Locus 3818

Sequence ID	2L_DroMel_CAF1
Location	11,143,331 – 11,143,451
Length	120
Max. P	0.857303

overview

Window 5

Location	11,143,331 – 11,143,424
Length	93
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	79.07
Mean single sequence MFE	-28.02
Consensus MFE	-20.09
Energy contribution	-20.32
Covariance contribution	0.22
Combinations/Pair	1.44
Mean z-score	-1.63
Structure conservation index	0.72
SVM decision value	0.81
SVM RNA-class probability	0.857303
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11143331 93 + 22407834
UACUCACCUGAAUGGCACGGGCUACAUCCGAGCCCCAAAUCGGUUUCGAGCUGACUACUAUGGAGAAUUUAUUCCAAUGGAAGGCGUUCAGCA
.......(((((((.(..(((((.......)))))....(((((.....)))))...((((((((......)))).))))..).))))))).. ( -26.40)
>DroPse_CAF1 13498 93 + 1
CACUCACCUGUAUGGCCCGUGCCACAUCUGAGCCCCAAAUGGGCUUGGAGCUCACUACGAUGGCAAACUUUUGCCAGUGGAAGGCGCUCAGCA
.......(((...(((((...((((.((..(((((.....)))))..))...........((((((....))))))))))..)).)))))).. ( -35.20)
>DroEre_CAF1 12547 93 + 1
CACUCACUUGAAUGGCGCGGGCCACAUCCGAGCCCCAAAUCGGCUUGGAGCUGACUACUAUGGAGAACUUAUUCCAAUGAAAGGCGUUCAGUA
.....(((.(((((.((..(..((..((((((((.......))))))))..)).)..)..(((((......)))))......).)))))))). ( -26.60)
>DroMoj_CAF1 12953 93 + 1
UGCUUACCUGUAUAGCGCUGGCCACAUCGGAGCCCCAAAUGGGCUUCGAGCUAACCACAAUGGCGAAUUUUUUCCAAUCAUAGGCAUUUAAUA
.(((.........)))....(((...(((((((((.....)))))))))((((.......))))..................)))........ ( -25.60)
>DroAna_CAF1 12319 92 + 1
-CCUCACCUGAAUGGCCCGGGCUACGUCAGAACCAAAGAUUGGUUUGGAACUGACAACGAUGGAAAACUUUUCCCAAUGAAAAGCACUCAGCA
-......((((.((((....)))).(((((..(((((......)))))..)))))............((((((.....))))))...)))).. ( -21.40)
>DroPer_CAF1 13636 93 + 1
CACUCACCUGUAUGGCCCGUGCCACAUCUGAGCCCCAAAUGGGCUUGGAGCUCACUACGAUGGCAAACUUUUGCCAGUGGAAAGCGCUCAGCA
.......(((..((((....))))..((..(((((.....)))))..))(((..((((..((((((....))))))))))..)))...))).. ( -32.90)
>consensus
CACUCACCUGAAUGGCCCGGGCCACAUCCGAGCCCCAAAUGGGCUUGGAGCUGACUACGAUGGAAAACUUUUUCCAAUGAAAGGCGCUCAGCA
............((((....))))..(((((((((.....)))))))))(((((......((((((....))))))(((.....)))))))). (-20.09 = -20.32 +   0.22)

alignment

secondary structure

dotplot

Window 6

Location	11,143,344 – 11,143,451
Length	107
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.46
Mean single sequence MFE	-33.45
Consensus MFE	-18.23
Energy contribution	-18.78
Covariance contribution	0.56
Combinations/Pair	1.39
Mean z-score	-1.65
Structure conservation index	0.54
SVM decision value	0.01
SVM RNA-class probability	0.537234
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11143344 107 + 22407834
GGCACGGGCUACAUCCGAGCCCCAAAUCGGUUUCGAGCUGACUACUAUGGAGAAUUUAUUCCAAUGGAAGGCGUUCAGCAGACUAAUAACACUUUUCGAGACCUGUG------
..((((((((.......)))))......(((((((((((((((.((((((((......)))).)))).))....))))).(........).....)))))))).)))------ ( -30.90)
>DroVir_CAF1 14066 107 + 1
AGCGCUAGCCACAUCGGAGCCCCAAAUGGGCUUUGAACUAACCACAAUUGCAAAUUUUUUCCAAUCAUAUGCACUUAAUAGGCUUAUAACACUUUUGGAGACCUACG------
.((....))....(((((((((.....))))))))).....................(((((((..(((.((.((....)))).))).......)))))))......------ ( -21.20)
>DroPse_CAF1 13511 113 + 1
GGCCCGUGCCACAUCUGAGCCCCAAAUGGGCUUGGAGCUCACUACGAUGGCAAACUUUUGCCAGUGGAAGGCGCUCAGCAGACUUAUCACACUCUUGGAGACCUUUAUGGGAA
..((((((((((.((..(((((.....)))))..))...........((((((....))))))))))((((..(((...(((..........)))..))).)))))))))).. ( -39.90)
>DroEre_CAF1 12560 107 + 1
GGCGCGGGCCACAUCCGAGCCCCAAAUCGGCUUGGAGCUGACUACUAUGGAGAACUUAUUCCAAUGAAAGGCGUUCAGUAGGCUGAUAACGCUUUUCGAGACCUGCA------
...(((((.((..((((((((.......))))))))..))....((.(((((......))))).((((((((((((((....))))..)))))))))))).))))).------ ( -41.40)
>DroMoj_CAF1 12966 107 + 1
AGCGCUGGCCACAUCGGAGCCCCAAAUGGGCUUCGAGCUAACCACAAUGGCGAAUUUUUUCCAAUCAUAGGCAUUUAAUAGACUUAUCACACUCUUAGAGACCUGUG------
..((((((.....(((((((((.....))))))))).....)).....)))).............((((((..(((((.((..........)).)))))..))))))------ ( -29.30)
>DroPer_CAF1 13649 113 + 1
GGCCCGUGCCACAUCUGAGCCCCAAAUGGGCUUGGAGCUCACUACGAUGGCAAACUUUUGCCAGUGGAAAGCGCUCAGCAGACUUAUCACACUCUUGGAGACCUUUAUGGGAA
..(((((.((((.((..(((((.....)))))..))...........((((((....))))))))))((((.((((...(((..........)))..))).)))))))))).. ( -38.00)
>consensus
GGCGCGGGCCACAUCCGAGCCCCAAAUGGGCUUGGAGCUAACUACAAUGGCAAACUUUUUCCAAUGAAAGGCGCUCAGCAGACUUAUAACACUCUUGGAGACCUGUA______
.......(((...(((((((((.....)))))))))...........((((((....))))))......)))......................................... (-18.23 = -18.78 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:09 2006