Locus 6225

Sequence ID	X_DroMel_CAF1
Location	15,826,756 – 15,826,939
Length	183
Max. P	0.998179

overview

Window 2

Location	15,826,756 – 15,826,874
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-26.28
Consensus MFE	-21.89
Energy contribution	-21.57
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-1.46
Structure conservation index	0.83
SVM decision value	0.45
SVM RNA-class probability	0.743009
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826756 118 + 22224390
UGCAUUCAAAUUAAUGCUUAACCAUAACCUUGUGUGUAUGUAAAUAUAAACUUGGCAGGUUGAUUUUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAU
.(((((......)))))((((((....((..((.(((((....))))).))..))..))))))........--..(((......)))......((((((((((....))))))))))... ( -27.10)
>DroSec_CAF1 5624 118 + 1
UGCAUUCAAAUUAGUGCUGAGCCAUAACCUUGUGUGUAUGUAAAUAUAAACCAGGCAGGUUGCUUAUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAU
..........((((((((.(((.....(((.((.(((((....))))).)).)))..(((...........--.))).....)))))))))))((((((((((....))))))))))... ( -33.30)
>DroSim_CAF1 5413 118 + 1
UGCAUGUAAAUUAUUGCUGAACCAUAACCUUGUGUGUAUGUAAAUAUAAACUAGGCAGGUUGCUUAUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAU
.(((.(((((..((.((..((((....(((.((.(((((....))))).)).)))..))))))..))..))--))).....))).........((((((((((....))))))))))... ( -26.40)
>DroEre_CAF1 6134 117 + 1
UGUAUUAAAAUAAAUGUUGAACCAUAACCGUGUGUGUAUGUAAAUAUAAACUAGGCAGGUUGCUUUUUUU---UACCAUUCUGCUGUCACUAAACAUACGUACAAGUGUAUGUAUGUGAU
.................(((.........((...(((((....))))).))..(((((..((........---...))..))))).)))....((((((((((....))))))))))... ( -21.20)
>DroYak_CAF1 5427 120 + 1
UGUAUUGAAAUAAAUAUUGAACCAUAACCGUGUGUAUAUGUAAAUAUAAACUAGGCAGGUUAAUUUUUUUUUCUACCAUUCUGCUGGCACCAAACAUACGUACAAGUGUAUGUAUGUGAU
......((((.(((.(((((.((....((..((.(((((....))))).))..))..))))))).))).))))..(((......)))......((((((((((....))))))))))... ( -23.40)
>consensus
UGCAUUCAAAUUAAUGCUGAACCAUAACCUUGUGUGUAUGUAAAUAUAAACUAGGCAGGUUGCUUUUUUUU__UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAU
.(((((......)))))..............((((((((....))))......((((((....................)))))).))))...((((((((((....))))))))))... (-21.89 = -21.57 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	15,826,796 – 15,826,906
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.00
Mean single sequence MFE	-27.06
Consensus MFE	-24.67
Energy contribution	-24.27
Covariance contribution	-0.40
Combinations/Pair	1.08
Mean z-score	-2.18
Structure conservation index	0.91
SVM decision value	3.03
SVM RNA-class probability	0.998179
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826796 110 + 22224390
UAAAUAUAAACUUGGCAGGUUGAUUUUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUGU----A----CAUGUGUAA
.............(((((..((.........--...))..))))).((((...((((((((((....))))))))))(((((.....)))))..........----.----...)))).. ( -28.90)
>DroSec_CAF1 5664 114 + 1
UAAAUAUAAACCAGGCAGGUUGCUUAUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUUUGUAGAUA----CAUAUGUAA
...(((((..((((.(((..((.(.......--.).))..)))))))..(((.((((((((((....))))))))))(((((.....))))).........)))...----..))))).. ( -28.50)
>DroSim_CAF1 5453 114 + 1
UAAAUAUAAACUAGGCAGGUUGCUUAUUUUU--UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUGUAGAUA----CAUAUGUAA
...(((((...(((((.....))))).....--......(((((.((......((((((((((....))))))))))(((((.....))))).....)).)))))..----..))))).. ( -28.20)
>DroEre_CAF1 6174 113 + 1
UAAAUAUAAACUAGGCAGGUUGCUUUUUUU---UACCAUUCUGCUGUCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUCUACAUAUG----UAUAUAA
....((((.((..(((((..((........---...))..)))))........((((((((((....))))))))))(((((.....)))))................)----).)))). ( -25.30)
>DroYak_CAF1 5467 120 + 1
UAAAUAUAAACUAGGCAGGUUAAUUUUUUUUUCUACCAUUCUGCUGGCACCAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCUUUUAUCUCUACAUAUAUACAUAUAUAA
.....(((((..((((.(((..(........)..))).....(((((((....((((((((((....))))))))))..)))...))))))))))))).......(((((....))))). ( -24.40)
>consensus
UAAAUAUAAACUAGGCAGGUUGCUUUUUUUU__UACCAUUCUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUGUACAUA____CAUAUGUAA
...(((((.....((((((....................))))))........((((((((((....))))))))))(((((.....))))).....................))))).. (-24.67 = -24.27 +  -0.40)

alignment

secondary structure

dotplot

Window 4

Location	15,826,834 – 15,826,939
Length	105
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	82.91
Mean single sequence MFE	-27.00
Consensus MFE	-20.72
Energy contribution	-20.50
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-2.96
Structure conservation index	0.77
SVM decision value	1.92
SVM RNA-class probability	0.982618
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15826834 105 + 22224390
CUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUGU----A----CAUGUGUAAAAUGUAACGUUACCUGUGGUACACAGCAAUAAA-------
.(((((((((...((((((((((....))))))))))(((((.....)))))..........----.----...))))..........((.(((...))))).))))).....------- ( -30.80)
>DroEre_CAF1 6211 115 + 1
CUGCUGUCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUCUACAUAUG----UAUAUAAAAUGUAAC-UAAACUGUGCCACCCAACAAUAAAUAAAUAA
.(((.(((((...(((((((......)))))))..))))))))...((((.((((((....(((((...----........)))))..-)))).)))))).................... ( -21.80)
>DroYak_CAF1 5507 119 + 1
CUGCUGGCACCAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCUUUUAUCUCUACAUAUAUACAUAUAUAAAAUGUAAC-UUAACUGUGCCACCCAACAAUAAAUAAAUAA
....((((((...((((((((((....))))))))))(((((.....))))).................(((((.......)))))..-......))))))................... ( -28.40)
>consensus
CUGCUGGCACUAAACAUACGUACAAGUGUAUGUAUGUGAUGCACUCGGCGUCAUUUAUCUCUACAUAU___CAUAUAUAAAAUGUAAC_UUAACUGUGCCACCCAACAAUAAAUAAAUAA
....((.(((...((((((((((....))))))))))(((((.....)))))...........................................))).))................... (-20.72 = -20.50 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:45 2006