Locus 4159

Sequence ID	2L_DroMel_CAF1
Location	11,959,241 – 11,959,377
Length	136
Max. P	0.979545

overview

Window 3

Location	11,959,241 – 11,959,341
Length	100
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.40
Mean single sequence MFE	-22.27
Consensus MFE	-7.40
Energy contribution	-7.64
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-1.68
Structure conservation index	0.33
SVM decision value	-0.04
SVM RNA-class probability	0.511406
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11959241 100 + 22407834
GGCAGUAAUG-------AAAUGUCUGGCAUUUCGUCCGUUUCCAUCAGCUAACC---AACCAA----------CCAACUGCCAACUCCAAGCUGACCACUCUUAACGGCCAGCUAGCAAU
((((((.(((-------(((((.....))))))))..(((......))).....---......----------...)))))).......(((((.((.........)).)))))...... ( -24.90)
>DroSec_CAF1 178616 92 + 1
GUCAGUAAUG-------AAAUGUCUGGCAUUUCGUCCGUUUCCAUCAGCUAAC---------------------CAACUGCCCACUUCAAGCUGACGACUCUCAACGGCCAGCUACCAAU
((((((..((-------((.((...((((.((.((..(((......)))..))---------------------.)).)))))).)))).))))))..........((.......))... ( -17.50)
>DroSim_CAF1 145059 92 + 1
GUCAGUAAUG-------AAAUGUCUGGCAUUUCGUCCGUUUCCAUCAGCUAAC---------------------CAACUGCCCACUUCAAGCUGACGACUCUCAACGGCCAGCUACCAAU
((((((..((-------((.((...((((.((.((..(((......)))..))---------------------.)).)))))).)))).))))))..........((.......))... ( -17.50)
>DroEre_CAF1 153578 84 + 1
GGCAGUAAUG-------AAAUGGCUGGCAUUUAGUCCGUUUCCAUCAGCUA-----CAGCUAC----------CCAACUGCCAACUCCAAG--------------CCGCCAGCUCCCAAU
((((((...(-------(((((((((.....))).)))))))....(((..-----..)))..----------...)))))).......((--------------(.....)))...... ( -21.80)
>DroYak_CAF1 149339 111 + 1
GGCAGUAAUGUCGGGCAAAAUGUCCGGCAUUUCGUCCGUUUCCAUCAGCUAUCCAACAGCCAAGUGCCAACUGCCAACUGCUAACUUCAAA---------CUGAACUGCCAGCUCCCAAU
((((((((((((((((.....)))))))))).............((((.........(((..(((((.....))..)))))).........---------)))))))))).......... ( -29.67)
>consensus
GGCAGUAAUG_______AAAUGUCUGGCAUUUCGUCCGUUUCCAUCAGCUAAC____A_C_A___________CCAACUGCCAACUUCAAGCUGAC_ACUCUCAACGGCCAGCUACCAAU
((((((...........(((((.....))))).....(((......)))...........................))))))...................................... ( -7.40 =  -7.64 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	11,959,274 – 11,959,377
Length	103
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	77.39
Mean single sequence MFE	-23.54
Consensus MFE	-13.58
Energy contribution	-15.66
Covariance contribution	2.08
Combinations/Pair	1.10
Mean z-score	-2.37
Structure conservation index	0.58
SVM decision value	1.84
SVM RNA-class probability	0.979545
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11959274 103 + 22407834
UCCAUCAGCUAACC---AACCAA----------CCAACUGCCAACUCCAAGCUGACCACUCUUAACGGCCAGCUAGCAAUUGGUGGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
......(((((((.---.....(----------((((.(((........(((((.((.........)).))))).))).)))))(....)...)))))))................ ( -23.50)
>DroSec_CAF1 178649 95 + 1
UCCAUCAGCUAAC---------------------CAACUGCCCACUUCAAGCUGACGACUCUCAACGGCCAGCUACCAAUUGGUGGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
....((((((...---------------------...............)))))).(((.......(((((((((((....)))(....)..))))))))(((.....)))))).. ( -23.47)
>DroSim_CAF1 145092 95 + 1
UCCAUCAGCUAAC---------------------CAACUGCCCACUUCAAGCUGACGACUCUCAACGGCCAGCUACCAAUUGGUGGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
....((((((...---------------------...............)))))).(((.......(((((((((((....)))(....)..))))))))(((.....)))))).. ( -23.47)
>DroEre_CAF1 153611 87 + 1
UCCAUCAGCUA-----CAGCUAC----------CCAACUGCCAACUCCAAG--------------CCGCCAGCUCCCAAUUGGUGGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
......(((..-----..)))..----------......(((((((....(--------------(((((((.......)))))))).....)))))))((((.....)))).... ( -24.70)
>DroYak_CAF1 149379 107 + 1
UCCAUCAGCUAUCCAACAGCCAAGUGCCAACUGCCAACUGCUAACUUCAAA---------CUGAACUGCCAGCUCCCAAUUGGUAGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
.......(((.......))).(((((((((((.....(((((((.......---------(((......))).......)))))))......))))))).))))............ ( -22.54)
>consensus
UCCAUCAGCUAAC____A_C_A___________CCAACUGCCAACUUCAAGCUGAC_ACUCUCAACGGCCAGCUACCAAUUGGUGGCAACUAAGUUGGCUACUUAUUAAGUGUCAU
.......................................(((((((....((((...........))))..((((((....)))))).....)))))))((((.....)))).... (-13.58 = -15.66 +   2.08)

alignment

secondary structure

dotplot

Window 5

Location	11,959,274 – 11,959,377
Length	103
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	77.39
Mean single sequence MFE	-30.74
Consensus MFE	-14.04
Energy contribution	-15.94
Covariance contribution	1.90
Combinations/Pair	1.08
Mean z-score	-1.82
Structure conservation index	0.46
SVM decision value	-0.05
SVM RNA-class probability	0.506616
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11959274 103 - 22407834
AUGACACUUAAUAAGUAGCCAACUUAGUUGCCACCAAUUGCUAGCUGGCCGUUAAGAGUGGUCAGCUUGGAGUUGGCAGUUGG----------UUGGUU---GGUUAGCUGAUGGA
....((.(((.(((.(((((((((...((((((...(((.(.(((((((((.......))))))))).).)))))))))..))----------))))))---).)))..))))).. ( -37.80)
>DroSec_CAF1 178649 95 - 1
AUGACACUUAAUAAGUAGCCAACUUAGUUGCCACCAAUUGGUAGCUGGCCGUUGAGAGUCGUCAGCUUGAAGUGGGCAGUUG---------------------GUUAGCUGAUGGA
......((.....(((((((((((.((((((((.....))))))))(.(((((..((((.....))))..))))).))))))---------------------))).)))...)). ( -28.30)
>DroSim_CAF1 145092 95 - 1
AUGACACUUAAUAAGUAGCCAACUUAGUUGCCACCAAUUGGUAGCUGGCCGUUGAGAGUCGUCAGCUUGAAGUGGGCAGUUG---------------------GUUAGCUGAUGGA
......((.....(((((((((((.((((((((.....))))))))(.(((((..((((.....))))..))))).))))))---------------------))).)))...)). ( -28.30)
>DroEre_CAF1 153611 87 - 1
AUGACACUUAAUAAGUAGCCAACUUAGUUGCCACCAAUUGGGAGCUGGCGG--------------CUUGGAGUUGGCAGUUGG----------GUAGCUG-----UAGCUGAUGGA
.....(((((((.....((((((((((((((((((.....))...))))))--------------))..)))))))).)))))----------))(((..-----..)))...... ( -28.10)
>DroYak_CAF1 149379 107 - 1
AUGACACUUAAUAAGUAGCCAACUUAGUUGCUACCAAUUGGGAGCUGGCAGUUCAG---------UUUGAAGUUAGCAGUUGGCAGUUGGCACUUGGCUGUUGGAUAGCUGAUGGA
...........(((((.(((((((((..(((((((....))(((((((....))))---------))).....)))))..))..)))))))))))).((((..(....)..)))). ( -31.20)
>consensus
AUGACACUUAAUAAGUAGCCAACUUAGUUGCCACCAAUUGGUAGCUGGCCGUUGAGAGU_GUCAGCUUGAAGUUGGCAGUUGG___________U_G_U____GUUAGCUGAUGGA
..((((((.....))).((((((((((((((((.....)))))))).........((((.....)))).)))))))).)))................................... (-14.04 = -15.94 +   1.90)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:06 2006