Locus 9043

Sequence ID	3R_DroMel_CAF1
Location	24,193,220 – 24,193,325
Length	105
Max. P	0.710473

overview

Window 3

Location	24,193,220 – 24,193,325
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.40
Mean single sequence MFE	-35.63
Consensus MFE	-19.32
Energy contribution	-20.52
Covariance contribution	1.20
Combinations/Pair	1.12
Mean z-score	-2.98
Structure conservation index	0.54
SVM decision value	0.12
SVM RNA-class probability	0.592020
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24193220 105 + 27905053
UGUUUAAAUUACCGGCUCCACGGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU------UGCUCAUCCGCCGUGUAUGCCGCGCAGCGGGUU---------AAACUC
.((((((....(((((..((((((..(((((((((((....((((((.....))))))....))))------))))).)).))))))...)))((...)))).))---------)))).. ( -40.60)
>DroPse_CAF1 17045 103 + 1
UGUUUAAAUUACCGUCUGC-UGGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCACGAGUACUGCUCAUCCGCCGUGUGUUAC-------GGCUA---------AAAAAA
........(((((((..((-((((..(((((((..(((.....(((((((.......))))))).....)))))))).)).)))).))...))-------)).))---------)..... ( -22.20)
>DroSim_CAF1 19711 105 + 1
UGUUUAAAUUACCGGCUCCACGGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU------UGCUCAUCCGCCGUGUAUGCCGCGCAGCGGGUU---------GAACUC
.((((((....(((((..((((((..(((((((((((....((((((.....))))))....))))------))))).)).))))))...)))((...)))).))---------)))).. ( -40.70)
>DroEre_CAF1 19154 105 + 1
UGUUUAAAUUACCGGCUCCACAGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU------UGCUCAUCCGCCGUGUAUGCUGCGCAGCGGGUU---------GAACUG
.((((((.....(((((....))).)).(((((((((....((((((.....))))))....))))------))))).(((((.((((.....)))).)))))))---------)))).. ( -35.40)
>DroYak_CAF1 17045 105 + 1
UGUUUAAAUUACCGGCUCCACAGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU------UGCUCAUCCGCCGUGUAUGCCGCGCAGCGGGUU---------GAACUG
.((((((.....(((((....))).)).(((((((((....((((((.....))))))....))))------))))).(((((.((((.....)))).)))))))---------)))).. ( -35.20)
>DroAna_CAF1 14539 108 + 1
UGCUUAACAUACCGACACC--GGCUGAAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU------UGCUCAUCCGCCGCGUAUGCC----AGCAGGUUACGGCGGUCGAAGCC
.((((.....((((.(..(--(((.((.(((((((((....((((((.....))))))....))))------))))).)).))))((((.(((----....))))))))))))..)))). ( -39.70)
>consensus
UGUUUAAAUUACCGGCUCCACGGCUCGAGGGCAAUGUAAUUAAGUUUUAAUCAAACUUUAAGGCAU______UGCUCAUCCGCCGUGUAUGCCGCGCAGCGGGUU_________GAACUC
............((((..((((((....(((((((((....((((((.....))))))....))))......)))))....))))))...)))).......................... (-19.32 = -20.52 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	24,193,220 – 24,193,325
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.40
Mean single sequence MFE	-32.43
Consensus MFE	-22.94
Energy contribution	-24.27
Covariance contribution	1.32
Combinations/Pair	1.11
Mean z-score	-2.28
Structure conservation index	0.71
SVM decision value	0.37
SVM RNA-class probability	0.710473
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24193220 105 - 27905053
GAGUUU---------AACCCGCUGCGCGGCAUACACGGCGGAUGAGCA------AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCCGUGGAGCCGGUAAUUUAAACA
..((((---------((.....(((.((((...((((((.((.(.(((------(((.....((((((.....)))))).....))))))).))..))))))..)))))))..)))))). ( -36.50)
>DroPse_CAF1 17045 103 - 1
UUUUUU---------UAGCC-------GUAACACACGGCGGAUGAGCAGUACUCGUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCCA-GCAGACGGUAAUUUAAACA
......---------..(((-------((.....)))))(((((((.....))))).))...((((((.....))))))..(((.((((((.((......-...)).)))))).)))... ( -24.40)
>DroSim_CAF1 19711 105 - 1
GAGUUC---------AACCCGCUGCGCGGCAUACACGGCGGAUGAGCA------AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCCGUGGAGCCGGUAAUUUAAACA
......---------.......(((.((((...((((((.((.(.(((------(((.....((((((.....)))))).....))))))).))..))))))..)))))))......... ( -33.90)
>DroEre_CAF1 19154 105 - 1
CAGUUC---------AACCCGCUGCGCAGCAUACACGGCGGAUGAGCA------AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCUGUGGAGCCGGUAAUUUAAACA
......---------.(((.(((.((((((.....(((.((....(((------(((.....((((((.....)))))).....))))))))))).)))))).))).))).......... ( -30.70)
>DroYak_CAF1 17045 105 - 1
CAGUUC---------AACCCGCUGCGCGGCAUACACGGCGGAUGAGCA------AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCUGUGGAGCCGGUAAUUUAAACA
......---------.......(((.((((...((((((.((.(.(((------(((.....((((((.....)))))).....))))))).))..))))))..)))))))......... ( -31.70)
>DroAna_CAF1 14539 108 - 1
GGCUUCGACCGCCGUAACCUGCU----GGCAUACGCGGCGGAUGAGCA------AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUUCAGCC--GGUGUCGGUAUGUUAAGCA
(((.......))).((((.((((----(((((...((((.((.(.(((------(((.....((((((.....)))))).....)))))).).)).)))--)))))))))).)))).... ( -37.40)
>consensus
GAGUUC_________AACCCGCUGCGCGGCAUACACGGCGGAUGAGCA______AUGCCUUAAAGUUUGAUUAAAACUUAAUUACAUUGCCCUCGAGCCGUGGAGCCGGUAAUUUAAACA
................(((.(((.((((((......((((.(((.(((.......)))....((((((.....)))))).....))))))).....)))))).))).))).......... (-22.94 = -24.27 +   1.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:25:25 2006