Locus 2288

Sequence ID	3R_DroMel_CAF1
Location	6,505,656 – 6,505,748
Length	92
Max. P	0.885773

overview

Window 9

Location	6,505,656 – 6,505,748
Length	92
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	76.66
Mean single sequence MFE	-22.58
Consensus MFE	-17.72
Energy contribution	-17.00
Covariance contribution	-0.72
Combinations/Pair	1.35
Mean z-score	-1.47
Structure conservation index	0.78
SVM decision value	0.94
SVM RNA-class probability	0.885773
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6505656 92 + 27905053
GAAGAUAAAUCAUCGGAAAAGAAAAAGA--GGGGCGGGAAAGUGGGCCCAUUUUCCGGAUGGUGCUCUAUGCACAAUUUACCC-----GUAGAUAUAU----G
....(((.(((.((......))......--(((.(.((((((((....)))))))).)...((((.....))))......)))-----...))).)))----. ( -25.00)
>DroSec_CAF1 270668 83 + 1
GAAGAUAAAUCAUCGGAA-A-------A--GGGACAGGAAAGUGGGCCUAUUUUCCGGAUGGUGGUCUGUGCACAAUGUACCC------UACAUAUAU----G
..((((..((((((((((-(-------(--(((.((......))..))).)))))).)))))).))))((((.....))))..------.........----. ( -20.10)
>DroSim_CAF1 299678 88 + 1
GAAGAUAAAUCAUCGGAAAA-------A--GGGGCAGGAAAGUGGGCCUAUUUUCCGGAUGGUGCUCUAUGCACAAUGUACCC------UACAUAUAUGUAUG
..(((...((((((((((((-------.--(((.(.........).))).)))))).))))))..)))(((((..(((((...------)))))...))))). ( -22.60)
>DroEre_CAF1 283891 82 + 1
UA-ACUAAAUCAUCGGAAAA-------GUGGGGGCAGGAAAGUGGGGCCAUUUUCCGGAUGGUGCUCUAUGCACAAUGCACCAUAUAUGU-------------
..-.................-------((((..(((((((((((....)))))))).....((((.....))))..))).))))......------------- ( -25.00)
>DroYak_CAF1 279933 93 + 1
GA-GAUAAAUCAUCGGAAAA-------A--GGGGCAGGAAAGUGGGGCCAUUUUCCGGAUGGUGCUCUAUGUACAAUGCACUAUAUACAUACAUAUAUACAUA
((-(....((((((((((((-------.--..(((...........))).)))))).)))))).)))((((((........(((((......))))))))))) ( -20.20)
>consensus
GAAGAUAAAUCAUCGGAAAA_______A__GGGGCAGGAAAGUGGGCCCAUUUUCCGGAUGGUGCUCUAUGCACAAUGUACCC______UACAUAUAU____G
..............................((.(((((((((((....)))))))).....((((.....))))..))).))..................... (-17.72 = -17.00 +  -0.72)

alignment

secondary structure

dotplot

Window 0

Location	6,505,656 – 6,505,748
Length	92
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	76.66
Mean single sequence MFE	-19.56
Consensus MFE	-8.67
Energy contribution	-9.27
Covariance contribution	0.60
Combinations/Pair	1.11
Mean z-score	-1.89
Structure conservation index	0.44
SVM decision value	0.24
SVM RNA-class probability	0.648110
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6505656 92 - 27905053
C----AUAUAUCUAC-----GGGUAAAUUGUGCAUAGAGCACCAUCCGGAAAAUGGGCCCACUUUCCCGCCCC--UCUUUUUCUUUUCCGAUGAUUUAUCUUC
.----..........-----((((((((.((((.....))))((((.((((((.((((..........)))).--........)))))))))))))))))).. ( -21.10)
>DroSec_CAF1 270668 83 - 1
C----AUAUAUGUA------GGGUACAUUGUGCACAGACCACCAUCCGGAAAAUAGGCCCACUUUCCUGUCCC--U-------U-UUCCGAUGAUUUAUCUUC
(----(((.(((((------...)))))))))..........((((.(((((..(((..((......))..))--)-------)-)))))))).......... ( -14.10)
>DroSim_CAF1 299678 88 - 1
CAUACAUAUAUGUA------GGGUACAUUGUGCAUAGAGCACCAUCCGGAAAAUAGGCCCACUUUCCUGCCCC--U-------UUUUCCGAUGAUUUAUCUUC
..((((....))))------(((((....((((.....))))((((.((((((..(((..........)))..--.-------))))))))))...))))).. ( -19.80)
>DroEre_CAF1 283891 82 - 1
-------------ACAUAUAUGGUGCAUUGUGCAUAGAGCACCAUCCGGAAAAUGGCCCCACUUUCCUGCCCCCAC-------UUUUCCGAUGAUUUAGU-UA
-------------.(((..(((((((.(((....))).))))))).((((((((((...((......))...))).-------)))))))))).......-.. ( -19.80)
>DroYak_CAF1 279933 93 - 1
UAUGUAUAUAUGUAUGUAUAUAGUGCAUUGUACAUAGAGCACCAUCCGGAAAAUGGCCCCACUUUCCUGCCCC--U-------UUUUCCGAUGAUUUAUC-UC
((((((((.((((((.......))))))))))))))......((((.((((((.(((...........)))..--.-------)))))))))).......-.. ( -23.00)
>consensus
C____AUAUAUGUA______GGGUACAUUGUGCAUAGAGCACCAUCCGGAAAAUGGGCCCACUUUCCUGCCCC__U_______UUUUCCGAUGAUUUAUCUUC
.............................((((.....))))((((.((((((((((........))))..............)))))))))).......... ( -8.67 =  -9.27 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:41 2006