Locus 5091

Sequence ID	3R_DroMel_CAF1
Location	13,424,186 – 13,424,323
Length	137
Max. P	0.574617

overview

Window 7

Location	13,424,186 – 13,424,287
Length	101
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	89.28
Mean single sequence MFE	-31.04
Consensus MFE	-22.32
Energy contribution	-23.30
Covariance contribution	0.98
Combinations/Pair	1.15
Mean z-score	-1.72
Structure conservation index	0.72
SVM decision value	0.01
SVM RNA-class probability	0.539807
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13424186 101 - 27905053
AAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCAAAUGCACGCGCACACACGCAAUUGCAACUAUGCAAUUAUCAAAUUAGUGCGGGGCGUGGCGG
......(((.......)))........((((((..(((...((((((((......)))(((((((....))))))).........)))))..))))))))) ( -34.40)
>DroSec_CAF1 49809 101 - 1
AAUUAACCCAUCAGACGGGCUUAUGAGCCGUCGACCGCAAAUGCACACGCACACACGCAAUUGCAACUAUGCAAUUAUCAAAUUAGUGCGGGGCGUGGCGG
.............(((((.((....)))))))..((((..((((...(((((......(((((((....))))))).........)))))..)))).)))) ( -32.16)
>DroSim_CAF1 52627 101 - 1
AAUUAACCCAUCAGACGGGCUUAUGAGCCGUCGACCGCAAAUGCACACGCACACACGCAAUUGCAACUAUGCAAUUAUCAAAUUAGUGCGGGGCGUGGCGG
.............(((((.((....)))))))..((((..((((...(((((......(((((((....))))))).........)))))..)))).)))) ( -32.16)
>DroEre_CAF1 50105 89 - 1
AAUUAACCCAUCAGACGGGCUUAUGAGCCGCCAAGCGCUAGUGCG----CACACACGCAGUUGC--------AAUUAUCAAAUUAGUGCGGGGCGUGGCGG
......(((.......)))........(((((..((((....)))----)....((((..((((--------(.(((......)))))))).))))))))) ( -29.80)
>DroYak_CAF1 54959 89 - 1
AAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCCAAUGCA----CACACACGCAAUUGC--------AAUUAUCAAAUUAGUGCGGGGCGUGGCGG
......(((.......)))........((((((..((((..((((----(......((....))--------((((....)))).))))).)))))))))) ( -26.70)
>consensus
AAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCAAAUGCAC_CGCACACACGCAAUUGCAACUAUGCAAUUAUCAAAUUAGUGCGGGGCGUGGCGG
......(((.......)))........((((((..(((...(((((..((......))(((((((....))))))).........)))))..))))))))) (-22.32 = -23.30 +   0.98)

alignment

secondary structure

dotplot

Window 8

Location	13,424,225 – 13,424,323
Length	98
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	89.67
Mean single sequence MFE	-23.04
Consensus MFE	-18.58
Energy contribution	-18.78
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.81
SVM decision value	0.08
SVM RNA-class probability	0.574617
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13424225 98 - 27905053
CUGGCCGCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCAAAUGCACGCGCACACACGCAAUU
......(((((....((((((...........(((((..((((((.......))).))))).)))(.....)))))))...)))))............ ( -24.50)
>DroSec_CAF1 49848 92 - 1
------CCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGUCGACCGCAAAUGCACACGCACACACGCAAUU
------..(((((..((((((...........((........)).....(((((.((....)))))))....))))))..)).)))............ ( -22.20)
>DroSim_CAF1 52666 92 - 1
------CCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGUCGACCGCAAAUGCACACGCACACACGCAAUU
------..(((((..((((((...........((........)).....(((((.((....)))))))....))))))..)).)))............ ( -22.20)
>DroEre_CAF1 50136 93 - 1
CUG-CCCCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGCCAAGCGCUAGUGCG----CACACACGCAGUU
(((-(...(((((.((((((...))))))..(((((..((.........))..)))))....)))))...((((....)))----)......)))).. ( -26.00)
>DroYak_CAF1 54990 94 - 1
CUGACCCCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCCAAUGCA----CACACACGCAAUU
........(((((.((((((...))))))...(((((..((((((.......))).))))).)))....)))))...(((.----.......)))... ( -20.30)
>consensus
CUG_CCCCGCGGUAAAUUUGCAACAAAUUAAAGGCCAAUUAACCCAUCAGACGGGCUUAUGAGCCGCCGACCGCAAAUGCAC_CGCACACACGCAAUU
........(((((.((((((...))))))...(((((..((((((.......))).))))).)))....)))))...(((............)))... (-18.58 = -18.78 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:56 2006