Locus 5302

Sequence ID	X_DroMel_CAF1
Location	13,870,349 – 13,870,469
Length	120
Max. P	0.805459

overview

Window 9

Location	13,870,349 – 13,870,469
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.50
Mean single sequence MFE	-31.02
Consensus MFE	-27.30
Energy contribution	-27.80
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.88
SVM decision value	0.31
SVM RNA-class probability	0.685030
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13870349 120 + 22224390
AAAUGACAUUAAAUUGUGCGCAAAAUAGCGGCAAAUAAAAUUUUACUGCGACUUUUUUGCGCUGCUUUUCUCGUCUGGCGCACAAAUGUAUGCAAUAUGUGGCAUUAGAAAUCCGCAUUA
...((.(((....((((((((.....(((((((((......)))...((((.....))))))))))...........))))))))....)))))..((((((.((.....)))))))).. ( -28.89)
>DroSec_CAF1 15754 120 + 1
AAAUGGCAUUAAAUUGUGCGCAAAAUAGCGGCAAAUAAAAUUUUACUGCGACUUUUUUGCGCUGCUUUUCUCGUUUGGCGCACAAAUGUAUGCAAUAUGUGGCAUUAGAAAUCCGCAUUA
.....((((....((((((((.(((((((((((((......)))...((((.....))))))))))......)))).))))))))....))))...((((((.((.....)))))))).. ( -33.30)
>DroEre_CAF1 13505 120 + 1
AAAUGGCAUUAAAUUGUGCGCAAAAUAGCGGCAAAUAAAAUUUUACUGCGACUUUUUUGCGAUGCUUUUCUCGUCUGGCGCACAAAUGUAUGCAAUACGUGGCACUAGAAAUCCGCAUUA
.....((((......))))((((((..((((.(((......))).)))).....))))))(((((........(((((.((....((((((...)))))).)).))))).....))))). ( -30.22)
>DroYak_CAF1 16105 120 + 1
AAAUGGCAUUAAAUUGUGCGCAAAAUAGCGGCAAAUAAAAUUUUACUGCGACUUUUUUGCGCUGCUUUUCUCGUCUGGCGCACAAAUGUAUGCAAUAUGUGGCAUUCGAAAUCCGCAUUA
.....((((....((((((((.....(((((((((......)))...((((.....))))))))))...........))))))))....))))...((((((.((.....)))))))).. ( -31.69)
>consensus
AAAUGGCAUUAAAUUGUGCGCAAAAUAGCGGCAAAUAAAAUUUUACUGCGACUUUUUUGCGCUGCUUUUCUCGUCUGGCGCACAAAUGUAUGCAAUAUGUGGCAUUAGAAAUCCGCAUUA
.....((((....((((((((((((..((((.(((......))).)))).....))))))...(((..........)))))))))....))))...((((((..........)))))).. (-27.30 = -27.80 +   0.50)

alignment

secondary structure

dotplot

Window 0

Location	13,870,349 – 13,870,469
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.50
Mean single sequence MFE	-29.91
Consensus MFE	-27.06
Energy contribution	-27.12
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-2.10
Structure conservation index	0.90
SVM decision value	0.63
SVM RNA-class probability	0.805459
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13870349 120 - 22224390
UAAUGCGGAUUUCUAAUGCCACAUAUUGCAUACAUUUGUGCGCCAGACGAGAAAAGCAGCGCAAAAAAGUCGCAGUAAAAUUUUAUUUGCCGCUAUUUUGCGCACAAUUUAAUGUCAUUU
...(((...(((((...((((((...((....))..)))).))......))))).)))((((((((.(((.((((...........)))).))).))))))))................. ( -29.50)
>DroSec_CAF1 15754 120 - 1
UAAUGCGGAUUUCUAAUGCCACAUAUUGCAUACAUUUGUGCGCCAAACGAGAAAAGCAGCGCAAAAAAGUCGCAGUAAAAUUUUAUUUGCCGCUAUUUUGCGCACAAUUUAAUGCCAUUU
...(((...(((((...((((((...((....))..)))).))......))))).)))((((((((.(((.((((...........)))).))).))))))))................. ( -29.50)
>DroEre_CAF1 13505 120 - 1
UAAUGCGGAUUUCUAGUGCCACGUAUUGCAUACAUUUGUGCGCCAGACGAGAAAAGCAUCGCAAAAAAGUCGCAGUAAAAUUUUAUUUGCCGCUAUUUUGCGCACAAUUUAAUGCCAUUU
.((((((..............))))))((((....((((((((..(.(((........))))...(((((.((.(((((......))))).)).)))))))))))))....))))..... ( -29.14)
>DroYak_CAF1 16105 120 - 1
UAAUGCGGAUUUCGAAUGCCACAUAUUGCAUACAUUUGUGCGCCAGACGAGAAAAGCAGCGCAAAAAAGUCGCAGUAAAAUUUUAUUUGCCGCUAUUUUGCGCACAAUUUAAUGCCAUUU
...(((...(((((..(((((((...((....))..)))).).))..)))))...)))((((((((.(((.((((...........)))).))).))))))))................. ( -31.50)
>consensus
UAAUGCGGAUUUCUAAUGCCACAUAUUGCAUACAUUUGUGCGCCAGACGAGAAAAGCAGCGCAAAAAAGUCGCAGUAAAAUUUUAUUUGCCGCUAUUUUGCGCACAAUUUAAUGCCAUUU
...(((...((((....((((((...((....))..)))).)).....))))...)))((((((((.(((.((((...........)))).))).))))))))................. (-27.06 = -27.12 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:21 2006