Locus 2732

Sequence ID	2R_DroMel_CAF1
Location	9,577,839 – 9,578,039
Length	200
Max. P	0.952124

overview

Window 8

Location	9,577,839 – 9,577,959
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	93.89
Mean single sequence MFE	-30.91
Consensus MFE	-28.61
Energy contribution	-28.17
Covariance contribution	-0.44
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.93
SVM decision value	0.01
SVM RNA-class probability	0.536831
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9577839 120 + 20766785
UCCGGCGGCUGCCUUUCAGUUUGUUUUCAAUGGUAGGAUGUUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGC
..(((((((.((...(((((.(((...(((((....((((...(((........)))...))))...)))))...))).))).((((((((....))))))))))...)).))))).)). ( -32.10)
>DroSim_CAF1 1251 116 + 1
UCCGGCGGCUGCCUUUCAGUUUGUUUUCAAUGGUAGGAUGCUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACA----UGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGC
(((((((.(((((..................)))))..))))))).......(((((((((.........((....))----.((((((((....)))))))))))))))))........ ( -31.77)
>DroYak_CAF1 2385 120 + 1
AUCGGCUACUGCCUUUCAGUUUGUUUUCAAUGGUAGGAUGCUGGGAAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCGCGC
.(((((..(((((..................)))))...)))))......(((((((((((.........((....)).....((((((((....)))))))))))))))))..)).... ( -28.87)
>consensus
UCCGGCGGCUGCCUUUCAGUUUGUUUUCAAUGGUAGGAUGCUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGC
.(((((..(((((..................)))))...)))))........(((((((((.........((....)).....((((((((....)))))))))))))))))........ (-28.61 = -28.17 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	9,577,879 – 9,577,999
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	96.11
Mean single sequence MFE	-28.63
Consensus MFE	-26.60
Energy contribution	-27.27
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.93
SVM decision value	1.13
SVM RNA-class probability	0.920084
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9577879 120 + 20766785
UUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUA
.(((((((..(((((((((((.........((....)).....((((((((....))))))))))))))))((((((....)))))).......)))..))))).))............. ( -29.70)
>DroSim_CAF1 1291 116 + 1
CUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACA----UGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUA
...(((((..(((((((((((.........((....))----.((((((((....))))))))))))))))((((((....)))))).......)))..)))))................ ( -29.60)
>DroYak_CAF1 2425 120 + 1
CUGGGAAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCGCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUA
...........................((((((........((((((((((....))))))))))...((.(((((......)))))..)).................))))))...... ( -26.60)
>consensus
CUGGGUAUCUGUUAACUAAUCAUUAAAUAUUGCAUACAUACUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUA
.(((((((..(((((((((((.........((....)).....((((((((....))))))))))))))))((((((....)))))).......)))..))))).))............. (-26.60 = -27.27 +   0.67)

alignment

secondary structure

dotplot

Window 0

Location	9,577,879 – 9,577,999
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	96.11
Mean single sequence MFE	-28.57
Consensus MFE	-27.07
Energy contribution	-27.07
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.47
Structure conservation index	0.95
SVM decision value	1.42
SVM RNA-class probability	0.952124
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9577879 120 - 20766785
UAUAUUUAUUGCGUGUGAUAUAAAUUUAUGCAAGCUGCCCGCGAGCAGCAACUAAUCGCUAUUUGUAAUCAAACAGCAAGUAUGUAUGCAAUAUUUAAUGAUUAGUUAACAGAUACCCAA
..(((((.(((((((...........)))))))(((((......)))))(((((((((((.((((....)))).)))((((((.......))))))...))))))))...)))))..... ( -29.30)
>DroSim_CAF1 1291 116 - 1
UAUAUUUAUUGCGUGUGAUAUAAAUUUAUGCAAGCUGCCCGCGAGCAGCAACUAAUCGCUAUUUGUAAUCAAACAGCA----UGUAUGCAAUAUUUAAUGAUUAGUUAACAGAUACCCAG
..(((((.(((((((...........)))))))(((((......)))))(((((((((((.((((....)))).))).----((....)).........))))))))...)))))..... ( -27.30)
>DroYak_CAF1 2425 120 - 1
UAUAUUUAUUGCGUGUGAUAUAAAUUUAUGCAAGCUGCCCGCGCGCAGCAACUAAUCGCUAUUUGUAAUCAAACAGCAAGUAUGUAUGCAAUAUUUAAUGAUUAGUUAACAGAUUCCCAG
........(((((((...........)))))))(((((......)))))(((((((((((.((((....)))).)))((((((.......))))))...))))))))............. ( -29.10)
>consensus
UAUAUUUAUUGCGUGUGAUAUAAAUUUAUGCAAGCUGCCCGCGAGCAGCAACUAAUCGCUAUUUGUAAUCAAACAGCAAGUAUGUAUGCAAUAUUUAAUGAUUAGUUAACAGAUACCCAG
........(((((((...........)))))))(((((......)))))(((((((((((.((((....)))).))).....((....)).........))))))))............. (-27.07 = -27.07 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	9,577,919 – 9,578,039
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.22
Mean single sequence MFE	-24.79
Consensus MFE	-21.79
Energy contribution	-21.90
Covariance contribution	0.11
Combinations/Pair	1.03
Mean z-score	-1.82
Structure conservation index	0.88
SVM decision value	-0.05
SVM RNA-class probability	0.506415
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9577919 120 + 20766785
CUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUAAUAAAAGUAACUUAAGAUUUCGAAAUCAAGAAAAUUCUAA
.((((((((((....))))))))))..((((((((((....))))))((((.................))))................))))..(((((((........))))..))).. ( -24.43)
>DroSim_CAF1 1329 118 + 1
--UGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUAAUAAAAGUAACAUAAGAUUUCGAAAUCAAGAAAAUUCUAA
--.((((((((....)))))))).....(((((((((....))))))((((.................))))................)))...(((((((........))))..))).. ( -23.23)
>DroYak_CAF1 2465 120 + 1
CUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCGCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUAAUAAAAGUAACUUAGGAUUUCGAAAUCAAGAAAAUUCUAA
.((((((((((....))))))))))..((((((((((.((.....)).)))....((((((..........))))))........)))))))(((((((((........).)))))))). ( -26.70)
>consensus
CUUGCUGUUUGAUUACAAAUAGCGAUUAGUUGCUGCUCGCGGGCAGCUUGCAUAAAUUUAUAUCACACGCAAUAAAUAUAAUAAAAGUAACUUAAGAUUUCGAAAUCAAGAAAAUUCUAA
.((((((((((....))))))))))...((((((((..((.....))..))....((((((..........))))))........))))))...(((((((........))))..))).. (-21.79 = -21.90 +   0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:07 2006