Locus 2473

Sequence ID	X_DroMel_CAF1
Location	6,590,340 – 6,590,484
Length	144
Max. P	0.941823

overview

Window 0

Location	6,590,340 – 6,590,453
Length	113
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.45
Mean single sequence MFE	-35.59
Consensus MFE	-25.46
Energy contribution	-26.84
Covariance contribution	1.38
Combinations/Pair	1.07
Mean z-score	-2.25
Structure conservation index	0.72
SVM decision value	1.32
SVM RNA-class probability	0.941823
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6590340 113 + 22224390
AAUCGGCUGGCGAUCAAAAAUAAGACUGCGGAUCAAACCGGUCGAAGGAGGCGGUGCUCCACCGCUCACCACUCACCGAUGGCCACUGACCAGUGACCACUCACCACUAA-------CCA
..((((.((((.(((........(((((.(.......))))))...((.(((((((...)))))))..)).......))).))))))))...((((....))))......-------... ( -35.70)
>DroSec_CAF1 6022 110 + 1
AAUCGGCCGGCGAUCAAAAAUAAGACUGCGGAUCAAACCGGUCGAAGGAGGCGGUACUCCACCGCUCACCACUCACCGAUGGCCACUGACCAGUGGCCAGUGACCACUCA----------
..((((((((.((((...............))))...))))))))..((((((((.....))))).......((((...((((((((....))))))))))))...))).---------- ( -43.86)
>DroEre_CAF1 6145 119 + 1
AAUCGGCCGGCGAUCAACAAUAAGACUGCGGAUCAAACCGGUCGA-GAAGGCGGUGCUCCACCGCUCACCACUGACCACUGACCACUGACCAGUCACCAGCCACCACUCACCACUGACCA
..((((((((.((((..((.......))..))))...))))))))-((.(((((((...))))))).....(((...((((.........))))...))).......))........... ( -32.70)
>DroYak_CAF1 5216 99 + 1
AAUCGGCCGGCGAUCAAAAAUAAGACUGCGGAUCAAACCGGUCGG-GAAGGCGUUGCUCCACCGCUCACCACUGACCACUGGCCACUGGCCA----CCAACCA---C-------------
....((((((.(..((.............((......))((((((-...((.(..((......)).).)).))))))..))..).)))))).----.......---.------------- ( -30.10)
>consensus
AAUCGGCCGGCGAUCAAAAAUAAGACUGCGGAUCAAACCGGUCGA_GAAGGCGGUGCUCCACCGCUCACCACUCACCAAUGGCCACUGACCAGUGACCAGCCACCACUCA__________
..((((((((.((((...............))))...)))))))).(..(((((((...)))))))..)..........(((.((((....)))).)))..................... (-25.46 = -26.84 +   1.38)

alignment

secondary structure

dotplot

Window 1

Location	6,590,340 – 6,590,453
Length	113
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.45
Mean single sequence MFE	-44.62
Consensus MFE	-32.05
Energy contribution	-32.68
Covariance contribution	0.63
Combinations/Pair	1.19
Mean z-score	-1.55
Structure conservation index	0.72
SVM decision value	0.08
SVM RNA-class probability	0.572819
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6590340 113 - 22224390
UGG-------UUAGUGGUGAGUGGUCACUGGUCAGUGGCCAUCGGUGAGUGGUGAGCGGUGGAGCACCGCCUCCUUCGACCGGUUUGAUCCGCAGUCUUAUUUUUGAUCGCCAGCCGAUU
.((-------(...(((((((((((((((....)))))))))(((((((.((.(.((((((...))))))).))))).)))).........................))))))))).... ( -43.40)
>DroSec_CAF1 6022 110 - 1
----------UGAGUGGUCACUGGCCACUGGUCAGUGGCCAUCGGUGAGUGGUGAGCGGUGGAGUACCGCCUCCUUCGACCGGUUUGAUCCGCAGUCUUAUUUUUGAUCGCCGGCCGAUU
----------....((((((((((((...))))))))))))(((((...((((((.((((((....)))))......((((((......)))..)))........).))))))))))).. ( -46.20)
>DroEre_CAF1 6145 119 - 1
UGGUCAGUGGUGAGUGGUGGCUGGUGACUGGUCAGUGGUCAGUGGUCAGUGGUGAGCGGUGGAGCACCGCCUUC-UCGACCGGUUUGAUCCGCAGUCUUAUUGUUGAUCGCCGGCCGAUU
((..((((.(..(((....)))..).))))..)).(((((.((((((((..((((((.(((((..((((.....-.....))))....))))).).)))))..)))))))).)))))... ( -48.50)
>DroYak_CAF1 5216 99 - 1
-------------G---UGGUUGG----UGGCCAGUGGCCAGUGGUCAGUGGUGAGCGGUGGAGCAACGCCUUC-CCGACCGGUUUGAUCCGCAGUCUUAUUUUUGAUCGCCGGCCGAUU
-------------.---(((((((----(((((...))))...((((((..((((((.(((((.(((.(((...-......)))))).))))).).)))))..))))))))))))))... ( -40.40)
>consensus
__________UGAGUGGUGACUGGUCACUGGUCAGUGGCCAGCGGUCAGUGGUGAGCGGUGGAGCACCGCCUCC_UCGACCGGUUUGAUCCGCAGUCUUAUUUUUGAUCGCCGGCCGAUU
...................((((((.....))))))((((.((((((((..((((((.(((((.....(((..........)))....))))).).)))))..)))))))).)))).... (-32.05 = -32.68 +   0.63)

alignment

secondary structure

dotplot

Window 2

Location	6,590,380 – 6,590,484
Length	104
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	72.82
Mean single sequence MFE	-26.16
Consensus MFE	-16.14
Energy contribution	-18.70
Covariance contribution	2.56
Combinations/Pair	1.05
Mean z-score	-1.74
Structure conservation index	0.62
SVM decision value	0.83
SVM RNA-class probability	0.861529
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6590380 104 + 22224390
GUCGAAGGAGGCGGUGCUCCACCGCUCACCACUCACCGAUGGCCACUGACCAGUGACCACUCACCACUAA-------CCAU--AC-------CACUCAGCAAAUCCUGCGGCAAAUCCGA
((((.(((((((((((...)))))))...........(((((.((((....)))).))).))........-------....--..-------...........)))).))))........ ( -29.20)
>DroSec_CAF1 6062 99 + 1
GUCGAAGGAGGCGGUACUCCACCGCUCACCACUCACCGAUGGCCACUGACCAGUGGCCAGUGACCACUCA--------------C-------CACUUACCAAAUCCUGCGGCAAAUCCGA
((((.((((((((((.....))))))......((((...((((((((....)))))))))))).......--------------.-------...........)))).))))........ ( -36.00)
>DroEre_CAF1 6185 119 + 1
GUCGA-GAAGGCGGUGCUCCACCGCUCACCACUGACCACUGACCACUGACCAGUCACCAGCCACCACUCACCACUGACCACUGACCACCCAUCAUCCACCAAAUCCUGCGACAAAUCCGA
(((((-(..(((((((...))))))).............(((....((..((((...(((.............)))...))))..))....)))...........)).))))........ ( -20.32)
>DroYak_CAF1 5256 84 + 1
GUCGG-GAAGGCGUUGCUCCACCGCUCACCACUGACCACUGGCCACUGGCCA----CCAACCA---C----------------------------UCACCAAAUCCUGCGGCAAAUCCCA
...((-((.((.......)).(((((((....)))....(((((...)))))----.......---.----------------------------............))))....)))). ( -19.10)
>consensus
GUCGA_GAAGGCGGUGCUCCACCGCUCACCACUCACCAAUGGCCACUGACCAGUGACCAGCCACCACUCA______________C_______CACUCACCAAAUCCUGCGGCAAAUCCGA
((((.(((((((((((...))))))).............(((.((((....)))).)))............................................)))).))))........ (-16.14 = -18.70 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:39 2006