Locus 6590

Sequence ID	3L_DroMel_CAF1
Location	17,492,954 – 17,493,067
Length	113
Max. P	0.960258

overview

Window 2

Location	17,492,954 – 17,493,067
Length	113
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.84
Mean single sequence MFE	-41.95
Consensus MFE	-29.47
Energy contribution	-29.33
Covariance contribution	-0.14
Combinations/Pair	1.25
Mean z-score	-2.35
Structure conservation index	0.70
SVM decision value	1.51
SVM RNA-class probability	0.960258
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17492954 113 + 23771897
-------AUUAAAUCACCUCAUAUUUUUGCCGCCAUCGCAGAUGAUGGCAAUCUUCGGCCACUGAUGGUUGUUGGCCGGCGUCAAUCGCCUGGCGCCGCCCAGCAGUGUAAUGGCCAGAU
-------.....(((................(((((((....))))))).......(((((.((....(((((((.((((((((......)))))))).)))))))..)).))))).))) ( -44.40)
>DroVir_CAF1 371 113 + 1
-------GAUAACCCACCUCAUGGUGUUAACGCCAUCGCAUAUGAUGGCUAUUUUUGGCCACUGAUGAUUAUUUGCUGGCGUCAAGCGUCUGGCGCCGCCCAGCAGUGUUAUGGCCAAGU
-------.......((((....)))).....(((((((....)))))))....((((((((....((((...(((((((.((...(((.....))).))))))))).)))))))))))). ( -41.60)
>DroGri_CAF1 542 120 + 1
GUUCAAGGCAAGCUCACCUCAUUGUGUUGACGCCAUCGCAAAUGAUGGCAAUCUUGGGCCACUGAUGAUUGUUGGCCGGUGUCAAGCGGCGAGCGCCGCCGAGCAAUGUGAUGGCUAAAU
..........(((.((.(.((((((.((((((((((((....))))))).......((((((........).)))))...)))))(((((....)))))...)))))).).))))).... ( -45.30)
>DroWil_CAF1 8737 112 + 1
--------UUGUCUUACCUCAUAUUUUUAACGUCAUCGCAAAUGAUGACUAUCUUGGGCCACUGAUGAUUGUUGGCCGGUGUCAAACGUCUAGCGCCGCCUAGCAGGGUAAUGGCUAGAU
--------(((...((((.............(((((((....))))))).......((((((........).))))))))).)))..(((((((...((((....))))....))))))) ( -32.80)
>DroMoj_CAF1 509 113 + 1
-------CCUAACUGACCUCAUGGUAUUAACGCCAUCGCAAAUUAUGGCAAUCUUCGGCCAUUGAUGAUUGUUGGCGGGCGUCAAGCGACGCGCGCCACCAAGCAAUGUGAUGGCCAAAU
-------........(((....)))......(((((((((....(((((........)))))...((.(((.(((((.(((((....))))).))))).))).)).)))))))))..... ( -46.10)
>DroPer_CAF1 32137 113 + 1
-------CUCUGCUCGCCUCAUGUUCUUGACGCCAUCACAAAUGAUGGCUAUCUUGGGCCACUGAUGAUUGUUGGCCGGCGUCAGGCGUCUAGCACCGCCCAGCAGUGUGAUGGCCAGGU
-------........((((((......))).((((((((......(((((......)))))......((((((((.(((.(..((....))..).))).))))))))))))))))..))) ( -41.50)
>consensus
_______CUUAACUCACCUCAUGGUGUUAACGCCAUCGCAAAUGAUGGCAAUCUUGGGCCACUGAUGAUUGUUGGCCGGCGUCAAGCGUCUAGCGCCGCCCAGCAGUGUGAUGGCCAAAU
...............................(((((((....))))))).......(((((.((...(((((((((.(((((..........)))))))).)))))).)).))))).... (-29.47 = -29.33 +  -0.14)

alignment

secondary structure

dotplot

Window 3

Location	17,492,954 – 17,493,067
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.84
Mean single sequence MFE	-39.98
Consensus MFE	-25.20
Energy contribution	-25.45
Covariance contribution	0.25
Combinations/Pair	1.31
Mean z-score	-2.20
Structure conservation index	0.63
SVM decision value	1.21
SVM RNA-class probability	0.931550
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17492954 113 - 23771897
AUCUGGCCAUUACACUGCUGGGCGGCGCCAGGCGAUUGACGCCGGCCAACAACCAUCAGUGGCCGAAGAUUGCCAUCAUCUGCGAUGGCGGCAAAAAUAUGAGGUGAUUUAAU-------
...((((((((....((.(((.(((((.(((....))).))))).))).))......)))))))).((((..((.((((((((....)))).......))))))..))))...------- ( -41.01)
>DroVir_CAF1 371 113 - 1
ACUUGGCCAUAACACUGCUGGGCGGCGCCAGACGCUUGACGCCAGCAAAUAAUCAUCAGUGGCCAAAAAUAGCCAUCAUAUGCGAUGGCGUUAACACCAUGAGGUGGGUUAUC-------
..((((((((.....((((((((((((.....))).)).).))))))...........)))))))).....((((((......)))))).....((((....)))).......------- ( -38.19)
>DroGri_CAF1 542 120 - 1
AUUUAGCCAUCACAUUGCUCGGCGGCGCUCGCCGCUUGACACCGGCCAACAAUCAUCAGUGGCCCAAGAUUGCCAUCAUUUGCGAUGGCGUCAACACAAUGAGGUGAGCUUGCCUUGAAC
....(((((((.(((((...((((((....))))))((((...(((((.(........)))))).......((((((......))))))))))...))))).)))).))).......... ( -45.00)
>DroWil_CAF1 8737 112 - 1
AUCUAGCCAUUACCCUGCUAGGCGGCGCUAGACGUUUGACACCGGCCAACAAUCAUCAGUGGCCCAAGAUAGUCAUCAUUUGCGAUGACGUUAAAAAUAUGAGGUAAGACAA--------
.((((((..(..((......))..).)))))).((((...((((((((.(........)))))).......((((((......)))))).............))).))))..-------- ( -30.00)
>DroMoj_CAF1 509 113 - 1
AUUUGGCCAUCACAUUGCUUGGUGGCGCGCGUCGCUUGACGCCCGCCAACAAUCAUCAAUGGCCGAAGAUUGCCAUAAUUUGCGAUGGCGUUAAUACCAUGAGGUCAGUUAGG-------
.(((((((((.....((.(((.(((((.(((((....))))).))))).))).))...)))))))))....(((((........))))).((((((((....)))..))))).------- ( -41.80)
>DroPer_CAF1 32137 113 - 1
ACCUGGCCAUCACACUGCUGGGCGGUGCUAGACGCCUGACGCCGGCCAACAAUCAUCAGUGGCCCAAGAUAGCCAUCAUUUGUGAUGGCGUCAAGAACAUGAGGCGAGCAGAG-------
..............((((((((((........)))))..(((((((((.(........))))))...(((.(((((((....))))))))))..........)))))))))..------- ( -43.90)
>consensus
AUCUGGCCAUCACACUGCUGGGCGGCGCUAGACGCUUGACGCCGGCCAACAAUCAUCAGUGGCCCAAGAUAGCCAUCAUUUGCGAUGGCGUCAAAAACAUGAGGUGAGUUAAC_______
((((((((((..........(((((((.(((....))).)))).)))...........)))))).......((((((......))))))............))))............... (-25.20 = -25.45 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:25:12 2006