Locus 2011

Sequence ID	3R_DroMel_CAF1
Location	5,707,612 – 5,707,722
Length	110
Max. P	0.898688

overview

Window 6

Location	5,707,612 – 5,707,722
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.48
Mean single sequence MFE	-25.81
Consensus MFE	-15.29
Energy contribution	-14.98
Covariance contribution	-0.30
Combinations/Pair	1.21
Mean z-score	-2.07
Structure conservation index	0.59
SVM decision value	0.73
SVM RNA-class probability	0.835477
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5707612 110 + 27905053
-----CACACAAAGGAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC----ACAGCGCAAAGCCGAAAAAUGUAUAAAAUAAAAUAAGAUGUCAACGUCACCAGU-UUGCGCCGA
-----.................(((..(((((((((....))))))))))))----.(.(((((((((........))..............((((....)))).....)-)))))).). ( -24.70)
>DroVir_CAF1 10108 114 + 1
AGACAUAUUUAACAAAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGCGGCUGGCAGAGC--A---GCGAAAAGUGUAUAGAA-AAGAGAAGACAUCAACGUCAGCAAAGUCGCGGCAA
......................(((.((((((((((....))))))))))((((((...((--(---.(.....))))......-..((.......))...))))))........))).. ( -29.00)
>DroSec_CAF1 10906 110 + 1
-----CACACAAAGGAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC----ACAGCGCAAAUUUCGGCUUUGUAUAAAAUAAAAUAAGAUGUCAACGUCACCAGU-UUGCGCCGA
-----.................(((..(((((((((....))))))))))))----.(.(((((((((..((.(((((.....)))))....((((....)))).)))))-)))))).). ( -28.40)
>DroEre_CAF1 6937 113 + 1
AAACGCACACAAAGGAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC----ACAGC--AAAGCCGAAAAAUGUAUAAAAUAAAAUAAGAUGUCAACGUCACCAGU-UUGCGCCGA
...((((.((...((.......(((..(((((((((....))))))))))))----.....--....)).......................((((....))))....))-.)))).... ( -23.29)
>DroYak_CAF1 11249 111 + 1
AAAC--ACACAAAGGAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC----ACAGC--AAAGCCGAAAAAUGUAUAAAAUAAAAUAAGAUGUCAACGUCACCGGU-UUGCGCCGA
....--.......((.......(((..(((((((((....))))))))))))----...((--(((.(((.....(((.....)))......((((....))))..))))-)))).)).. ( -26.20)
>DroAna_CAF1 6818 109 + 1
ACUAGCAUAAUACAAAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC----AGAG-----AACCGAAAAGUGGAUAAAAUAAAAGAAGACGUCAACGUCACCAGC-UCACGUUG-
..((((................(((..(((((((((....))))))))))))----.(((-----..(((.....)))..............((((....)))).....)-))..))))- ( -23.30)
>consensus
A_AC_CACACAAAGGAGAAGAAGCCACGCAUGAAAAUUGCUUUUCAUGUGGC____ACAGC__AAAGCCGAAAAAUGUAUAAAAUAAAAUAAGAUGUCAACGUCACCAGU_UUGCGCCGA
.............((.(.....(((..(((((((((....))))))))))))........................................((((....))))..........).)).. (-15.29 = -14.98 +  -0.30)

alignment

secondary structure

dotplot

Window 7

Location	5,707,612 – 5,707,722
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.48
Mean single sequence MFE	-28.14
Consensus MFE	-18.08
Energy contribution	-17.53
Covariance contribution	-0.55
Combinations/Pair	1.30
Mean z-score	-2.10
Structure conservation index	0.64
SVM decision value	1.00
SVM RNA-class probability	0.898688
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5707612 110 - 27905053
UCGGCGCAA-ACUGGUGACGUUGACAUCUUAUUUUAUUUUAUACAUUUUUCGGCUUUGCGCUGU----GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUCCUUUGUGUG-----
.((((((((-(..(....)(((((.....(((........)))......)))))))))))))).----((((((((((((....)))))))..))))).................----- ( -29.90)
>DroVir_CAF1 10108 114 - 1
UUGCCGCGACUUUGCUGACGUUGAUGUCUUCUCUU-UUCUAUACACUUUUCGC---U--GCUCUGCCAGCCGCAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUUUGUUAAAUAUGUCU
..((((((((...((....))....))).......-...............((---(--(......)))).(((((((((....))))))))))))))...................... ( -28.00)
>DroSec_CAF1 10906 110 - 1
UCGGCGCAA-ACUGGUGACGUUGACAUCUUAUUUUAUUUUAUACAAAGCCGAAAUUUGCGCUGU----GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUCCUUUGUGUG-----
.((((((((-(.((((....(((....................))).))))...))))))))).----((((((((((((....)))))))..))))).................----- ( -28.95)
>DroEre_CAF1 6937 113 - 1
UCGGCGCAA-ACUGGUGACGUUGACAUCUUAUUUUAUUUUAUACAUUUUUCGGCUUU--GCUGU----GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUCCUUUGUGUGCGUUU
..((((((.-((.((.((................................((((...--)))).----((((((((((((....)))))))..)))))....)).))...)).)))))). ( -27.70)
>DroYak_CAF1 11249 111 - 1
UCGGCGCAA-ACCGGUGACGUUGACAUCUUAUUUUAUUUUAUACAUUUUUCGGCUUU--GCUGU----GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUCCUUUGUGU--GUUU
...((((((-(.(((..(.(((((.....(((........)))......))))).).--.))).----((((((((((((....)))))))..))))).........)))))))--.... ( -27.70)
>DroAna_CAF1 6818 109 - 1
-CAACGUGA-GCUGGUGACGUUGACGUCUUCUUUUAUUUUAUCCACUUUUCGGUU-----CUCU----GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUUUGUAUUAUGCUAGU
-........-((((((((((....))))..............((((.....(((.-----....----))).((((((((....)))))))).)))).................)))))) ( -26.60)
>consensus
UCGGCGCAA_ACUGGUGACGUUGACAUCUUAUUUUAUUUUAUACAUUUUUCGGCUUU__GCUGU____GCCACAUGAAAAGCAAUUUUCAUGCGUGGCUUCUUCUCCUUUGUGUG_GU_U
((((((((.......)).))))))............................................((((((((((((....)))))))..)))))...................... (-18.08 = -17.53 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:11 2006