Locus 7836

Sequence ID	3L_DroMel_CAF1
Location	20,982,093 – 20,982,293
Length	200
Max. P	0.954564

overview

Window 4

Location	20,982,093 – 20,982,213
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.97
Mean single sequence MFE	-23.16
Consensus MFE	-21.32
Energy contribution	-21.82
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.92
SVM decision value	0.05
SVM RNA-class probability	0.558338
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20982093 120 + 23771897
CGUACGUGUAUGUAUUCGACUGUCUGCCGCCUCAGCCGCAGUCGACGUCGCUGCCACCGCUUAAAUAUCCCCAAAAACGUCCCUUGAAUUCAUAUACAUAUAUAUUUUUUAUAUAUCCAU
.....(((((((.((((((..(.((((.((....)).)))).)(((((............................)))))..)))))).)))))))(((((((.....))))))).... ( -26.49)
>DroSim_CAF1 7164 120 + 1
CGUACGUGUAUGUAUUCGACUGUCUGCCGCCUCAGCCGCAGUCGACGUCGCUGCCGCCGCUUAAAUAUCCCCAAAAACGUCCCUUGAAUUCAUAUACAUAUAUAUUUUUUAUAUAUCCAU
.....(((((((.((((((..(.((((.((....)).)))).)(((((............................)))))..)))))).)))))))(((((((.....))))))).... ( -26.49)
>DroEre_CAF1 2859 120 + 1
CGUACGUGUAUGUAUUCGCCUGUCUGCCGCCUCUACCGCAGUCGACGUCGCUGCCACCGCUUAAAUAUCCCCAAAAACGUCCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUAUCCAU
.....(((((((..(((....(.((((.(......).)))).)(((((............................)))))....)))..)))))))(((((((.....))))))).... ( -20.19)
>DroYak_CAF1 5851 120 + 1
CGUACGUGUAUGUAUUCGCCUGUCUGCCGCCUCUACCGCAGUCGACGUCGCUGCCACCGCUUAAAAAUCCCCAAAAACGUCCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUACCCAU
.....(((((((..(((....(.((((.(......).)))).)(((((............................)))))....)))..))))))).((((((.....))))))..... ( -19.49)
>consensus
CGUACGUGUAUGUAUUCGACUGUCUGCCGCCUCAACCGCAGUCGACGUCGCUGCCACCGCUUAAAUAUCCCCAAAAACGUCCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUAUCCAU
.....(((((((.(((((...(.((((.(......).)))).)(((((............................)))))...))))).))))))).((((((.....))))))..... (-21.32 = -21.82 +   0.50)

alignment

secondary structure

dotplot

Window 5

Location	20,982,133 – 20,982,253
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.09
Mean single sequence MFE	-30.25
Consensus MFE	-30.61
Energy contribution	-30.55
Covariance contribution	-0.06
Combinations/Pair	1.11
Mean z-score	-1.84
Structure conservation index	1.01
SVM decision value	1.44
SVM RNA-class probability	0.954564
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20982133 120 - 23771897
UUUCUUUUCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGGACGUUUUUGGGGAUAUUUAAGCGGUGGCAGCGACGUCGAC
.......((((...((((((((((.((((.((((((....(((.(((((((.....))))))).)))....)))))).)).))...))))))))))....))))((((......)))).. ( -30.80)
>DroSim_CAF1 7204 116 - 1
U----UUUCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGGACGUUUUUGGGGAUAUUUAAGCGGCGGCAGCGACGUCGAC
.----..((((...((((((((((.((((.((((((....(((.(((((((.....))))))).)))....)))))).)).))...))))))))))....))))((((......)))).. ( -32.50)
>DroEre_CAF1 2899 116 - 1
-U---UUCCGCGUUAUAUUUUUAAUCGCUGUUGAGUGUAGAUGGAUAUAUAAAAUAUAUAUAUGUAUAUGAUUUCAAGGGACGUUUUUGGGGAUAUUUAAGCGGUGGCAGCGACGUCGAC
-.---..((((...((((((((((.((((.(((((.....(((.(((((((.....))))))).))).....))))).)).))...))))))))))....))))((((......)))).. ( -29.20)
>DroYak_CAF1 5891 117 - 1
UU---UUCCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGGUAUAUAAAAUAUAUAUAUGUAUAUGAUUUCAAGGGACGUUUUUGGGGAUUUUUAAGCGGUGGCAGCGACGUCGAC
..---..((((.....((((((((.((((.(((((.....(((.(((((((.....))))))).))).....))))).)).))...))))))))......))))((((......)))).. ( -28.50)
>consensus
UU___UUCCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGGACGUUUUUGGGGAUAUUUAAGCGGUGGCAGCGACGUCGAC
.......((((...((((((((((.((((.((((((....(((.(((((((.....))))))).)))....)))))).)).))...))))))))))....))))((((......)))).. (-30.61 = -30.55 +  -0.06)

alignment

secondary structure

dotplot

Window 6

Location	20,982,173 – 20,982,293
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.09
Mean single sequence MFE	-14.43
Consensus MFE	-11.20
Energy contribution	-11.95
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.78
SVM decision value	-0.05
SVM RNA-class probability	0.510574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20982173 120 + 23771897
CCCUUGAAUUCAUAUACAUAUAUAUUUUUUAUAUAUCCAUCUACACUCAACGGCGAUUAAAAAUAUAUCGCGAAAAGAAAAAAUAUAAAAACGAACUUCAAAGUGAAAUUCGAAAUUCCU
.....(((((..........((((((((((...............(.....)(((((.........)))))......))))))))))....((((.(((.....))).)))).))))).. ( -15.40)
>DroSim_CAF1 7244 116 + 1
CCCUUGAAUUCAUAUACAUAUAUAUUUUUUAUAUAUCCAUCUACACUCAACGGCGAUUAAAAAUAUAUCGCGAAA----AAAACAUAAAAACAAACUUCAAAGUGAAAUUCGAAAUUCCU
...((((((((((....(((((((.....)))))))................(((((.........)))))....----.......................))).)))))))....... ( -14.40)
>DroEre_CAF1 2939 116 + 1
CCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUAUCCAUCUACACUCAACAGCGAUUAAAAAUAUAACGCGGAA---A-AAAUAUAAAAACGAACUUCAAAGUGAAAUUCGAAAUUCCU
.((((((..........(((((((.....)))))))..........))))..(((.(((......))))))))..---.-...........((((.(((.....))).))))........ ( -13.45)
>DroYak_CAF1 5931 117 + 1
CCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUACCCAUCUACACUCAACGGCGAUUAAAAAUAUAUCGCGGAA---AAAAAUAUAAAAACGAACUUCAAAGUGAAAUUCGAAAUUCCU
.((((((...........((((((.....))))))...........))))..(((((.........)))))))..---.............((((.(((.....))).))))........ ( -14.45)
>consensus
CCCUUGAAAUCAUAUACAUAUAUAUAUUUUAUAUAUCCAUCUACACUCAACGGCGAUUAAAAAUAUAUCGCGAAA___AAAAAUAUAAAAACGAACUUCAAAGUGAAAUUCGAAAUUCCU
...((((((((((.....((((((.....)))))).................(((((.........)))))...............................))).)))))))....... (-11.20 = -11.95 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	20,982,173 – 20,982,293
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.09
Mean single sequence MFE	-25.07
Consensus MFE	-23.75
Energy contribution	-23.69
Covariance contribution	-0.06
Combinations/Pair	1.12
Mean z-score	-1.84
Structure conservation index	0.95
SVM decision value	1.15
SVM RNA-class probability	0.922383
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20982173 120 - 23771897
AGGAAUUUCGAAUUUCACUUUGAAGUUCGUUUUUAUAUUUUUUCUUUUCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGG
..((((((((((......)))))))))).....................(((((.........)))))(.((((((....(((.(((((((.....))))))).)))....)))))).). ( -26.20)
>DroSim_CAF1 7244 116 - 1
AGGAAUUUCGAAUUUCACUUUGAAGUUUGUUUUUAUGUUUU----UUUCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGG
..((((((((((......)))))))))).............----....(((((.........)))))(.((((((....(((.(((((((.....))))))).)))....)))))).). ( -24.00)
>DroEre_CAF1 2939 116 - 1
AGGAAUUUCGAAUUUCACUUUGAAGUUCGUUUUUAUAUUU-U---UUCCGCGUUAUAUUUUUAAUCGCUGUUGAGUGUAGAUGGAUAUAUAAAAUAUAUAUAUGUAUAUGAUUUCAAGGG
.(((((.....))))).(((((((((.(((..((((((((-.---..(.((((((......))).))).)..))))))))(((.(((((((.....))))))).))))))))))))))). ( -24.00)
>DroYak_CAF1 5931 117 - 1
AGGAAUUUCGAAUUUCACUUUGAAGUUCGUUUUUAUAUUUUU---UUCCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGGUAUAUAAAAUAUAUAUAUGUAUAUGAUUUCAAGGG
.((((...((((((((.....)))))))).............---))))(((((.........)))))(.(((((.....(((.(((((((.....))))))).))).....))))).). ( -26.09)
>consensus
AGGAAUUUCGAAUUUCACUUUGAAGUUCGUUUUUAUAUUUUU___UUCCGCGAUAUAUUUUUAAUCGCCGUUGAGUGUAGAUGGAUAUAUAAAAAAUAUAUAUGUAUAUGAAUUCAAGGG
.((((...((((((((.....))))))))................))))(((((.........)))))(.((((((....(((.(((((((.....))))))).)))....)))))).). (-23.75 = -23.69 +  -0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:15 2006