Locus 6040

Sequence ID	X_DroMel_CAF1
Location	15,505,606 – 15,505,805
Length	199
Max. P	0.999900

overview

Window 3

Location	15,505,606 – 15,505,715
Length	109
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	91.58
Mean single sequence MFE	-32.54
Consensus MFE	-29.90
Energy contribution	-29.58
Covariance contribution	-0.32
Combinations/Pair	1.14
Mean z-score	-2.70
Structure conservation index	0.92
SVM decision value	4.45
SVM RNA-class probability	0.999900
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15505606 109 + 22224390
GAUUUCCAUCGUAUAAUGCUUGACAAAUGCUCCGGCUAACGAUCGGCAUAUAU----AAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAUCAUCAUUUGUGCGAUUGA
....((.(((((((((....(((...(((((.((.....))...)))))....----........(((((((....((.....))..))))))))))....))))))))).)) ( -31.70)
>DroSec_CAF1 66247 109 + 1
GAUUUCCAUCGUAUAAUGCUUGACAAAUGCCCCGGCUAACGAUCGGCAUAUAUUAU-UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU---AAUUUGUGCGAUUGA
....((.(((((((((..........(((((.((.....))...))))).......-.......((((((((....((.....))..))))))))---...))))))))).)) ( -32.60)
>DroSim_CAF1 78558 109 + 1
GAUUUCCAUCGUAUAAUGCUUGACAAAUGCCCCGGCUAACGAUCGGCAUAUAUUAU-UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU---CAUUUGUGCGAUUGA
....((.(((((((((....(((...(((((.((.....))...))))).......-........(((((((....((.....))..))))))))---)).))))))))).)) ( -32.60)
>DroEre_CAF1 67731 106 + 1
GAUUUCCAUCGCAUAAUGUUUGACAAAUGCCCCGGCUAACGAUUGGCAUAUAUUA----UAUUAAUGGGCCACAAGGGACCUUCCAUUGGGCCAU---CAAUUGUGCGAUUGA
....((.((((((((((...(((...(((((.((.....))...)))))......----........((((.(((.((.....)).))))))).)---)))))))))))).)) ( -32.60)
>DroYak_CAF1 72122 110 + 1
GAUUUCCAUUCCAUAAUGUUUGACAAAUGCCCCGGCUAACGAUCGGCAUAUAUUAUGGAUAUAAAUGGCCCACAAGGGACCUUCCAUUGGGCCGU---CAAUUGUGCGAUUGA
.........((((((((((.......(((((.((.....))...))))))))))))))).....((((((((....((.....))..))))))))---(((((....))))). ( -33.21)
>consensus
GAUUUCCAUCGUAUAAUGCUUGACAAAUGCCCCGGCUAACGAUCGGCAUAUAUUAU_UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU___CAUUUGUGCGAUUGA
....((.(((((((((..........(((((.((.....))...)))))...............((((((((....((.....))..))))))))......))))))))).)) (-29.90 = -29.58 +  -0.32)

alignment

secondary structure

dotplot

Window 4

Location	15,505,639 – 15,505,755
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.99
Mean single sequence MFE	-28.45
Consensus MFE	-22.10
Energy contribution	-21.98
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.74
Structure conservation index	0.78
SVM decision value	0.45
SVM RNA-class probability	0.739575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15505639 116 + 22224390
GGCUAACGAUCGGCAUAUAU----AAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAUCAUCAUUUGUGCGAUUGAUAUACAUGUUCCGAAAUUGAUUGAGAUUUGAUUUUGGGAA
......((((((.((((...----.......((((((((....((.....))..)))))))).......)))))))))).........(((((((((..(.......)..))))))))). ( -35.13)
>DroSec_CAF1 66280 109 + 1
GGCUAACGAUCGGCAUAUAUUAU-UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU---AAUUUGUGCGAUUGAUAUACAUAUUCCCAAAUUGAUUGAGAUUUGAUU-------
......((((((.((((.((((.-........(((((((....((.....))..))))))))---))).)))))))))).............((((((......))))))...------- ( -28.10)
>DroSim_CAF1 78591 109 + 1
GGCUAACGAUCGGCAUAUAUUAU-UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU---CAUUUGUGCGAUUGAUAUACAUAUUCCCAAAUUGAUUGAGAUUUGAUU-------
......((((((.(((((((...-.)))...((((((((....((.....))..))))))))---....)))))))))).............((((((......))))))...------- ( -26.80)
>DroEre_CAF1 67764 113 + 1
GGCUAACGAUUGGCAUAUAUUA----UAUUAAUGGGCCACAAGGGACCUUCCAUUGGGCCAU---CAAUUGUGCGAUUGAUAUACAUAUUCUGAAAUUGAUUGAGAUUUGAAUUCGAAAA
.((((.....))))........----.....(((((((.(((.((.....)).)))))))((---(((((....)))))))...))).(((.(((.(..(.......)..).)))))).. ( -23.90)
>DroYak_CAF1 72155 117 + 1
GGCUAACGAUCGGCAUAUAUUAUGGAUAUAAAUGGCCCACAAGGGACCUUCCAUUGGGCCGU---CAAUUGUGCGAUUGAAAUACAAAUUCGGAAAUUGAUUGAGAUUUGAAAUUGAAAA
......(((((((((((((((...)))))).((((((((....((.....))..))))))))---....))).)))))).....(((.((((((..((....))..)))))).))).... ( -28.30)
>consensus
GGCUAACGAUCGGCAUAUAUUAU_UAUAUUAAUGGCCCACAAGGGACCUUCCAUUGGGCCAU___CAUUUGUGCGAUUGAUAUACAUAUUCCGAAAUUGAUUGAGAUUUGAUUU_G__AA
......((((((.((((..............((((((((....((.....))..)))))))).......))))))))))..............(((((......)))))........... (-22.10 = -21.98 +  -0.12)

alignment

secondary structure

dotplot

Window 5

Location	15,505,715 – 15,505,805
Length	90
Sequences	4
Columns	102
Reading direction	reverse
Mean pairwise identity	71.20
Mean single sequence MFE	-13.31
Consensus MFE	-6.47
Energy contribution	-7.23
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	0.49
SVM decision value	2.00
SVM RNA-class probability	0.985223
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15505715 90 - 22224390
-----------AAUCCGCAGGAUAUAAUUCUAA-AAGUCACUCCUGACAUCUUGCCAAACACUUCCCAAAAUCAAAUCUCAAUCAAUUUCGGAACAUGUAUA
-----------.....(((((((.((....)).-..((((....)))))))))))...(((.((((.(((................))).))))..)))... ( -10.39)
>DroSec_CAF1 66356 79 - 1
-----------AAUCCGCAGGAUAUAAUUCUAAAAAGUCAUUUCUGACAUCUUCCCA------------AAUCAAAUCUCAAUCAAUUUGGGAAUAUGUAUA
-----------......(((((...................)))))((((.((((((------------(((.............))))))))).))))... ( -14.83)
>DroSim_CAF1 78667 79 - 1
-----------AAUCCGCAGGAUAUAAUUUUAAAAAGUCACUCCUGACAUCUUCCCA------------AAUCAAAUCUCAAUCAAUUUGGGAAUAUGUAUA
-----------......(((((....((((....))))...)))))((((.((((((------------(((.............))))))))).))))... ( -17.32)
>DroYak_CAF1 72232 94 - 1
UUAACAGUUCA-----AAAGGAUAUAAAUCCAG-AAGUCACUCCUGACAUUUA--CAGACACUUUUCAAUUUCAAAUCUCAAUCAAUUUCCGAAUUUGUAUU
...(((((((.-----...((((....)))).(-((((((....)))).....--..((......))...)))..................))).))))... ( -10.70)
>consensus
___________AAUCCGCAGGAUAUAAUUCUAA_AAGUCACUCCUGACAUCUUCCCA____________AAUCAAAUCUCAAUCAAUUUCGGAAUAUGUAUA
.....................(((((..........((((....))))............................((((((.....))))))...))))). ( -6.47 =  -7.23 +   0.75)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:42 2006