Locus 5227

Sequence ID	2L_DroMel_CAF1
Location	14,769,809 – 14,769,969
Length	160
Max. P	0.969733

overview

Window 9

Location	14,769,809 – 14,769,929
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.33
Mean single sequence MFE	-29.55
Consensus MFE	-27.04
Energy contribution	-27.26
Covariance contribution	0.23
Combinations/Pair	1.06
Mean z-score	-2.36
Structure conservation index	0.92
SVM decision value	1.12
SVM RNA-class probability	0.918397
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14769809 120 + 22407834
AAUAAUGUUCCUCUUCUGAAUUAGCUUUCAAUGUGGUAUUUUCCACAUCGAAAUUAUUUUGCAGAUCCCAUGUUUUGGGAGAUUUUUCACCGUUGCGGUACUGUCGCCAUACUGAAAGAA
..............((((...(((.((((.((((((......)))))).))))))).....))))(((((.....)))))..(((((((..((.((((.....)))).))..))))))). ( -30.10)
>DroSec_CAF1 16330 120 + 1
AAUAAUAUUAAUCUUAUGAAUUAGCAUUCAAUGUGGUAUUUUCCACAUCGAAAUUAUUUUGCAAAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGA
.......................((((((.((((((......)))))).))).......)))...(((((.....)))))..(((((((....((((((......)))))).))))))). ( -28.31)
>DroSim_CAF1 14039 120 + 1
AAUAAUAUUAAUCUUCUGAAUUAGCAUUCAAUGUGGUAUUUUCCACAUCGAAAUUAUUUUGCAGAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGA
..............((((........(((.((((((......)))))).))).........))))(((((.....)))))..(((((((....((((((......)))))).))))))). ( -30.23)
>consensus
AAUAAUAUUAAUCUUCUGAAUUAGCAUUCAAUGUGGUAUUUUCCACAUCGAAAUUAUUUUGCAGAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGA
..............((((........(((.((((((......)))))).))).........))))(((((.....)))))..(((((((....((((((......)))))).))))))). (-27.04 = -27.26 +   0.23)

alignment

secondary structure

dotplot

Window 0

Location	14,769,809 – 14,769,929
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.33
Mean single sequence MFE	-29.45
Consensus MFE	-26.57
Energy contribution	-26.47
Covariance contribution	-0.11
Combinations/Pair	1.07
Mean z-score	-3.03
Structure conservation index	0.90
SVM decision value	1.65
SVM RNA-class probability	0.969733
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14769809 120 - 22407834
UUCUUUCAGUAUGGCGACAGUACCGCAACGGUGAAAAAUCUCCCAAAACAUGGGAUCUGCAAAAUAAUUUCGAUGUGGAAAAUACCACAUUGAAAGCUAAUUCAGAAGAGGAACAUUAUU
((((((.....(((((.((((((((...))))).......(((((.....))))).)))).......(((((((((((......))))))))))))))).....)))))).......... ( -33.10)
>DroSec_CAF1 16330 120 - 1
UCCUUUCAGUAUGGCGACAGUACCACAAAAGUGAAAGAUCUCCCAAAACUUGGGAUUUGCAAAAUAAUUUCGAUGUGGAAAAUACCACAUUGAAUGCUAAUUCAUAAGAUUAAUAUUAUU
..((((((.(.(((........)))....).))))))...........(((((((((.(((.......((((((((((......))))))))))))).))))).))))............ ( -26.41)
>DroSim_CAF1 14039 120 - 1
UCCUUUCAGUAUGGCGACAGUACCACAAAAGUGAAAGAUCUCCCAAAACUUGGGAUCUGCAAAAUAAUUUCGAUGUGGAAAAUACCACAUUGAAUGCUAAUUCAGAAGAUUAAUAUUAUU
..((((((.(.(((........)))....).))))))((((((((.....)))))((((.........((((((((((......))))))))))........)))).))).......... ( -28.83)
>consensus
UCCUUUCAGUAUGGCGACAGUACCACAAAAGUGAAAGAUCUCCCAAAACUUGGGAUCUGCAAAAUAAUUUCGAUGUGGAAAAUACCACAUUGAAUGCUAAUUCAGAAGAUUAAUAUUAUU
..((((.....(((((.(((...(((....))).......(((((.....))))).))))........((((((((((......)))))))))).)))).....))))............ (-26.57 = -26.47 +  -0.11)

alignment

secondary structure

dotplot

Window 1

Location	14,769,849 – 14,769,969
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-30.27
Consensus MFE	-28.99
Energy contribution	-28.67
Covariance contribution	-0.33
Combinations/Pair	1.09
Mean z-score	-1.44
Structure conservation index	0.96
SVM decision value	-0.03
SVM RNA-class probability	0.516316
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14769849 120 + 22407834
UUCCACAUCGAAAUUAUUUUGCAGAUCCCAUGUUUUGGGAGAUUUUUCACCGUUGCGGUACUGUCGCCAUACUGAAAGAAUAAAAUCGGUGUGACUCAGGACAUCCGUAUAAACGCUUGC
...((((((((..(((((((.(((.(((((.....)))))(((.....((((...))))...)))......)))..)))))))..)))))))).....((....)).............. ( -30.30)
>DroSec_CAF1 16370 120 + 1
UUCCACAUCGAAAUUAUUUUGCAAAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGAUAAAAUCGGUGUGACUCAGAACAUCCGUAUAAAUGCUUGC
...((((((((..(((((.......(((((.....)))))...((((((....((((((......)))))).)))))))))))..))))))))........................... ( -29.40)
>DroSim_CAF1 14079 120 + 1
UUCCACAUCGAAAUUAUUUUGCAGAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGAUAAAAUCGGUGUGACUCAGAACAUCCGUAUAAACGCUUGC
...((((((((..(((((.......(((((.....)))))...((((((....((((((......)))))).)))))))))))..))))))))........((..(((....)))..)). ( -31.10)
>consensus
UUCCACAUCGAAAUUAUUUUGCAGAUCCCAAGUUUUGGGAGAUCUUUCACUUUUGUGGUACUGUCGCCAUACUGAAAGGAUAAAAUCGGUGUGACUCAGAACAUCCGUAUAAACGCUUGC
...((((((((..(((((.......(((((.....)))))...((((((....((((((......)))))).)))))))))))..))))))))........((..(((....)))..)). (-28.99 = -28.67 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:09 2006