Locus 1326

Sequence ID	2R_DroMel_CAF1
Location	5,137,533 – 5,137,635
Length	102
Max. P	0.996079

overview

Window 9

Location	5,137,533 – 5,137,635
Length	102
Sequences	4
Columns	102
Reading direction	forward
Mean pairwise identity	94.61
Mean single sequence MFE	-37.45
Consensus MFE	-35.04
Energy contribution	-35.35
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.63
Structure conservation index	0.94
SVM decision value	2.13
SVM RNA-class probability	0.988562
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5137533 102 + 20766785
UGAUGCAUAAUGAUAUGGGACGCGAGACGCGUCCCAUUACCCACACGCAGGGAACAGGGAGCAGGACAUCUAGAGCUGGAGAGCUAAGUCCUGGCCAUUAGA
..............((((((((((...))))))))))..(((.......))).....((..((((((......((((....))))..)))))).))...... ( -35.60)
>DroSec_CAF1 13465 102 + 1
UGAUGCAUAAUGAUAUGGGACGCGAGACGCGUCCCAUUACCCACACGCAGGGAACAGGGAGCAGGACAUCUAGAGCUGGAGAGCUAAGUCCUGGCCAUUAGA
..............((((((((((...))))))))))..(((.......))).....((..((((((......((((....))))..)))))).))...... ( -35.60)
>DroEre_CAF1 12302 102 + 1
UGAUGCAUAAUGAUAUGGGACGCGGGACGCGUCCCAUUACCCACACGCAGGGAACUGGGCUCAGGACAACUAGAGCUCGAGAGCUAAGUCCUGGCCAUUAUA
.........(((((((((((((((...))))))))))..........(((....)))(((.((((((......((((....))))..)))))))))))))). ( -40.50)
>DroYak_CAF1 13299 102 + 1
UGAUGCAUAGUGAUAUGGGACGCGAGACGCGUCCCAUUACCCACACGCAGGGAACAGGGCUCAGGACAUCUAGAGCUGAAGAGCUAAGUUCUGGCCAUUAUA
...(((...(((..((((((((((...))))))))))....)))..)))(....)..(((.((((((......((((....))))..)))))))))...... ( -38.10)
>consensus
UGAUGCAUAAUGAUAUGGGACGCGAGACGCGUCCCAUUACCCACACGCAGGGAACAGGGAGCAGGACAUCUAGAGCUGGAGAGCUAAGUCCUGGCCAUUAGA
..............((((((((((...))))))))))..(((.......))).....(((.((((((......((((....))))..)))))))))...... (-35.04 = -35.35 +   0.31)

alignment

secondary structure

dotplot

Window 0

Location	5,137,533 – 5,137,635
Length	102
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	94.61
Mean single sequence MFE	-38.30
Consensus MFE	-36.91
Energy contribution	-37.47
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-3.27
Structure conservation index	0.96
SVM decision value	2.65
SVM RNA-class probability	0.996079
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5137533 102 - 20766785
UCUAAUGGCCAGGACUUAGCUCUCCAGCUCUAGAUGUCCUGCUCCCUGUUCCCUGCGUGUGGGUAAUGGGACGCGUCUCGCGUCCCAUAUCAUUAUGCAUCA
......((.((((((..((((....))))......))))))..))........((((((..((((.(((((((((...)))))))))))))..))))))... ( -36.80)
>DroSec_CAF1 13465 102 - 1
UCUAAUGGCCAGGACUUAGCUCUCCAGCUCUAGAUGUCCUGCUCCCUGUUCCCUGCGUGUGGGUAAUGGGACGCGUCUCGCGUCCCAUAUCAUUAUGCAUCA
......((.((((((..((((....))))......))))))..))........((((((..((((.(((((((((...)))))))))))))..))))))... ( -36.80)
>DroEre_CAF1 12302 102 - 1
UAUAAUGGCCAGGACUUAGCUCUCGAGCUCUAGUUGUCCUGAGCCCAGUUCCCUGCGUGUGGGUAAUGGGACGCGUCCCGCGUCCCAUAUCAUUAUGCAUCA
......(((((((((..((((....))))......)))))).)))........((((((..((((.(((((((((...)))))))))))))..))))))... ( -43.00)
>DroYak_CAF1 13299 102 - 1
UAUAAUGGCCAGAACUUAGCUCUUCAGCUCUAGAUGUCCUGAGCCCUGUUCCCUGCGUGUGGGUAAUGGGACGCGUCUCGCGUCCCAUAUCACUAUGCAUCA
......((((((.((..((((....))))......)).))).)))........(((((((((...((((((((((...)))))))))).)))).)))))... ( -36.60)
>consensus
UAUAAUGGCCAGGACUUAGCUCUCCAGCUCUAGAUGUCCUGAGCCCUGUUCCCUGCGUGUGGGUAAUGGGACGCGUCUCGCGUCCCAUAUCAUUAUGCAUCA
......(((((((((..((((....))))......)))))).)))........(((((((((...((((((((((...)))))))))).)))).)))))... (-36.91 = -37.47 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:17 2006