Locus 6835

Sequence ID	3R_DroMel_CAF1
Location	18,085,299 – 18,085,452
Length	153
Max. P	0.829794

overview

Window 3

Location	18,085,299 – 18,085,393
Length	94
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.98
Mean single sequence MFE	-23.52
Consensus MFE	-11.90
Energy contribution	-12.07
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.51
SVM decision value	0.10
SVM RNA-class probability	0.584807
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18085299 94 + 27905053
CUGUGCAGGCGAAGGAUGUU-UGUGCAUAUUUUAAAG------------------GCGAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
.((((((....(((...(((-((.(((..((((....------------------..))))..))))))))((((((((.....))))).))).)))...))))))....... ( -26.00)
>DroVir_CAF1 130512 103 + 1
UGGGU---UGGGCUCUCUUU-GGUGCAUAUUUUAAAGC------GCCGCCACUAGACGAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
((.((---(.((((((((.(-(((((..........))------)))).....))).)).....))).))).))......(((.((((((.(((......)))))))))))). ( -22.80)
>DroGri_CAF1 129635 109 + 1
AUGGU---GCAAGUGGUGUU-GGUGCAUAUUUUAAAGCAUUGCCGUCGCCGCGGCACAAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
...((---((..((((((.(-(((((..........))...)))).))))))((((.......))))....)))).....(((.((((((.(((......)))))))))))). ( -32.60)
>DroSec_CAF1 116518 83 + 1
-----------AAGGAUGUU-UGUGCAUAUUUUAAAG------------------GCGAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
-----------...((((..-(((((((........(------------------((((...)))))....((((((((.....))))).)))......)))))))...)))) ( -21.30)
>DroWil_CAF1 127811 93 + 1
CUGGCA--UUCAACAAUGUUGCCUGCAUAUUUUAAAG------------------GCGAAACUUACCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
((((((--((....))))((((((...........))------------------))))......))))...........(((.((((((.(((......)))))))))))). ( -18.00)
>DroAna_CAF1 113804 90 + 1
UUGCC----AGAAAAAUGUU-UGUGCAUAUUUUAAAG------------------GCGAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
.....----...........-(((((((........(------------------((((...)))))....((((((((.....))))).)))......)))))))....... ( -20.40)
>consensus
CUGGC____CGAAGGAUGUU_UGUGCAUAUUUUAAAG__________________GCGAAACUUGCCAGACGCACAUUUUACAUAAAUGUUGCACUUAAAUGCACAUUUUGUC
......................((((((.................................((....))..((((((((.....))))).)))......))))))........ (-11.90 = -12.07 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	18,085,353 – 18,085,452
Length	99
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	79.72
Mean single sequence MFE	-27.00
Consensus MFE	-13.22
Energy contribution	-14.22
Covariance contribution	1.00
Combinations/Pair	1.12
Mean z-score	-2.55
Structure conservation index	0.49
SVM decision value	0.71
SVM RNA-class probability	0.829794
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18085353 99 - 27905053
AAACCC--------------CUUGA----AAGCACUUCU-GGUCCCAACGGUGGGAACAGGGGACAGGGCAACAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
....((--------------((((.----...))(((((-(.(((((....))))).))))))..))))..(((((...(((((((((((((....)))).)))))).)))..))))) ( -29.60)
>DroSec_CAF1 116561 92 - 1
AAACCC--------------CUUGA----AAGCACUUCU-GGUCCCAACGGUGGGAACAGGGG-------GACAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
...(((--------------((((.----.....(....-).(((((....))))).))))))-------)(((((...(((((((((((((....)))).)))))).)))..))))) ( -30.20)
>DroEre_CAF1 120745 91 - 1
AAACCC--------------CUUGA----AAGCACUUCU-GUUCCCAACGGUGGGA-CAGGGC-------AACAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
......--------------.....----..((((((((-((.((((....)))))-))).((-------(.((((.......)))))))....)))))).((((((.....)))))) ( -23.80)
>DroWil_CAF1 127864 96 - 1
AAAUUC--------------CUUGGGGCUAGGUCCUUCUUGGCAUCAACAUCCACA-AGCAGC-------AGCAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
......--------------((((((((((((.....))))))........)).))-))....-------.(((((...(((((((((((((....)))).)))))).)))..))))) ( -21.60)
>DroYak_CAF1 121957 91 - 1
AAACCC--------------CUUGA----AAGCACUUCU-GCUCCCAACGGUGAGA-CGGGGC-------AACAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
...(((--------------((((.----.((((....)-)))..))).(......-))))).-------.(((((...(((((((((((((....)))).)))))).)))..))))) ( -22.90)
>DroAna_CAF1 113854 105 - 1
AAACCCCCAAGGAGCCGGCACUUGA----AGGCACUUCG-GCUCCCAGCGGUAGCU-GGUGGC-------AGCAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
......(((.(((((((((......----..))....))-)))))((((....)))-).))).-------.(((((...(((((((((((((....)))).)))))).)))..))))) ( -33.90)
>consensus
AAACCC______________CUUGA____AAGCACUUCU_GGUCCCAACGGUGGGA_CAGGGC_______AACAUUAUGACAAAAUGUGCAUUUAAGUGCAACAUUUAUGUAAAAUGU
....................................(((...(((((....)))))...))).........(((((...(((((((((((((....)))).)))))).)))..))))) (-13.22 = -14.22 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:07 2006