Locus 6831

Sequence ID	3R_DroMel_CAF1
Location	18,059,662 – 18,059,766
Length	104
Max. P	0.785776

overview

Window 7

Location	18,059,662 – 18,059,766
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.36
Mean single sequence MFE	-29.37
Consensus MFE	-20.20
Energy contribution	-20.98
Covariance contribution	0.78
Combinations/Pair	1.05
Mean z-score	-1.73
Structure conservation index	0.69
SVM decision value	0.40
SVM RNA-class probability	0.721810
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18059662 104 + 27905053
-----CUGGCUUU-UGUUUUUGUUGG-------GGGCUUAAUGCGCUUUAAGCCCGCUGGAACUUU---GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGU
-----...(((..-.(((((....(.-------((((((((......)))))))).).)))))...---))).(((((....(((((((((.........))))))))))))))...... ( -32.10)
>DroEre_CAF1 105304 108 + 1
-----CUGGCUUU-UGUUUUUGUUGGG---GAGGGGCUUAAUGCGCUUUAAGCCCGCUGGAACUUU---GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGU
-----(..((.((-(.((......)).---)))((((((((......))))))))))..)......---....(((((....(((((((((.........))))))))))))))...... ( -30.20)
>DroWil_CAF1 110792 115 + 1
-----UUGCCUUUCUCUCUCUGUUGGUUUCUAUGAGGUUAAUGCGCUUUAAGCUCGUUGGAACUUUUUGGGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGC
-----..........(.(((....((((((.(((((.((((......)))).))))).))))))....))).)(((((....(((((((((.........))))))))))))))...... ( -31.00)
>DroYak_CAF1 106314 110 + 1
UGCUUCUGGCUUU-UGUUUUUGUUGGG------GGGCUUAAUGCGCUUUAAGCCCGCUGGAACUUU---GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGU
.(((..(((((..-........(..(.------((((((((......)))))))).)..)......---...))))).....(((((((((.........)))))))))..)))...... ( -33.11)
>DroAna_CAF1 98935 108 + 1
U--UACUGUCUUU-UGUUUUUGUUGGG------GGACUUAAUGCGCUUUAAGCCCGCUGGAACUUU---GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGC
.--(((((.....-.(((((....(.(------((.(((((......)))))))).).)))))..)---))))(((((....(((((((((.........))))))))))))))...... ( -26.30)
>DroPer_CAF1 125150 105 + 1
-----NNNNNNNN-NNNNNNNNNNNNN------NNNNUUAAUGCGCUUUAAGCUCGUUGGAACUUU---GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCCCCCCU
-----........-.............------....((((((.((.....)).))))))......---((.((((((....(((((((((.........)))))))))))))))))... ( -23.50)
>consensus
_____CUGGCUUU_UGUUUUUGUUGGG______GGGCUUAAUGCGCUUUAAGCCCGCUGGAACUUU___GGUGGCCAUUUAAAAUUUGUGCCGACAUAAAGCAUAAAUUAUGGCGUUUGU
.................................((((((((......))))))))..................(((((....(((((((((.........))))))))))))))...... (-20.20 = -20.98 +   0.78)

alignment

secondary structure

dotplot

Window 8

Location	18,059,662 – 18,059,766
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.36
Mean single sequence MFE	-21.29
Consensus MFE	-16.70
Energy contribution	-17.20
Covariance contribution	0.50
Combinations/Pair	1.09
Mean z-score	-1.68
Structure conservation index	0.78
SVM decision value	0.57
SVM RNA-class probability	0.785776
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18059662 104 - 27905053
ACAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC---AAAGUUCCAGCGGGCUUAAAGCGCAUUAAGCCC-------CCAACAAAAACA-AAAGCCAG-----
......((((((((((.((((.......)))).)))))....)))))....---.........(.((((((((......))))))))-------.)..........-........----- ( -21.80)
>DroEre_CAF1 105304 108 - 1
ACAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC---AAAGUUCCAGCGGGCUUAAAGCGCAUUAAGCCCCUC---CCCAACAAAAACA-AAAGCCAG-----
......((((((((((.((((.......)))).)))))....)))))....---...(((..((.((((((((......)))))))))).---...))).......-........----- ( -22.60)
>DroWil_CAF1 110792 115 - 1
GCAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACCCAAAAAGUUCCAACGAGCUUAAAGCGCAUUAACCUCAUAGAAACCAACAGAGAGAGAAAGGCAA-----
......(((.........(((((.....(((.((.........))))).......((((((....)))))))))))........(((.............))).......)))..----- ( -19.92)
>DroYak_CAF1 106314 110 - 1
ACAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC---AAAGUUCCAGCGGGCUUAAAGCGCAUUAAGCCC------CCCAACAAAAACA-AAAGCCAGAAGCA
......((((((((((.((((.......)))).)))))....)))))....---...(((...(.((((((((......))))))))------)..))).......-...((.....)). ( -22.60)
>DroAna_CAF1 98935 108 - 1
GCAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC---AAAGUUCCAGCGGGCUUAAAGCGCAUUAAGUCC------CCCAACAAAAACA-AAAGACAGUA--A
......((((((((((.((((.......)))).)))))....)))))....---...(((...(.((((((((......))))))))------)..))).......-..........--. ( -19.20)
>DroPer_CAF1 125150 105 - 1
AGGGGGGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC---AAAGUUCCAACGAGCUUAAAGCGCAUUAANNNN------NNNNNNNNNNNNN-NNNNNNNN-----
.((..(((((((((((.((((.......)))).)))))....)))))).))---.((((((....))))))................------.............-........----- ( -21.60)
>consensus
ACAAACGCCAUAAUUUAUGCUUUAUGUCGGCACAAAUUUUAAAUGGCCACC___AAAGUUCCAGCGGGCUUAAAGCGCAUUAAGCCC______CCCAACAAAAACA_AAAGCCAG_____
......((((((((((.((((.......)))).)))))....)))))..................((((((((......))))))))................................. (-16.70 = -17.20 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:01 2006