Locus 2086

Sequence ID	3R_DroMel_CAF1
Location	5,939,481 – 5,939,581
Length	100
Max. P	0.787384

overview

Window 8

Location	5,939,481 – 5,939,581
Length	100
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	69.49
Mean single sequence MFE	-27.87
Consensus MFE	-5.76
Energy contribution	-6.98
Covariance contribution	1.22
Combinations/Pair	1.22
Mean z-score	-2.42
Structure conservation index	0.21
SVM decision value	0.50
SVM RNA-class probability	0.761351
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5939481 100 + 27905053
AUGUGAUAAGGUCAGCAUAAGCUAAAUAUUUGGUCACGCUGGCGAGCGGACUUGUGAGUUCGGAAAACUCACA-CUGCUGACCAC--UGCUGAUCGAGAUAAU
.........((((((((..............((((.((((....))))))))((((((((.....))))))))-.))))))))..--................ ( -32.90)
>DroPse_CAF1 56125 78 + 1
-UGCGAUGGGGUCACCGAAUGUUAAAAAUUUCGUAA-------------AUUUAUAGCUGCGGGGA---AAAA-CUGCUGAC-------CCAAUCAAGAUAAU
-...(((.((((((......((((.(((((.....)-------------)))).)))).((((...---....-))))))))-------)).)))........ ( -20.20)
>DroSec_CAF1 52891 102 + 1
AUGUGAUAAGGUCAGCAGAAGCUAAAUAUUUGGUCACGCUGGGUAGCGGACUUGUGAGUUCGGAGAACUCACA-CUGCUGACCAUCCAUCCAAUCGAGAUAAU
(((.(((..(((((((((.............((((.((((....))))))))(((((((((...)))))))))-))))))))))))))).............. ( -38.60)
>DroSim_CAF1 41634 103 + 1
AUGUGAUAAGGUCAGCAGAAGCUAAAUAUUUGGUCACGCUGGGUAGCGGACUUGUGAGUUCGGAAAACUCACAAACGCUGACCAUCCAUCCAAUCGAGAUAAU
(((.(((..(((((((................(((.((((....)))))))(((((((((.....)))))))))..))))))))))))).............. ( -33.10)
>DroEre_CAF1 43340 89 + 1
AUGUGAUAAGGUCAGCAGAAGCCAAAUAGCUGGUCACGGUGGGCAGUGGACUUGUAGGAUCGGAAACC-AAAA-CU------------GCCGAUGGAGAUAAU
.........(..((((............))))..).(.((.((((((.((((....)).))(....).-...)-))------------))).)).)....... ( -22.90)
>DroYak_CAF1 44725 82 + 1
AUGUGAUAAGGUCAGCAGAAGCUAAGUAUCUGGUCACGAUGGCCAGUGGACUUGUGGGAUCGGAAAAC---------------------CCAAUAGAGAUAAU
.........(((((((....)))((((..((((((.....))))))...))))....))))((.....---------------------))............ ( -19.50)
>consensus
AUGUGAUAAGGUCAGCAGAAGCUAAAUAUUUGGUCACGCUGGGCAGCGGACUUGUGAGUUCGGAAAAC_CACA_CUGCUGAC_______CCAAUCGAGAUAAU
..(((((.((((.(((....)))....)))).))))).........((((((....))))))......................................... ( -5.76 =  -6.98 +   1.22)

alignment

secondary structure

dotplot

Window 9

Location	5,939,481 – 5,939,581
Length	100
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	69.49
Mean single sequence MFE	-25.27
Consensus MFE	-4.25
Energy contribution	-4.47
Covariance contribution	0.22
Combinations/Pair	1.22
Mean z-score	-2.65
Structure conservation index	0.17
SVM decision value	0.58
SVM RNA-class probability	0.787384
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5939481 100 - 27905053
AUUAUCUCGAUCAGCA--GUGGUCAGCAG-UGUGAGUUUUCCGAACUCACAAGUCCGCUCGCCAGCGUGACCAAAUAUUUAGCUUAUGCUGACCUUAUCACAU
................--..((((((((.-(((((((((...))))))))).(((((((....)))).)))...............))))))))......... ( -31.90)
>DroPse_CAF1 56125 78 - 1
AUUAUCUUGAUUGG-------GUCAGCAG-UUUU---UCCCCGCAGCUAUAAAU-------------UUACGAAAUUUUUAACAUUCGGUGACCCCAUCGCA-
........(((.((-------((((((.(-(...---.....)).)))......-------------...((((..........))))..))))).)))...- ( -15.60)
>DroSec_CAF1 52891 102 - 1
AUUAUCUCGAUUGGAUGGAUGGUCAGCAG-UGUGAGUUCUCCGAACUCACAAGUCCGCUACCCAGCGUGACCAAAUAUUUAGCUUCUGCUGACCUUAUCACAU
...........((((((...(((((((((-(((((((((...))))))))).(((((((....)))).)))..............))))))))).)))).)). ( -38.40)
>DroSim_CAF1 41634 103 - 1
AUUAUCUCGAUUGGAUGGAUGGUCAGCGUUUGUGAGUUUUCCGAACUCACAAGUCCGCUACCCAGCGUGACCAAAUAUUUAGCUUCUGCUGACCUUAUCACAU
...........((((((...(((((((..((((((((((...))))))))))(((((((....)))).)))................))))))).)))).)). ( -34.50)
>DroEre_CAF1 43340 89 - 1
AUUAUCUCCAUCGGC------------AG-UUUU-GGUUUCCGAUCCUACAAGUCCACUGCCCACCGUGACCAGCUAUUUGGCUUCUGCUGACCUUAUCACAU
............(((------------((-((((-(.............))))...))))))....((((..((....(..((....))..).))..)))).. ( -16.82)
>DroYak_CAF1 44725 82 - 1
AUUAUCUCUAUUGG---------------------GUUUUCCGAUCCCACAAGUCCACUGGCCAUCGUGACCAGAUACUUAGCUUCUGCUGACCUUAUCACAU
.............(---------------------(((...((((.(((.........)))..)))).)))).((((.(((((....)))))...)))).... ( -14.40)
>consensus
AUUAUCUCGAUUGG_______GUCAGCAG_UGUG_GUUUUCCGAACCCACAAGUCCGCUACCCAGCGUGACCAAAUAUUUAGCUUCUGCUGACCUUAUCACAU
..................................................................((((........(((((....))))).....)))).. ( -4.25 =  -4.47 +   0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:00 2006