCGCCUCAUCUCCAGCAACACUGCAGCUCAG
.((((((((((........((((....).)))(((.....))).))))((((.((((((....))))))....)))).....((((.(((.(......).))))))).....)))))).. ( -40.60)
>consensus
CGAGCUGGCCCAUAAAAUCGAGGGAAACACUUGUAAAGUCUGCCGGGCGACCAGAAAGGGAGCCCUUUCCUAUGGUCUCAUAUUGCAUGGCGCCUCAUCUCGAGCAACACUGCAGCUCAG
.((((((((((((......((((....).)))((((.(((.....)))(((((((((((....))))))...))))).....)))))))).))).........(((....)))))))).. (-38.80 = -39.47 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:17 2006