Locus 4710

Sequence ID	X_DroMel_CAF1
Location	12,249,924 – 12,250,072
Length	148
Max. P	0.924260

overview

Window 9

Location	12,249,924 – 12,250,032
Length	108
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	87.68
Mean single sequence MFE	-27.03
Consensus MFE	-22.40
Energy contribution	-22.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.73
Structure conservation index	0.83
SVM decision value	1.16
SVM RNA-class probability	0.924260
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12249924 108 - 22224390
ACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAAAGGCUUUUG-----CCACUCCCAUCGCCCUCC-C
.((((..((((....))))((((.((.((((((((((((.(((.((..(.....)..)).))).))))))))))))(....)))...))-----))......))))......-. ( -28.20)
>DroSec_CAF1 17947 113 - 1
ACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAAAGGCUUUUCCAGCCCCACCACCCUCCCUCUCC-C
.................((((....(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).)...((((.....))))...........))))...-. ( -26.40)
>DroEre_CAF1 13179 107 - 1
ACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUUGAAAGGCUUUUCCACCACCACCA-------CCACCCC
.................(((((...((((((((((((((.(((.((..(.....)..)).))).))))))))))))))....))))).............-------....... ( -26.50)
>consensus
ACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAAAGGCUUUUCCA_C_CCACCACC_UC_CCCUCC_C
.................(((((...(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).)....)))))........................... (-22.40 = -22.40 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	12,249,952 – 12,250,072
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.58
Mean single sequence MFE	-25.07
Consensus MFE	-25.26
Energy contribution	-25.07
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.54
Structure conservation index	1.01
SVM decision value	1.05
SVM RNA-class probability	0.906303
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12249952 120 + 22224390
UUCGAAAGUUGCCGUCUAAAUAUUAUUUUACACGAUGCUUUAACGGCAACUUUUGCAUGCCUCAUAAUAAUAAUAAUCGUCAUAAUGCCGCCAGGCAACAACUGUUUCAUUAAAAGAAAA
..(((((((((((((.((((((((.........)))).)))))))))))))))))..............................((((....)))).......((((.......)))). ( -25.00)
>DroSec_CAF1 17980 120 + 1
UUCGAAAGUUGCCGUCUAAAUAUUAUUUUACACGAUGCUUUAACGGCAACUUUUGCAUGCCUCAUAAUAAUAAUAAUCGUCAUAAUGCCGCCAGGCAACAACUGUUUCAUUAAAAGAAAA
..(((((((((((((.((((((((.........)))).)))))))))))))))))..............................((((....)))).......((((.......)))). ( -25.00)
>DroEre_CAF1 13206 120 + 1
UUCAAAAGUUGCCGUCUAAAUAUUAUUUUACACGAUGCUUUAACGGCAACUUUUGCAUGCCUCAUAAUAAUAAUAAUCGUCAUAAUGCCGCCAGGCAACAACUGUUUCAUUAAAAGAAAA
..(((((((((((((.((((((((.........)))).)))))))))))))))))..............................((((....)))).......((((.......)))). ( -25.30)
>DroYak_CAF1 6396 120 + 1
UUCGAAAGUUGCCGUCUAAAUAUUAUUUUACACGAUGCUUUAACGGCAACUUUUGCAUGCCUCAUAAUAAUAAUAAUCGUCAUAAUGCCGCCAGGCAACAACUGUUUCAUUAAAAGAAAA
..(((((((((((((.((((((((.........)))).)))))))))))))))))..............................((((....)))).......((((.......)))). ( -25.00)
>consensus
UUCGAAAGUUGCCGUCUAAAUAUUAUUUUACACGAUGCUUUAACGGCAACUUUUGCAUGCCUCAUAAUAAUAAUAAUCGUCAUAAUGCCGCCAGGCAACAACUGUUUCAUUAAAAGAAAA
..(((((((((((((.((((((((.........)))).)))))))))))))))))..............................((((....)))).......((((.......)))). (-25.26 = -25.07 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	12,249,952 – 12,250,072
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	99.58
Mean single sequence MFE	-29.82
Consensus MFE	-28.80
Energy contribution	-28.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.97
SVM decision value	0.33
SVM RNA-class probability	0.691356
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12249952 120 - 22224390
UUUUCUUUUAAUGAAACAGUUGUUGCCUGGCGGCAUUAUGACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAA
...((((.((((((((.((((((((((....)))).....)))))).)).)))))).))))....(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).).. ( -28.80)
>DroSec_CAF1 17980 120 - 1
UUUUCUUUUAAUGAAACAGUUGUUGCCUGGCGGCAUUAUGACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAA
...((((.((((((((.((((((((((....)))).....)))))).)).)))))).))))....(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).).. ( -28.80)
>DroEre_CAF1 13206 120 - 1
UUUUCUUUUAAUGAAACAGUUGUUGCCUGGCGGCAUUAUGACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUUGAA
...((((.((((((((.((((((((((....)))).....)))))).)).)))))).))))....((((((((((((((.(((.((..(.....)..)).))).)))))))))))))).. ( -32.90)
>DroYak_CAF1 6396 120 - 1
UUUUCUUUUAAUGAAACAGUUGUUGCCUGGCGGCAUUAUGACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAA
...((((.((((((((.((((((((((....)))).....)))))).)).)))))).))))....(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).).. ( -28.80)
>consensus
UUUUCUUUUAAUGAAACAGUUGUUGCCUGGCGGCAUUAUGACGAUUAUUAUUAUUAUGAGGCAUGCAAAAGUUGCCGUUAAAGCAUCGUGUAAAAUAAUAUUUAGACGGCAACUUUCGAA
...((((.((((((((.((((((((((....)))).....)))))).)).)))))).))))....(.((((((((((((.(((.((..(.....)..)).))).)))))))))))).).. (-28.80 = -28.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:35 2006