Locus 6524

Sequence ID	2L_DroMel_CAF1
Location	18,354,045 – 18,354,156
Length	111
Max. P	0.979113

overview

Window 0

Location	18,354,045 – 18,354,156
Length	111
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	78.22
Mean single sequence MFE	-33.95
Consensus MFE	-21.08
Energy contribution	-21.02
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-2.42
Structure conservation index	0.62
SVM decision value	1.83
SVM RNA-class probability	0.979113
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18354045 111 + 22407834
GAGAAGCAGAUUGUGCGGCAGAUUGCUCAUUUGAC---UUUUGUUGCAACUGUCGCAGUAUUUGCAAUUGCGUCUGUAUCUGUUGCUGUCGCUGUGACUGCGACUGUGACUGCU
.(((.((((((..((((((((.((((.((......---...))..))))))))))))......((....)))))))).)))((..(.(((((.......))))).)..)).... ( -40.90)
>DroSec_CAF1 197868 111 + 1
NNNNNNNNNNNNNNNNNNNNNNNUGCUCAUUUGAU---UUUUGUUGCAACUGUCGCAGUAUUUGCAAUUGUGUCUGUAUCUGUUGCUGUCGCUGUGACUGCGACUGUGACUGAU
................................(((---....((((((((((...))))...))))))...)))...(((.((..(.(((((.......))))).)..)).))) ( -23.70)
>DroSim_CAF1 205876 111 + 1
GAGAAGCAGAUUGUGCGGCAGAUUGCUCAUUUGAU---UUUUGUUGCAACUGUCGCAGUAUUUGCAAUUGUGUCUGUAUCUGUUGCUGUCGCUGUGACUGCGACUGUGACUGCU
.(((.((((((..((((((((.((((.((......---...))..))))))))))))((....))......)))))).)))((..(.(((((.......))))).)..)).... ( -38.80)
>DroYak_CAF1 208328 114 + 1
CUGAUGGUGAUUGAAGCUGAGAUUGCUCAUCUGACUGUUUUUGUAGCAACAGUCGCAGUAUUUGCAACUGCGUCUGUAUCUCUUGCUGUCGCUGUGACUGCUCUUUUAAACGCU
...((((((((...(((.(((((((((((............)).))))((((.((((((.......)))))).)))))))))..)))))))))))................... ( -32.40)
>consensus
GAGAAGCAGAUUGUGCGGCAGAUUGCUCAUUUGAC___UUUUGUUGCAACUGUCGCAGUAUUUGCAAUUGCGUCUGUAUCUGUUGCUGUCGCUGUGACUGCGACUGUGACUGCU
..........................................((((((...((((((((....(((((.............)))))....)))))))))))))).......... (-21.08 = -21.02 +  -0.06)

alignment

secondary structure

dotplot

Window 1

Location	18,354,045 – 18,354,156
Length	111
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	78.22
Mean single sequence MFE	-24.81
Consensus MFE	-12.88
Energy contribution	-14.63
Covariance contribution	1.75
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.52
SVM decision value	0.22
SVM RNA-class probability	0.640385
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18354045 111 - 22407834
AGCAGUCACAGUCGCAGUCACAGCGACAGCAACAGAUACAGACGCAAUUGCAAAUACUGCGACAGUUGCAACAAAA---GUCAAAUGAGCAAUCUGCCGCACAAUCUGCUUCUC
(((((.....(((((.......))))).((..(((((......(((((((((.....))))...))))).......---.((....))...)))))..)).....))))).... ( -27.20)
>DroSec_CAF1 197868 111 - 1
AUCAGUCACAGUCGCAGUCACAGCGACAGCAACAGAUACAGACACAAUUGCAAAUACUGCGACAGUUGCAACAAAA---AUCAAAUGAGCANNNNNNNNNNNNNNNNNNNNNNN
.(((......(((((.......))))).(((((.(.......)....(((((.....)))))..))))).......---......))).......................... ( -17.30)
>DroSim_CAF1 205876 111 - 1
AGCAGUCACAGUCGCAGUCACAGCGACAGCAACAGAUACAGACACAAUUGCAAAUACUGCGACAGUUGCAACAAAA---AUCAAAUGAGCAAUCUGCCGCACAAUCUGCUUCUC
(((((.....(((((.......))))).((((...............))))......((((.(((((((.......---.........)))).))).))))....))))).... ( -25.45)
>DroYak_CAF1 208328 114 - 1
AGCGUUUAAAAGAGCAGUCACAGCGACAGCAAGAGAUACAGACGCAGUUGCAAAUACUGCGACUGUUGCUACAAAAACAGUCAGAUGAGCAAUCUCAGCUUCAAUCACCAUCAG
(((..........((.(((.....))).))..(((((......(((((.......)))))(((((((........))))))).........))))).))).............. ( -29.30)
>consensus
AGCAGUCACAGUCGCAGUCACAGCGACAGCAACAGAUACAGACACAAUUGCAAAUACUGCGACAGUUGCAACAAAA___AUCAAAUGAGCAAUCUGCCGCACAAUCUGCUUCUC
..........((((((((....((((..((.............))..))))....)))))))).(((((...................)))))..................... (-12.88 = -14.63 +   1.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:17 2006