Locus 5651

Sequence ID	2R_DroMel_CAF1
Location	17,954,456 – 17,954,599
Length	143
Max. P	0.918242

overview

Window 8

Location	17,954,456 – 17,954,559
Length	103
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-32.25
Consensus MFE	-26.89
Energy contribution	-27.20
Covariance contribution	0.31
Combinations/Pair	1.08
Mean z-score	-2.13
Structure conservation index	0.83
SVM decision value	1.12
SVM RNA-class probability	0.918242
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17954456 103 + 20766785
UUUCUCUCAUUCUCAUUCAUUCAUUCGAUUGUCGCUGGCUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGA
.........................((((((..(((((((.(.(((((((..((((((((......))))))))))))----))).).)))..)))).))))))... ( -31.20)
>DroSec_CAF1 11723 103 + 1
UUUCCCUCAUUCUCAUUCAUUCAUUCGAUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGA
......................(((.((((..((((.(((...(((((((..((((((((......))))))))))))----))))))))))..)))).)))..... ( -31.70)
>DroSim_CAF1 7457 103 + 1
UUUCCCUCAUUCUCAUUCAUUCAUUCGAUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGA
......................(((.((((..((((.(((...(((((((..((((((((......))))))))))))----))))))))))..)))).)))..... ( -31.70)
>DroEre_CAF1 16440 97 + 1
UUUCUC------UCAUUCAUUCAUUCGAUUGUCGCUGGCUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGCGGGCGGCAGUGGC----GUUCAGCUGCGA
......------..............((.((((((((.(.....((((((..((((((((......))))))))))))))..).)))))))----).))........ ( -34.40)
>consensus
UUUCCCUCAUUCUCAUUCAUUCAUUCGAUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC____GGUAGUGGCGGUAGUUCAGUUGCGA
............................((((.(((((...(.(((((((..((((((((......))))))))..)...........)))))).).))))).)))) (-26.89 = -27.20 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	17,954,483 – 17,954,599
Length	116
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.35
Mean single sequence MFE	-37.70
Consensus MFE	-31.14
Energy contribution	-31.70
Covariance contribution	0.56
Combinations/Pair	1.06
Mean z-score	-2.43
Structure conservation index	0.83
SVM decision value	0.92
SVM RNA-class probability	0.881732
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17954483 116 + 20766785
AUUGUCGCUGGCUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGACUUUCCCACAAUCAAUUCAAUUGCAUUAAAAAGUCACUUC
........((((((..(((((((..((((((((......))))))))))))----))).((((.((.((((.......)))).)))))).....................)))))).... ( -34.40)
>DroSec_CAF1 11750 116 + 1
AUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGACUUUGCCACAAUCAAUUCAAUUGCAUUAAAAAGUCACUUC
........((((((..(((((((..((((((((......))))))))))))----))).(((((((.((((.......))))))))))).....................)))))).... ( -38.50)
>DroSim_CAF1 7484 116 + 1
AUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC----GGUAGUGGCGGUAGUUCAGUUGCGACUUUGCCACAAUCAAUUCAAUUGCAUUAAAAAGUCACUUC
........((((((..(((((((..((((((((......))))))))))))----))).(((((((.((((.......))))))))))).....................)))))).... ( -38.50)
>DroEre_CAF1 16461 116 + 1
AUUGUCGCUGGCUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGCGGGCGGCAGUGGC----GUUCAGCUGCGACUGUGCCACAAUCAAUUCAAUUGCAUUAAAAAGUCACUUC
........((((((....(((((..((((((((......)))))))))))))((((.((((.((----(......))).)))))))).......................)))))).... ( -39.40)
>consensus
AUUGUCGCUGACUUCAAUCGCCUUUCAUCAGCUUUCAUCGGCUGAUGGGGC____GGUAGUGGCGGUAGUUCAGUUGCGACUUUGCCACAAUCAAUUCAAUUGCAUUAAAAAGUCACUUC
(((((((((.(((......((((..((((((((......))))))))))))....))))))))))))...........((((((....((((.......))))......))))))..... (-31.14 = -31.70 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	17,954,483 – 17,954,599
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.35
Mean single sequence MFE	-33.65
Consensus MFE	-29.08
Energy contribution	-29.32
Covariance contribution	0.25
Combinations/Pair	1.04
Mean z-score	-1.60
Structure conservation index	0.86
SVM decision value	0.17
SVM RNA-class probability	0.614712
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17954483 116 - 20766785
GAAGUGACUUUUUAAUGCAAUUGAAUUGAUUGUGGGAAAGUCGCAACUGAACUACCGCCACUACC----GCCCCAUCAGCCGAUGAAAGCUGAUGAAAGGCGAUUGAAGCCAGCGACAAU
...((((((((((...((((((.....)))))).))))))))))....................(----((..(((((((........)))))))...(((.......))).)))..... ( -34.60)
>DroSec_CAF1 11750 116 - 1
GAAGUGACUUUUUAAUGCAAUUGAAUUGAUUGUGGCAAAGUCGCAACUGAACUACCGCCACUACC----GCCCCAUCAGCCGAUGAAAGCUGAUGAAAGGCGAUUGAAGUCAGCGACAAU
...((((((((....(((((((.....)))))))..))))))))...........(((.(((.((----(((.(((((((........)))))))...))))...).)))..)))..... ( -32.90)
>DroSim_CAF1 7484 116 - 1
GAAGUGACUUUUUAAUGCAAUUGAAUUGAUUGUGGCAAAGUCGCAACUGAACUACCGCCACUACC----GCCCCAUCAGCCGAUGAAAGCUGAUGAAAGGCGAUUGAAGUCAGCGACAAU
...((((((((....(((((((.....)))))))..))))))))...........(((.(((.((----(((.(((((((........)))))))...))))...).)))..)))..... ( -32.90)
>DroEre_CAF1 16461 116 - 1
GAAGUGACUUUUUAAUGCAAUUGAAUUGAUUGUGGCACAGUCGCAGCUGAAC----GCCACUGCCGCCCGCCCCAUCAGCCGAUGAAAGCUGAUGAAAGGCGAUUGAAGCCAGCGACAAU
...((.((...(((((........)))))..)).))...(((((.(((...(----(((...((.....))..(((((((........)))))))...)))).....)))..)))))... ( -34.20)
>consensus
GAAGUGACUUUUUAAUGCAAUUGAAUUGAUUGUGGCAAAGUCGCAACUGAACUACCGCCACUACC____GCCCCAUCAGCCGAUGAAAGCUGAUGAAAGGCGAUUGAAGCCAGCGACAAU
...((((((((....(((((((.....)))))))..))))))))...........(((...............(((((((........)))))))...(((.......))).)))..... (-29.08 = -29.32 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:51:03 2006