Locus 2027

Sequence ID	X_DroMel_CAF1
Location	5,569,947 – 5,570,057
Length	110
Max. P	0.913681

overview

Window 9

Location	5,569,947 – 5,570,057
Length	110
Sequences	3
Columns	111
Reading direction	forward
Mean pairwise identity	87.39
Mean single sequence MFE	-30.30
Consensus MFE	-24.52
Energy contribution	-24.97
Covariance contribution	0.45
Combinations/Pair	1.05
Mean z-score	-2.74
Structure conservation index	0.81
SVM decision value	1.09
SVM RNA-class probability	0.913681
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5569947 110 + 22224390
CAAAAAAAAAAAAAAGUAAGACUAUGUACAAAACCG-AGGCAAGUGUAGUGUGCUUGCAAAUUUGCGCACAGUGGGACAGGUGGCGCCGCACAGUGGGUGCACACCACCCA
....................(((.((..((((....-..((((((.......))))))...))))..)).)))(((...(((((((((........))))).)))).))). ( -32.70)
>DroSec_CAF1 2963 111 + 1
AAAAAAAAAGAAAAAAAAAGAGUAUAUAUAAAACCAAAGGGAAGAGUAGCUUGCUUGCAAAUUUGCGCACAGUGGGACAGGUGGCGCCACACAGUGGGUGCACACCACCCA
......................................(((.......(((..(((((........))).))..)).).(((((((((........))))).)))).))). ( -29.00)
>DroSim_CAF1 2952 104 + 1
AAAAAAA-------AAGAAGAGUAUAUAUAAAACCAAAGGGAAGAGUAGCUUGCUUGCAAAUUUGCGCACAGUGGGACAGGUGGCGCCGCACAGUGGGUGCACACCACCCA
.......-------........................(((.......(((..(((((........))).))..)).).(((((((((........))))).)))).))). ( -29.20)
>consensus
AAAAAAAAA_AAAAAAAAAGAGUAUAUAUAAAACCAAAGGGAAGAGUAGCUUGCUUGCAAAUUUGCGCACAGUGGGACAGGUGGCGCCGCACAGUGGGUGCACACCACCCA
......................................(((.......((((((((((........))).)))))).).(((((((((........))))).)))).))). (-24.52 = -24.97 +   0.45)

alignment

secondary structure

dotplot

Window 0

Location	5,569,947 – 5,570,057
Length	110
Sequences	3
Columns	111
Reading direction	reverse
Mean pairwise identity	87.39
Mean single sequence MFE	-27.60
Consensus MFE	-23.45
Energy contribution	-23.23
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-1.83
Structure conservation index	0.85
SVM decision value	0.28
SVM RNA-class probability	0.666104
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5569947 110 - 22224390
UGGGUGGUGUGCACCCACUGUGCGGCGCCACCUGUCCCACUGUGCGCAAAUUUGCAAGCACACUACACUUGCCU-CGGUUUUGUACAUAGUCUUACUUUUUUUUUUUUUUG
.(((((((((((((.....)))).)))))))))((...((((((..((((...(((((.........)))))..-....))))..))))))...))............... ( -34.20)
>DroSec_CAF1 2963 111 - 1
UGGGUGGUGUGCACCCACUGUGUGGCGCCACCUGUCCCACUGUGCGCAAAUUUGCAAGCAAGCUACUCUUCCCUUUGGUUUUAUAUAUACUCUUUUUUUUUCUUUUUUUUU
.(((((((.(((...(((.(((.((((.....)))).))).))).(((....)))..))).)))))))........................................... ( -24.30)
>DroSim_CAF1 2952 104 - 1
UGGGUGGUGUGCACCCACUGUGCGGCGCCACCUGUCCCACUGUGCGCAAAUUUGCAAGCAAGCUACUCUUCCCUUUGGUUUUAUAUAUACUCUUCUU-------UUUUUUU
.(((((((.(((...(((.(((.((((.....)))).))).))).(((....)))..))).))))))).............................-------....... ( -24.30)
>consensus
UGGGUGGUGUGCACCCACUGUGCGGCGCCACCUGUCCCACUGUGCGCAAAUUUGCAAGCAAGCUACUCUUCCCUUUGGUUUUAUAUAUACUCUUAUUUUUU_UUUUUUUUU
.(((((((((((((.....)))).))))))))).......(((..(((....)))..)))................................................... (-23.45 = -23.23 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:31 2006