Locus 3948

Sequence ID	X_DroMel_CAF1
Location	10,508,101 – 10,508,316
Length	215
Max. P	0.992676

overview

Window 2

Location	10,508,101 – 10,508,216
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	91.65
Mean single sequence MFE	-38.90
Consensus MFE	-31.60
Energy contribution	-33.20
Covariance contribution	1.60
Combinations/Pair	1.06
Mean z-score	-2.54
Structure conservation index	0.81
SVM decision value	2.34
SVM RNA-class probability	0.992676
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10508101 115 + 22224390
CCAGCUAUCCGGGAUGCCAGUUGAUGCUACACACAUAGUUGCCAUUUGCAGCCAGCGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCGUCGCAUCGCAACGCAUCGCAUUAGCAG
...((((...(.(((((.(((....))).........(((((....((((((.(((........))))))))).......((((((...)))))))))))))))).)..)))).. ( -39.90)
>DroSec_CAF1 39492 115 + 1
CCAGCUAUCCGGGAUGCCAGUUGAUGCUACACACAUAGUUGCCAUUUGCAGCCAGCGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCGUCGCAUUGCAACGCAUCGCAUUAGCAG
...((((...(.(((((((((((((((..........(((((.....))))).((((((.....))))))(((((.....))))))))))).))))....))))).)..)))).. ( -38.10)
>DroSim_CAF1 42786 115 + 1
CCAGCUAUCCGGGAUGCCAGUUGAUGCUACACACAUAGUUGCCAUUUGCAGCCAGCGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCGUCGCAUUGCAACGCAUCGCAUUAGCAG
...((((...(.(((((((((((((((..........(((((.....))))).((((((.....))))))(((((.....))))))))))).))))....))))).)..)))).. ( -38.10)
>DroEre_CAF1 40285 115 + 1
CCAGCUAUGCUGCAUGCCAGUUGAUGCUGCACACAUAGUUGCCAUUUGCAGGCAGCGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCCUCGCAACGCAACGCAUCGCAUUAGCAG
...((((((((((.(((.(((....))))))......(((((...((((((((((((((.....))))))(((((.....))))))))).)))).))))))))..))).)))).. ( -44.70)
>DroYak_CAF1 41002 107 + 1
CCAGCUCUCUAGCAUGCCACAUG--------CACAUAGUUGCCAUUUGCUGGCAACGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCGUCGCAUCGCAACGCAUCGCAUUAGCAG
...((......(((((...))))--------).....(((((....(((.((((((........))))))))).......((((((...)))))))))))))...((....)).. ( -33.70)
>consensus
CCAGCUAUCCGGGAUGCCAGUUGAUGCUACACACAUAGUUGCCAUUUGCAGCCAGCGAUUUCCAGUUGCUGCAUCAUUCAGAUGCGCGUCGCAUCGCAACGCAUCGCAUUAGCAG
...((((...(.(((((.(((....))).........(((((....(((((.((((........))))))))).......((((((...)))))))))))))))).)..)))).. (-31.60 = -33.20 +   1.60)

alignment

secondary structure

dotplot

Window 3

Location	10,508,101 – 10,508,216
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	91.65
Mean single sequence MFE	-41.32
Consensus MFE	-32.48
Energy contribution	-33.92
Covariance contribution	1.44
Combinations/Pair	1.11
Mean z-score	-2.06
Structure conservation index	0.79
SVM decision value	1.15
SVM RNA-class probability	0.922817
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10508101 115 - 22224390
CUGCUAAUGCGAUGCGUUGCGAUGCGACGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGCUGGCUGCAAAUGGCAACUAUGUGUGUAGCAUCAACUGGCAUCCCGGAUAGCUGG
.(((((..((((((((((((...)))))))(((((.....)))))...........)))))..((((((.(((....).))...))))))......)))))..((((....)))) ( -40.90)
>DroSec_CAF1 39492 115 - 1
CUGCUAAUGCGAUGCGUUGCAAUGCGACGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGCUGGCUGCAAAUGGCAACUAUGUGUGUAGCAUCAACUGGCAUCCCGGAUAGCUGG
.(((((..((((((((((((...)))))))(((((.....)))))...........)))))..((((((.(((....).))...))))))......)))))..((((....)))) ( -40.90)
>DroSim_CAF1 42786 115 - 1
CUGCUAAUGCGAUGCGUUGCAAUGCGACGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGCUGGCUGCAAAUGGCAACUAUGUGUGUAGCAUCAACUGGCAUCCCGGAUAGCUGG
.(((((..((((((((((((...)))))))(((((.....)))))...........)))))..((((((.(((....).))...))))))......)))))..((((....)))) ( -40.90)
>DroEre_CAF1 40285 115 - 1
CUGCUAAUGCGAUGCGUUGCGUUGCGAGGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGCUGCCUGCAAAUGGCAACUAUGUGUGCAGCAUCAACUGGCAUGCAGCAUAGCUGG
..((((.(((.....(((((.((((.(((((((((.....)))))(((...........)))))))))))...)))))..(((((((((......)).))))))))))))))... ( -42.70)
>DroYak_CAF1 41002 107 - 1
CUGCUAAUGCGAUGCGUUGCGAUGCGACGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGUUGCCAGCAAAUGGCAACUAUGUG--------CAUGUGGCAUGCUAGAGAGCUGG
.(((((((((((((((((((...)))))))(((((.....)))))...........)))(((((((.....))))))).....)--------))).))))).(((....)))... ( -41.20)
>consensus
CUGCUAAUGCGAUGCGUUGCGAUGCGACGCGCAUCUGAAUGAUGCAGCAACUGGAAAUCGCUGGCUGCAAAUGGCAACUAUGUGUGUAGCAUCAACUGGCAUCCCGGAUAGCUGG
.(((((..((((((((((((...)))))))(((((.....)))))...........)))))..((((((.(((....).))...))))))......)))))..((((....)))) (-32.48 = -33.92 +   1.44)

alignment

secondary structure

dotplot

Window 4

Location	10,508,216 – 10,508,316
Length	100
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	83.20
Mean single sequence MFE	-28.50
Consensus MFE	-17.80
Energy contribution	-17.60
Covariance contribution	-0.20
Combinations/Pair	1.25
Mean z-score	-2.27
Structure conservation index	0.62
SVM decision value	0.69
SVM RNA-class probability	0.823738
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10508216 100 - 22224390
UACCCCCACAGCAAAUCCUCCCGCUCUUGCUGUGGCAACUCCUCCAUUCAUCAG---CUGCCAGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
.....(((((((((............)))))))))........((((......(---(.(((((.((.((((.....)))).)).))))).)).....)))). ( -29.80)
>DroSec_CAF1 39607 100 - 1
UCCUCCCACAGCAAAUCCUCCCGCUACUGAUGUGGCAUCUCCUCCAUUCAUCAG---CUGCCAGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
.....(((((............(((((....))))).................(---(.(((((.((.((((.....)))).)).))))).))....))))). ( -27.30)
>DroSim_CAF1 42901 100 - 1
UACUCCCACAGCAAAUCCUCCCGCUACUGAUGUGGCAUCUCCUCCAUUCAUCAG---CUGCCAGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
.....(((((............(((((....))))).................(---(.(((((.((.((((.....)))).)).))))).))....))))). ( -27.30)
>DroEre_CAF1 40400 100 - 1
ACCUCCCACACCCAAUCCUCCCGCUCAUGCUGUGGCAUCUCCACCAUUCAUCAG---CUGCCAGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
.....((((((...........(((.(((..((((........)))).))).))---).(((((.((.((((.....)))).)).)))))......)))))). ( -28.90)
>DroAna_CAF1 43532 94 - 1
ACCGCCCUUGUUCAUGCCACACACUCAUCAUCUGG---------CAGUCGUCAGUCGUUGUCGGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
...............(((((((.........((((---------((((.(.((..((....))..)).).))))))))..(((....)))......))))))) ( -29.20)
>consensus
UCCUCCCACAGCAAAUCCUCCCGCUCAUGAUGUGGCAUCUCCUCCAUUCAUCAG___CUGCCAGUUGUCAAUUGUCAGUUGUCACUUGGCUGCCUCGUGUGGC
.....(((((..........((((.......))))........................(((((.((.((((.....)))).)).))))).......))))). (-17.80 = -17.60 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:12:30 2006