Locus 324

Sequence ID	3L_DroMel_CAF1
Location	942,374 – 942,468
Length	94
Max. P	0.998844

overview

Window 4

Location	942,374 – 942,468
Length	94
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	74.12
Mean single sequence MFE	-27.00
Consensus MFE	-6.58
Energy contribution	-6.78
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.87
Structure conservation index	0.24
SVM decision value	3.25
SVM RNA-class probability	0.998844
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 942374 94 + 23771897
ACAGACCGCAAUCGAAACCGAAAUCGAAAUGGGAAUCAGAAU------------CCGAGUCUGAAUCGGA------AUCGGAAUCGGAAUCCGAGG-----CGAGUCACAAUCAAAA
...((((((..((((........))))....(((.((.((.(------------((((.((((...))))------.))))).)).)).)))...)-----)).))).......... ( -28.80)
>DroSec_CAF1 77420 82 + 1
ACAGAC------------CGAAAUCGAAGUGGGAAUCGGAAU------------CCGAGUCUGAAUCGGA------AUCUGAAUCGGAAUCCGAGG-----CGACUCACAAUCAAAA
.....(------------(((..((......))..))))...------------..(((((.(..(((((------.((((...)))).)))))..-----)))))).......... ( -23.80)
>DroSim_CAF1 69330 100 + 1
ACAGACCGCAAUCGAAACCGAAAUCGAAAUGGGAAUCGGAAU------------CCGAGUCUGAAUCGGAAUCGGAAUCUCAAUCGGAAUCCGAGG-----CGAGUCACAAUCAAAA
...((((((..((((........))))..(((((.((.((.(------------((((.......))))).)).)).))))).((((...)))).)-----)).))).......... ( -31.20)
>DroEre_CAF1 79320 111 + 1
ACAGACCGCAAUCGAAACCGAAAUCGAAAUGCGAAUCGGCAUCCCAAUCCGCAUCCGAAUGUGAAUCGGA------UUCGCAAUCGCAAUCCGAGGCAAUGCGAGUCACAAUCAAAA
...(((((((.(((....)))..(((..(((((.((.((....)).)).))))).)))...((..(((((------((.((....)))))))))..)).)))).))).......... ( -32.60)
>DroYak_CAF1 81247 83 + 1
ACAGACCGCAAUCGAAACCGAAAUCGAAAUGGGAAUCGGAAU------------CCGAAUCUGAAUCGGA------AUCGCA-UCGCAAUC----GCAAUCCGAGG-----------
.....(((...((((........))))..)))...(((((.(------------((((.......)))))------......-..((....----))..)))))..----------- ( -18.60)
>consensus
ACAGACCGCAAUCGAAACCGAAAUCGAAAUGGGAAUCGGAAU____________CCGAGUCUGAAUCGGA______AUCGCAAUCGGAAUCCGAGG_____CGAGUCACAAUCAAAA
..................(((..((((........))))...............((((.......))))..............)))............................... ( -6.58 =  -6.78 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	942,374 – 942,468
Length	94
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	74.12
Mean single sequence MFE	-29.52
Consensus MFE	-9.62
Energy contribution	-11.86
Covariance contribution	2.24
Combinations/Pair	1.05
Mean z-score	-2.48
Structure conservation index	0.33
SVM decision value	2.44
SVM RNA-class probability	0.994025
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 942374 94 - 23771897
UUUUGAUUGUGACUCG-----CCUCGGAUUCCGAUUCCGAU------UCCGAUUCAGACUCGG------------AUUCUGAUUCCCAUUUCGAUUUCGGUUUCGAUUGCGGUCUGU
..........(((.((-----(.(((((..((((...(((.------...((.(((((.....------------..))))).)).....)))...)))).)))))..))))))... ( -26.20)
>DroSec_CAF1 77420 82 - 1
UUUUGAUUGUGAGUCG-----CCUCGGAUUCCGAUUCAGAU------UCCGAUUCAGACUCGG------------AUUCCGAUUCCCACUUCGAUUUCG------------GUCUGU
....(((((.(((((.-----..((((...))))....)))------)))))))(((((.(((------------(...(((........)))..))))------------))))). ( -23.50)
>DroSim_CAF1 69330 100 - 1
UUUUGAUUGUGACUCG-----CCUCGGAUUCCGAUUGAGAUUCCGAUUCCGAUUCAGACUCGG------------AUUCCGAUUCCCAUUUCGAUUUCGGUUUCGAUUGCGGUCUGU
..........(((.((-----(.(((((..(((((((((((((.((.(((((.......))))------------).)).)).....)))))))..)))).)))))..))))))... ( -29.20)
>DroEre_CAF1 79320 111 - 1
UUUUGAUUGUGACUCGCAUUGCCUCGGAUUGCGAUUGCGAA------UCCGAUUCACAUUCGGAUGCGGAUUGGGAUGCCGAUUCGCAUUUCGAUUUCGGUUUCGAUUGCGGUCUGU
....(((((..(.(((....((((((((((((....)).))------))))).......(((((((((((((((....)))))))))).)))))....)))..))))..)))))... ( -41.30)
>DroYak_CAF1 81247 83 - 1
-----------CCUCGGAUUGC----GAUUGCGA-UGCGAU------UCCGAUUCAGAUUCGG------------AUUCCGAUUCCCAUUUCGAUUUCGGUUUCGAUUGCGGUCUGU
-----------...((((((((----(((((.((-(.(((.------..(((....((.((((------------...)))).)).....)))...)))))).))))))))))))). ( -27.40)
>consensus
UUUUGAUUGUGACUCG_____CCUCGGAUUCCGAUUGCGAU______UCCGAUUCAGACUCGG____________AUUCCGAUUCCCAUUUCGAUUUCGGUUUCGAUUGCGGUCUGU
........................((((((.((((((...........((((.......))))...............((((.((.......))..))))...)))))).)))))). ( -9.62 = -11.86 +   2.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:15 2006