Locus 3334

Sequence ID	2R_DroMel_CAF1
Location	11,340,271 – 11,340,417
Length	146
Max. P	0.660911

overview

Window 6

Location	11,340,271 – 11,340,381
Length	110
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	89.33
Mean single sequence MFE	-27.38
Consensus MFE	-23.12
Energy contribution	-23.88
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.660911
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11340271 110 + 20766785
AUCGUCGCUGCGAUCAGCGAUCAGCAGAAAUCAUCGUCAUCAUCAUCAUCGAUCCGGCGAUCCAGAGCCCUUCGACUUUCGUCGAAUGCACUGAAAGAAAAUAUAUAC-----AU
.(((((((((.((((.((.....)).((.....))...............))))))))))).(((.((..((((((....)))))).)).)))...))..........-----.. ( -28.70)
>DroSec_CAF1 127995 110 + 1
AUCGUCGCUGCGAUCAGCGAUCAGCAGAAAUCAUCGUCAUCAUCAUCAUCGAUCCGGCGAUUCAGAGCUCUUCGACUUUCGUCGAAUGCACUGAGAGAAAUAAUAUAU-----AU
.(((((((((.((((.((.....)).((.....))...............)))))))))))((((.((..((((((....)))))).)).))))))............-----.. ( -30.70)
>DroSim_CAF1 133733 105 + 1
AUCGUCGCUGCGAUCAGCGAUCAGCAGAAAUCAUC---AUCAUCAUCAUCGAUCCGGCGAUUCAGAGCCCUUCGACUUUCGUCAAAUGCACCGAGAGAAAAAAU--AU-----AU
...(((((((....)))))))..............---..........((((...(((........)))..))))((((((..........)))))).......--..-----.. ( -22.00)
>DroYak_CAF1 131096 115 + 1
AUCGUCGCUGCGAUCAGCGAUCAGCAAAAAUCAUCGUCAUCAUCAUCAUCGAUCCGGCGAUCCAGAGCCCUUCGACUUUCGUCGAUUGCACUGAGAAAAAAUGUAUACUAUGUUU
...(((((((....)))))))..(((.......(((((...(((......)))..)))))(((((.((...(((((....)))))..)).))).)).....)))........... ( -28.10)
>consensus
AUCGUCGCUGCGAUCAGCGAUCAGCAGAAAUCAUCGUCAUCAUCAUCAUCGAUCCGGCGAUCCAGAGCCCUUCGACUUUCGUCGAAUGCACUGAGAGAAAAAAUAUAC_____AU
...(((((((.((((.((.....)).((.....))...............))))))))))).(((.((...(((((....)))))..)).)))...................... (-23.12 = -23.88 +   0.75)

alignment

secondary structure

dotplot

Window 7

Location	11,340,306 – 11,340,417
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	82.82
Mean single sequence MFE	-27.25
Consensus MFE	-19.80
Energy contribution	-19.43
Covariance contribution	-0.37
Combinations/Pair	1.14
Mean z-score	-1.59
Structure conservation index	0.73
SVM decision value	0.17
SVM RNA-class probability	0.615249
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11340306 111 - 20766785
GGA----AUCUCAUUUAAAUUUUUUUGUGUUAUAUAGCUUAU-----GUAUAUAUUUUCUUUCAGUGCAUUCGACGAAAGUCGAAGGGCUCUGGAUCGCCGGAUCGAUGAUGAUGAUGAC
...----.(((((((...(((..((((.((((((((.....)-----)))))........(((((.((.((((((....))))))..)).)))))..))))))..)))...))))).)). ( -29.10)
>DroSec_CAF1 128030 109 - 1
GGA----AUCACAUUUAAAUUUAUUU--GUUAUAUAGCUUAU-----AUAUAUUAUUUCUCUCAGUGCAUUCGACGAAAGUCGAAGAGCUCUGAAUCGCCGGAUCGAUGAUGAUGAUGAC
...----.(((((((...(((.((((--(.((((((.....)-----))))).........((((.((.((((((....))))))..)).)))).....))))).)))...)))).))). ( -28.10)
>DroSim_CAF1 133768 104 - 1
GGA----AUCACAUUUAAAUUCAUUU--GUUAUAUAGCUUAU-----AU--AUUUUUUCUCUCGGUGCAUUUGACGAAAGUCGAAGGGCUCUGAAUCGCCGGAUCGAUGAUGAUGAU---
...----((((((((...((((....--..((((((...)))-----))--).........((((.((.((((((....))))))..)).))))......)))).)))).))))...--- ( -23.00)
>DroYak_CAF1 131131 118 - 1
GGAAUGCAUCCCAAUUCAAUUUCUUU--GUUAUAUAUACAAAACAUAGUAUACAUUUUUUCUCAGUGCAAUCGACGAAAGUCGAAGGGCUCUGGAUCGCCGGAUCGAUGAUGAUGAUGAC
.((((........)))).......(.--.((((.(((((........)))))((((...((.(((.((..(((((....)))))...)).)))((((....)))))).))))))))..). ( -28.80)
>consensus
GGA____AUCACAUUUAAAUUUAUUU__GUUAUAUAGCUUAU_____AUAUAUAUUUUCUCUCAGUGCAUUCGACGAAAGUCGAAGGGCUCUGAAUCGCCGGAUCGAUGAUGAUGAUGAC
............................(((((............................((((.((.((((((....))))))..)).))))((((......)))).)))))...... (-19.80 = -19.43 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:02 2006