Locus 1779

Sequence ID	2R_DroMel_CAF1
Location	6,648,130 – 6,648,261
Length	131
Max. P	0.986551

overview

Window 8

Location	6,648,130 – 6,648,233
Length	103
Sequences	4
Columns	112
Reading direction	forward
Mean pairwise identity	94.88
Mean single sequence MFE	-25.93
Consensus MFE	-25.84
Energy contribution	-25.65
Covariance contribution	-0.19
Combinations/Pair	1.03
Mean z-score	-2.27
Structure conservation index	1.00
SVM decision value	2.05
SVM RNA-class probability	0.986551
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6648130 103 + 20766785
---------UGUUUGUGUUUGUUUUUGCAUAUCUGCAUCCGAACAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACA
---------.(((((((((......((((....)))).((((((((((..........(((.....)))(((((......))))).))))))))))...))))))))).... ( -25.00)
>DroSec_CAF1 197506 103 + 1
---------UGUUUGUGUUUGUUUUUGCAUAUCUGCAUCCGAACAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACA
---------.(((((((((......((((....)))).((((((((((..........(((.....)))(((((......))))).))))))))))...))))))))).... ( -25.00)
>DroSim_CAF1 185255 103 + 1
---------UGUUUGUGUCUGUUUUUGCAUAUCUGCAUCCGAACAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACA
---------.(((((((((......((((....)))).((((((((((..........(((.....)))(((((......))))).))))))))))...))))))))).... ( -27.50)
>DroYak_CAF1 205514 112 + 1
UUGUGCUUGCGUUUGUGUUUGUUUUUGCAUAUCUGCAUCCGAACAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACA
(((((..((((..(((((........)))))..)))).((((((((((..........(((.....)))(((((......))))).)))))))))).....)))))...... ( -26.20)
>consensus
_________UGUUUGUGUUUGUUUUUGCAUAUCUGCAUCCGAACAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACA
..........(((((((((......((((....)))).((((((((((..........(((.....)))(((((......))))).))))))))))...))))))))).... (-25.84 = -25.65 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	6,648,130 – 6,648,233
Length	103
Sequences	4
Columns	112
Reading direction	reverse
Mean pairwise identity	94.88
Mean single sequence MFE	-19.75
Consensus MFE	-19.20
Energy contribution	-19.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.97
SVM decision value	0.85
SVM RNA-class probability	0.867069
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6648130 103 - 20766785
UGUAAUUUAUGUCAAGCCAAACAAAAAACAACGAAAUUGUUGUGGCACAUAACCGAGAGCAGCACUUUGUUCGGAUGCAGAUAUGCAAAAACAAACACAAACA---------
(((...((((((...(((((((((............))))).))))))))))((((..((((....)))))))).((((....))))...)))..........--------- ( -19.20)
>DroSec_CAF1 197506 103 - 1
UGUAAUUUAUGUCAAGCCAAACAAAAAACAACGAAAUUGUUGUGGCACAUAACCGAGAGCAGCACUUUGUUCGGAUGCAGAUAUGCAAAAACAAACACAAACA---------
(((...((((((...(((((((((............))))).))))))))))((((..((((....)))))))).((((....))))...)))..........--------- ( -19.20)
>DroSim_CAF1 185255 103 - 1
UGUAAUUUAUGUCAAGCCAAACAAAAAACAACGAAAUUGUUGUGGCACAUAACCGAGAGCAGCACUUUGUUCGGAUGCAGAUAUGCAAAAACAGACACAAACA---------
.....(((.((((..(((((((((............))))).))))......((((..((((....)))))))).((((....))))......)))).)))..--------- ( -20.90)
>DroYak_CAF1 205514 112 - 1
UGUAAUUUAUGUCAAGCCAAACAAAAAACAACGAAAUUGUUGUGGCACAUAACCGAGAGCAGCACUUUGUUCGGAUGCAGAUAUGCAAAAACAAACACAAACGCAAGCACAA
(((...((((((...(((((((((............))))).))))))))))((((..((((....)))))))).((((....))))...)))........(....)..... ( -19.70)
>consensus
UGUAAUUUAUGUCAAGCCAAACAAAAAACAACGAAAUUGUUGUGGCACAUAACCGAGAGCAGCACUUUGUUCGGAUGCAGAUAUGCAAAAACAAACACAAACA_________
(((...((((((...(((((((((............))))).))))))))))((((..((((....)))))))).((((....))))...)))................... (-19.20 = -19.20 +  -0.00)

alignment

secondary structure

dotplot

Window 0

Location	6,648,161 – 6,648,261
Length	100
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-24.25
Consensus MFE	-21.37
Energy contribution	-21.53
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.38
Structure conservation index	0.88
SVM decision value	0.24
SVM RNA-class probability	0.649120
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6648161 100 + 20766785
GAA------CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAGCACGCA
...------....((((((.......((((((((((.(((((............)))))))))...))))))......(((......))).......))))))... ( -23.90)
>DroSec_CAF1 197537 100 + 1
GAA------CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAGCACGCA
...------....((((((.......((((((((((.(((((............)))))))))...))))))......(((......))).......))))))... ( -23.90)
>DroSim_CAF1 185286 100 + 1
GAA------CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAUCACGCA
...------....((((((.....(((.....))).........((((((((((.((((......)))).)))..)))))))))))))((.............)). ( -23.12)
>DroEre_CAF1 198925 100 + 1
GAA------CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAGCACGCA
...------....((((((.......((((((((((.(((((............)))))))))...))))))......(((......))).......))))))... ( -23.90)
>DroYak_CAF1 205554 100 + 1
GAA------CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAGCACGCA
...------....((((((.......((((((((((.(((((............)))))))))...))))))......(((......))).......))))))... ( -23.90)
>DroAna_CAF1 212874 91 + 1
GAAUGUGUGCAAAGUGCUGCUCUUGGUUAUGUGCCACAACAAUUUCAUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCA---------------CGCA
...(((((((....(((((.......((((((((((.(((((............)))))))))...))))))....)))))...)))---------------)))) ( -26.80)
>consensus
GAA______CAAAGUGCUGCUCUCGGUUAUGUGCCACAACAAUUUCGUUGUUUUUUGUUUGGCUUGACAUAAAUUACAGCGACAGCACGCAAAACUUCAGCACGCA
.............(((((((.((.(.((((((((((.(((((............)))))))))...))))))....))).).)))))).................. (-21.37 = -21.53 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:58 2006