Locus 7947

Sequence ID	3R_DroMel_CAF1
Location	21,326,575 – 21,326,728
Length	153
Max. P	0.997272

overview

Window 0

Location	21,326,575 – 21,326,673
Length	98
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	77.69
Mean single sequence MFE	-21.62
Consensus MFE	-13.48
Energy contribution	-14.28
Covariance contribution	0.80
Combinations/Pair	1.11
Mean z-score	-1.60
Structure conservation index	0.62
SVM decision value	0.04
SVM RNA-class probability	0.555540
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21326575 98 - 27905053
UCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGCCAACAAAAAAAGG------AGCACAGUG------UGGAAAAUGCUGUGACAACGAUAGUCGACUAUCAGC
......((((....)))).((((((............))))))........(.------.((((((((------(.....)))))))).)..)(((((....)))))... ( -25.40)
>DroSec_CAF1 18917 92 - 1
UCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGCCAACAAAAAAAGG------AGCACGCCG------------ACAGUGUGAAAGCGAUAGUCGACUAUCAGA
...(((((((....)))..((((((............))))))..........------..(((((..------------...))))).))))(((((....)))))... ( -21.30)
>DroSim_CAF1 18044 92 - 1
UCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGCCAACAAAAAAAGG------AGCACGCCG------------ACAGUGUGAAAGCGAUAGUCGACUAUCAGA
...(((((((....)))..((((((............))))))..........------..(((((..------------...))))).))))(((((....)))))... ( -21.30)
>DroEre_CAF1 19114 80 - 1
UCAGUUUGCAAACAUGCAUUUGGCCAACAGCCAACGGGGCCAACAAAAAA------------------------UCAAACAAGCUGUGA------CGUUCGACUAUCAGA
.(((((((((....)))..((((((............)))))).......------------------------......))))))...------............... ( -14.60)
>DroYak_CAF1 17887 110 - 1
UCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGCCAACAAAAAAAAGAAAACGAACACGCCGACAGUGUGGAAAAAGCUGUGAAAACGAUAGUCGACUAUCAGA
...((((....(((.((..((((((............))))))..................(((((.....)))))......)))))..))))(((((....)))))... ( -25.50)
>consensus
UCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGCCAACAAAAAAAGG______AGCACGCCG______U__AA_AAGCUGUGAAAACGAUAGUCGACUAUCAGA
.((((.((((....)))).((((((............)))))).......................................)))).......(((((....)))))... (-13.48 = -14.28 +   0.80)

alignment

secondary structure

dotplot

Window 1

Location	21,326,633 – 21,326,728
Length	95
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.98
Mean single sequence MFE	-36.63
Consensus MFE	-14.34
Energy contribution	-14.37
Covariance contribution	0.03
Combinations/Pair	1.26
Mean z-score	-3.33
Structure conservation index	0.39
SVM decision value	2.75
SVM RNA-class probability	0.996777
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21326633 95 + 27905053
GCCCUGUUGGCUUUUGGCCAAAUGCAUGUUUGCAAACUGAAG------C---GGCUGACAAUUAACUAAUGUCAGCCGCACAAAGUUCAG-------UUUGUAGAUGUUGG
((....(((((.....)))))..))(((((((((((((((((------(---((((((((.........))))))))))......)))))-------)))))))))))... ( -42.20)
>DroVir_CAF1 13931 101 + 1
GCCGCGUUGGCUUUUGGCCAACUGCAUGUUUGCUAACGGACAAACCUCC---GGCUGACAAUUAACAAAUGUCCACAGCGCACAACUUGC-------GCCAAGGAUGCGGG
.((((((..((..(((((.(((.....))).)))))((((......)))---)))..))...........((((...(((((.....)))-------))...)))))))). ( -37.50)
>DroGri_CAF1 14516 111 + 1
GCCGUAUUGGCUUUUGGCCAACUGCUUGUUUGCAAACCAAAAACCCCCACAAGGCUGACAAUUAACAAAUGUCAACGGCACAGAAGCUUCCCCAAAAGCCAAGGAUGCGGG
.((((((((((((((((......((((.(.(((.............((....)).(((((.........)))))...))).).))))....))))))))))...)))))). ( -34.50)
>DroEre_CAF1 19154 95 + 1
GCCCCGUUGGCUGUUGGCCAAAUGCAUGUUUGCAAACUGAAG------C---GGCUGACAAUUAACUAAUGUCAGCCGCACAAAGUUUCG-------CUUGGAGAUGUGGG
..(((.(((((.....)))))..((((.((.(((((((...(------(---((((((((.........))))))))))....))))).)-------)...)).))))))) ( -38.30)
>DroYak_CAF1 17957 95 + 1
GCCCUGUUGGCUUUUGGCCAAAUGCAUGUUUGCAAACUGAAG------C---GGCUGACAAUUAACUAAUGUCAGCCGCACAAAGUUUCG-------UUCGGAGAUGUGGG
.(((..(((((.....)))))..((((.((((.(((((...(------(---((((((((.........))))))))))....)))))..-------..)))).))))))) ( -36.60)
>DroMoj_CAF1 13381 101 + 1
GCCGUGUUGGCUUUUGGCCAACUGCAUGUUUGCUAGCCGAAAACCUCCA---AGCUGACAAUUAACAAAUGUCAACGGUGCAAAACUUGU-------GCCAAAGAUGCGGG
.(((((((((.(((((((.....(((....)))..))))))).))....---.(.(((((.........))))).)((..((.....)).-------.))...))))))). ( -30.70)
>consensus
GCCCUGUUGGCUUUUGGCCAAAUGCAUGUUUGCAAACUGAAA______C___GGCUGACAAUUAACAAAUGUCAACCGCACAAAAUUUCG_______GCCAAAGAUGCGGG
(((...(((((.....)))))..(((....)))...................)))(((((.........)))))....((((...(((.............))).)))).. (-14.34 = -14.37 +   0.03)

alignment

secondary structure

dotplot

Window 2

Location	21,326,633 – 21,326,728
Length	95
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.98
Mean single sequence MFE	-35.47
Consensus MFE	-16.29
Energy contribution	-15.77
Covariance contribution	-0.53
Combinations/Pair	1.26
Mean z-score	-3.16
Structure conservation index	0.46
SVM decision value	2.83
SVM RNA-class probability	0.997272
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21326633 95 - 27905053
CCAACAUCUACAAA-------CUGAACUUUGUGCGGCUGACAUUAGUUAAUUGUCAGCC---G------CUUCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGC
((........((((-------(((((......((((((((((.........))))))))---)------))))))))))...........(((((.....)))))..)).. ( -34.90)
>DroVir_CAF1 13931 101 - 1
CCCGCAUCCUUGGC-------GCAAGUUGUGCGCUGUGGACAUUUGUUAAUUGUCAGCC---GGAGGUUUGUCCGUUAGCAAACAUGCAGUUGGCCAAAAGCCAACGCGGC
.((((.(((.((((-------(((.....))))))).)))..(((((((((.(.(((((---...)).))).).)))))))))......((((((.....)))))))))). ( -38.20)
>DroGri_CAF1 14516 111 - 1
CCCGCAUCCUUGGCUUUUGGGGAAGCUUCUGUGCCGUUGACAUUUGUUAAUUGUCAGCCUUGUGGGGGUUUUUGGUUUGCAAACAAGCAGUUGGCCAAAAGCCAAUACGGC
...((.((((..(...)..)))).))......((((((((((.........)))))))...(((..((((((((((((((......))))...))))))))))..)))))) ( -40.20)
>DroEre_CAF1 19154 95 - 1
CCCACAUCUCCAAG-------CGAAACUUUGUGCGGCUGACAUUAGUUAAUUGUCAGCC---G------CUUCAGUUUGCAAACAUGCAUUUGGCCAACAGCCAACGGGGC
(((..........(-------(.(((((....((((((((((.........))))))))---)------)...)))))))..........(((((.....))))).))).. ( -35.70)
>DroYak_CAF1 17957 95 - 1
CCCACAUCUCCGAA-------CGAAACUUUGUGCGGCUGACAUUAGUUAAUUGUCAGCC---G------CUUCAGUUUGCAAACAUGCAUUUGGCCAAAAGCCAACAGGGC
(((...........-------..(((((....((((((((((.........))))))))---)------)...)))))(((....)))..(((((.....)))))..))). ( -33.20)
>DroMoj_CAF1 13381 101 - 1
CCCGCAUCUUUGGC-------ACAAGUUUUGCACCGUUGACAUUUGUUAAUUGUCAGCU---UGGAGGUUUUCGGCUAGCAAACAUGCAGUUGGCCAAAAGCCAACACGGC
...(((.(((....-------..)))...))).(((((((((.........))))))).---((..((((((.(((((((.........))))))).))))))..)).)). ( -30.60)
>consensus
CCCACAUCUUCGAC_______CCAAACUUUGUGCGGCUGACAUUAGUUAAUUGUCAGCC___G______CUUCAGUUUGCAAACAUGCAGUUGGCCAAAAGCCAACACGGC
..........................(((((....(((((((.........)))))))....................((......))..(((((.....)))))))))). (-16.29 = -15.77 +  -0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:47 2006