Locus 5164

Sequence ID	3R_DroMel_CAF1
Location	13,554,857 – 13,554,995
Length	138
Max. P	0.835102

overview

Window 8

Location	13,554,857 – 13,554,955
Length	98
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	76.89
Mean single sequence MFE	-27.96
Consensus MFE	-17.82
Energy contribution	-19.18
Covariance contribution	1.36
Combinations/Pair	1.22
Mean z-score	-1.80
Structure conservation index	0.64
SVM decision value	0.73
SVM RNA-class probability	0.835102
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13554857 98 + 27905053
UGGCUAUAUUAUUUAUUACUUUCCCAACUGCACGACUCCCACGCACCUGGAUAAAAACA---------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCG
.(((...................(((..(((...........)))..))).........---------------------.((((((((.((((((....)))))).))))))))))). ( -28.70)
>DroSec_CAF1 7789 98 + 1
AGGCUAUAUUAUUUAUUACUUUCCCAACUGCACGACUCCCACGCACCUGCAUAAAAACC---------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCG
.(((......................................((....)).........---------------------.((((((((.((((((....)))))).))))))))))). ( -25.60)
>DroSim_CAF1 7960 98 + 1
AGGCUAUAUUAUUUAUUACUUUCCCAACUGCACGACUCCCACGCACCUGCAUAAAAACC---------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCG
.(((......................................((....)).........---------------------.((((((((.((((((....)))))).))))))))))). ( -25.60)
>DroEre_CAF1 21365 92 + 1
AUGGCAUAUUAUUUACCGCGUUCGCAACUGCAAGACUCCCACGCAGCUGCAUUAAAGCCACUAUU---------------------------UCCGCAGGUGGAAGAGGUGGAGUGCCG
..(((((................(((.((((...........)))).))).......(((((.((---------------------------((((....)))))).))))).))))). ( -30.50)
>DroYak_CAF1 8053 119 + 1
AUGCAAUAUUGUGUAUUACUUUCGCAACUGCACGACUCCCACGCACCUGCACUAAAACCACUAUUUCCACCAUUUUCACCAUUUCCACCAUUUCCACAGGUGGAAGAGGUGGAGUGCCG
.((((...(((((.........))))).)))).......(((((....))........................((((((.((((((((.........)))))))).)))))))))... ( -29.40)
>consensus
AGGCUAUAUUAUUUAUUACUUUCCCAACUGCACGACUCCCACGCACCUGCAUAAAAACC_____________________UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCG
.............................((((.........((....)).................................((((((.((((((....)))))).)))))))))).. (-17.82 = -19.18 +   1.36)

alignment

secondary structure

dotplot

Window 9

Location	13,554,897 – 13,554,995
Length	98
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	72.09
Mean single sequence MFE	-35.86
Consensus MFE	-20.61
Energy contribution	-22.70
Covariance contribution	2.09
Combinations/Pair	1.34
Mean z-score	-1.47
Structure conservation index	0.57
SVM decision value	0.42
SVM RNA-class probability	0.730961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13554897 98 + 27905053
ACGCACCUGGAUAAAAACA----------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCGCUGCGAGGGCGAUGGACUGAAUCGCGUACCGCAAACCCUG
.((((.(.((.........----------------------(((((((((.((((((....)))))).)))))))))))).))))((((.(((.......)))(((...)))...)))). ( -33.10)
>DroSec_CAF1 7829 98 + 1
ACGCACCUGCAUAAAAACC----------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCGUUGCGAGGGCGACGGGCUGAAUCGCGUACCGCAAACCCUG
((((....((.........----------------------(((((((((.((((((....)))))).)))))))))(((((((....)))))))))......))))............. ( -36.90)
>DroSim_CAF1 8000 98 + 1
ACGCACCUGCAUAAAAACC----------------------UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCGUUGCGAGGGCGACGGACUGAAUCGCGUACCGCAAACCCUG
((((...............----------------------(((((((((.((((((....)))))).)))))))))(((((((....)))))))........))))............. ( -36.40)
>DroEre_CAF1 21405 92 + 1
ACGCAGCUGCAUUAAAGCCACUAUU----------------------------UCCGCAGGUGGAAGAGGUGGAGUGCCGCUGCGAGGGCGACGGACUGAACCGCGUGCCGCAGACCCUG
.((((((.(((((....(((((.((----------------------------((((....)))))).)))))))))).))))))(((((..(((((........)).)))..).)))). ( -42.10)
>DroYak_CAF1 8093 119 + 1
ACGCACCUGCACUAAAACCACUAUUUCC-ACCAUUUUCACCAUUUCCACCAUUUCCACAGGUGGAAGAGGUGGAGUGCCGUUGCGAGGGCGACGGACUUAACCGCGUGCCGCAAACCCUG
..((((..((..................-........((((.((((((((.........)))))))).))))((((.(((((((....)))))))))))....))))))........... ( -39.40)
>DroAna_CAF1 7357 100 + 1
--GCACGAGAAGA--AACA-CU------AACCAC-------UUUUAUACAACAUC--CAGAGCGAGGAGGUGGAGUGCCGGUGUGAGGGGGAGGCGCUCACCCGAGUACCGCAAACAUUA
--((.........--....-..------..((((-------((((..........--........)))))))).(((((((.(((((.(.....).)))))))).)))).))........ ( -27.27)
>consensus
ACGCACCUGCAUAAAAACC______________________UAUUCCACUAUUUCCGCAGGCGGAGGAGGUGGAGUGCCGUUGCGAGGGCGACGGACUGAACCGCGUACCGCAAACCCUG
..((((..(........)..........................((((((.((((((....)))))).))))))))))..(((((.(.(((.(((......)))))).))))))...... (-20.61 = -22.70 +   2.09)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:07 2006