Locus 987

Sequence ID	3R_DroMel_CAF1
Location	3,166,781 – 3,166,935
Length	154
Max. P	0.760994

overview

Window 5

Location	3,166,781 – 3,166,895
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-31.93
Consensus MFE	-30.22
Energy contribution	-30.67
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.95
SVM decision value	0.16
SVM RNA-class probability	0.610439
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3166781 114 + 27905053
GUUACAGUUUCUAAUUUAUGACAAAUGCACAUGCCCGUCUUGAAGUUUUUGGCCUGGCCAGAAACUCGGCUCAAAU------CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUU
...................(((....((....))..)))((((((((((((((...))))))))))....))))..------.(((.(((((((.......))))))).)))........ ( -30.80)
>DroSec_CAF1 14862 114 + 1
GUUACAGUUUCUAAUUUAUGACAAAUGCACAUGCCCGUCUUGAAGUUUUUGGCCUGACCAGAAACUCGGCUGAAAU------CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUU
....(((((.....((((.(((....((....))..))).))))((((((((.....))))))))..)))))....------.(((.(((((((.......))))))).)))........ ( -32.30)
>DroEre_CAF1 6503 120 + 1
GUUACAGUUUCUAAUUUAUGACAAAUGCACAUGCCCGUCUUGAAGUUUUUGGCCUGGCCAGAAACUGAGCUGAAAUCCGAAACUGGACUGGACCGAGCUCAGGUCCCGCCCACCUCCAUU
(((.(((((((....(((.(((....((....))..))).)))((((((((((...))))))))))............)))))))))).(((((.......))))).............. ( -32.70)
>consensus
GUUACAGUUUCUAAUUUAUGACAAAUGCACAUGCCCGUCUUGAAGUUUUUGGCCUGGCCAGAAACUCGGCUGAAAU______CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUU
....(((((.....((((.(((....((....))..))).))))((((((((.....))))))))..)))))...........(((.(((((((.......))))))).)))........ (-30.22 = -30.67 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	3,166,781 – 3,166,895
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-38.83
Consensus MFE	-34.09
Energy contribution	-34.20
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.88
SVM decision value	0.23
SVM RNA-class probability	0.646087
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3166781 114 - 27905053
AAUGGAGGUGGGCUGGACCUGGGCUUGGUCCAGUCCAG------AUUUGAGCCGAGUUUCUGGCCAGGCCAAAAACUUCAAGACGGGCAUGUGCAUUUGUCAUAAAUUAGAAACUGUAAC
..(((((.(((((((((((.......))))))))))).------.((((.(((..((.....))..)))))))..))))).((((.((....))...))))................... ( -39.40)
>DroSec_CAF1 14862 114 - 1
AAUGGAGGUGGGCUGGACCUGGGCUUGGUCCAGUCCAG------AUUUCAGCCGAGUUUCUGGUCAGGCCAAAAACUUCAAGACGGGCAUGUGCAUUUGUCAUAAAUUAGAAACUGUAAC
..(((((.(((((((((((.......))))))))))).------.)))))....(((((((((.....))...........((((.((....))...)))).......)))))))..... ( -38.50)
>DroEre_CAF1 6503 120 - 1
AAUGGAGGUGGGCGGGACCUGAGCUCGGUCCAGUCCAGUUUCGGAUUUCAGCUCAGUUUCUGGCCAGGCCAAAAACUUCAAGACGGGCAUGUGCAUUUGUCAUAAAUUAGAAACUGUAAC
..(((((.(((((.(((((.......))))).))))).)))))..........(((((((((((...)))...........((((.((....))...)))).......)))))))).... ( -38.60)
>consensus
AAUGGAGGUGGGCUGGACCUGGGCUUGGUCCAGUCCAG______AUUUCAGCCGAGUUUCUGGCCAGGCCAAAAACUUCAAGACGGGCAUGUGCAUUUGUCAUAAAUUAGAAACUGUAAC
........(((((((((((.......))))))))))).................((((((((((...)))...........((((.((....))...)))).......)))))))..... (-34.09 = -34.20 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	3,166,821 – 3,166,935
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-40.97
Consensus MFE	-38.15
Energy contribution	-38.27
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.80
Structure conservation index	0.93
SVM decision value	0.50
SVM RNA-class probability	0.760994
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3166821 114 + 27905053
UGAAGUUUUUGGCCUGGCCAGAAACUCGGCUCAAAU------CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUUUGUGUAUCGUCACUCGAGGAAACUUAUUGGGCGAUGGGUU
.((.(((((((((...)))))))))))(((((....------.(((.(((((((.......))))))).))).............((((((....(((....)))....))))))))))) ( -42.60)
>DroSec_CAF1 14902 114 + 1
UGAAGUUUUUGGCCUGACCAGAAACUCGGCUGAAAU------CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUUUGUGUAUCGUCACUCGAGGAAACUUAUUGGGCGAUGGGUU
.((.((((((((.....))))))))))(((((..((------((((.((......)).)))))).)))))(((........)))(((((((....(((....)))....))))))).... ( -39.30)
>DroEre_CAF1 6543 120 + 1
UGAAGUUUUUGGCCUGGCCAGAAACUGAGCUGAAAUCCGAAACUGGACUGGACCGAGCUCAGGUCCCGCCCACCUCCAUUUGUGUAUCGUCACUCGAGGAAACUUAUUGGGCGAUGGGUU
...((((((((((...)))))))))).......((((((..........(((((.......)))))((((((.........(((......)))..(((....)))..)))))).)))))) ( -41.00)
>consensus
UGAAGUUUUUGGCCUGGCCAGAAACUCGGCUGAAAU______CUGGACUGGACCAAGCCCAGGUCCAGCCCACCUCCAUUUGUGUAUCGUCACUCGAGGAAACUUAUUGGGCGAUGGGUU
...(((((((((.....))))))))).((((............(((.(((((((.......))))))).)))............(((((((....(((....)))....))))))))))) (-38.15 = -38.27 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:39 2006