Locus 4342

Sequence ID	2L_DroMel_CAF1
Location	12,453,995 – 12,454,155
Length	160
Max. P	0.954444

overview

Window 0

Location	12,453,995 – 12,454,115
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-40.73
Consensus MFE	-37.24
Energy contribution	-37.80
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.90
Structure conservation index	0.91
SVM decision value	0.35
SVM RNA-class probability	0.701776
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12453995 120 - 22407834
UCAUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUUGGUGGUGCAAAUCGAUAUCCUUCGGGCACUUCCGGAUUUAAUUUGAUAAAAGAUCCGGUGGCC
.....(((((((.((((((.((.......)).))))))((((((((...)))))))).)))))))....(((......)))(((....((((((((...........))))))))..))) ( -43.00)
>DroSec_CAF1 26777 118 - 1
UCGUCGCAC-ACAG-GGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUCGGGCACUUCCGGAUUUAUUUUGAUGAAAGAACCGGUGGCC
.....((.(-((..-((.((.....((((((.((((..((((((((...))))))))((.(((((...((((......))))))))).))))))..))))))......)).)).))))). ( -36.80)
>DroSim_CAF1 26193 120 - 1
UCGUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUCGGGCACUUCCGGAUUUAUUUUGAUGAAAGAACCGGUGGCC
.....(((((((.((((((.((.......)).))))))((((((((...)))))))).)))))))....(((......)))(((....((((.(((.(((....))).)))))))..))) ( -42.40)
>consensus
UCGUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUCGGGCACUUCCGGAUUUAUUUUGAUGAAAGAACCGGUGGCC
.....(((((((.((((((.((.......)).))))))((((((((...)))))))).)))))))....(((......)))(((....((((.(((.((.....)).))).))))..))) (-37.24 = -37.80 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	12,454,035 – 12,454,155
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	85.00
Mean single sequence MFE	-29.97
Consensus MFE	-27.83
Energy contribution	-28.50
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-0.82
Structure conservation index	0.93
SVM decision value	0.06
SVM RNA-class probability	0.563262
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12454035 120 + 22407834
GAAGGAUAUCGAUUUGCACCACCAAAGCAAGAGACUUGCUUCAAGGACGAUUCUAGUCACGAUCCCCUGUGGUGCGAUGAGCAAAUUCUCUCCUCGAAUUUUGAGUGCAAUGGCCUAAUA
..(((((.((((.(((((((((..(((((((...)))))))..(((..((((........)))).)))))))))))).(((......)))...))))))))).((.((....)))).... ( -29.30)
>DroSec_CAF1 26817 118 + 1
GAAGGAUAUCGAUUUGCACCACCGAAGCAAGAGACUUGCUUCAAGGACGAUUCUAGUCACGAUCC-CUGU-GUGCGACGAGCAAAUUCUCUCCUCGANNNNNNNNNNNNNNNNNNNNNNN
((.(((.......((((((((..((((((((...))))))))...(((.......))).......-.)).-)))))).(((......))))))))......................... ( -25.30)
>DroSim_CAF1 26233 120 + 1
GAAGGAUAUCGAUUUGCACCACCGAAGCAAGAGACUUGCUUCAAGGACGAUUCUAGUCACGAUCCCCUGUGGUGCGACGAGCAAAUUCUCUCCUCGAAUUUUGAGUGCAAUGGCCUAAUA
..(((...(((..(((((((((.((((((((...)))))))).(((..((((........)))).)))))))))))))))((((((((.......))))).....))).....))).... ( -35.30)
>consensus
GAAGGAUAUCGAUUUGCACCACCGAAGCAAGAGACUUGCUUCAAGGACGAUUCUAGUCACGAUCCCCUGUGGUGCGACGAGCAAAUUCUCUCCUCGAAUUUUGAGUGCAAUGGCCUAAUA
((.(((.......(((((((((.((((((((...))))))))...(((.......)))..........))))))))).(((......))))))))......................... (-27.83 = -28.50 +   0.67)

alignment

secondary structure

dotplot

Window 2

Location	12,454,035 – 12,454,155
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	85.00
Mean single sequence MFE	-34.40
Consensus MFE	-33.09
Energy contribution	-33.53
Covariance contribution	0.45
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.96
SVM decision value	1.44
SVM RNA-class probability	0.954444
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12454035 120 - 22407834
UAUUAGGCCAUUGCACUCAAAAUUCGAGGAGAGAAUUUGCUCAUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUUGGUGGUGCAAAUCGAUAUCCUUC
......((....))...........((((((((......)))...(((((((.((((((.((.......)).))))))((((((((...)))))))).))))))).........))))). ( -34.90)
>DroSec_CAF1 26817 118 - 1
NNNNNNNNNNNNNNNNNNNNNNNUCGAGGAGAGAAUUUGCUCGUCGCAC-ACAG-GGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUC
.........................((((((((......)))...((((-((((-((((.((.......)).))))))((((((((...)))))))).)).)))).........))))). ( -30.00)
>DroSim_CAF1 26233 120 - 1
UAUUAGGCCAUUGCACUCAAAAUUCGAGGAGAGAAUUUGCUCGUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUC
....(((..((((............((.(((........))).))(((((((.((((((.((.......)).))))))((((((((...)))))))).)))))))....))))..))).. ( -38.30)
>consensus
UAUUAGGCCAUUGCACUCAAAAUUCGAGGAGAGAAUUUGCUCGUCGCACCACAGGGGAUCGUGACUAGAAUCGUCCUUGAAGCAAGUCUCUUGCUUCGGUGGUGCAAAUCGAUAUCCUUC
.........................((((((((......)))...(((((((.((((((.((.......)).))))))((((((((...)))))))).))))))).........))))). (-33.09 = -33.53 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:30 2006