Locus 8485

Sequence ID	3R_DroMel_CAF1
Location	22,638,524 – 22,638,661
Length	137
Max. P	0.909488

overview

Window 3

Location	22,638,524 – 22,638,632
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	91.67
Mean single sequence MFE	-30.73
Consensus MFE	-27.12
Energy contribution	-27.93
Covariance contribution	0.81
Combinations/Pair	1.12
Mean z-score	-1.79
Structure conservation index	0.88
SVM decision value	1.07
SVM RNA-class probability	0.909488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22638524 108 + 27905053
UUGGGCAGUUAUCGGAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCGGGCGAAAUGAUGUGUAAUAC
(((((.(((((((((.(((.....)))...))))))))).)))))..(((((............)))))....(((((((((.(((....)))...)))))))))... ( -34.60)
>DroSec_CAF1 86420 108 + 1
UUGGGCAGUUAUCGGAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUAC
(((((.(((((((((.(((.....)))...))))))))).)))))..(((((............)))))....(((((((((.(((....)))...)))))))))... ( -34.60)
>DroSim_CAF1 88240 108 + 1
UCGGGCAGUUAUCGAAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUAC
(((((((((((((....)...)))))))).)))).............(((((............)))))....(((((((((.(((....)))...)))))))))... ( -30.30)
>DroEre_CAF1 94662 107 + 1
U-GGGCAGUUAUCAGAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCACAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUAU
(-(((.(((((((((.(((.....)))...))))))))).))))(((((...((((.......))))..)))))((((((((.(((....)))...)))))))).... ( -35.10)
>DroYak_CAF1 90050 108 + 1
UCGGGCACUUAUCGGAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCCUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCUGGCGAAAUGAUGUGUAAUAU
..(((...(((((((.(((.....)))...)))))))...)))....(((.(((.........))))))....(((((((((.(((....)))...)))))))))... ( -29.20)
>DroAna_CAF1 87969 107 + 1
AUGGGCAGUUAUCGAAAGCUAAUGGCAGAGCUGAUAAUUCCACAAAU-GCCUUUCUUGUCCUUGGACCAUAAUUCACGCAUCGACGCAGGCCAAAUGAUGUGAGAUAU
..(((((((((.(....).))))((((.....((....))......)-))).....)))))............((.(((((((............))))))).))... ( -20.60)
>consensus
UUGGGCAGUUAUCGGAAGUUAAUGGCUGCGCUGAUAAUUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUAC
..(((.(((((((((.(((.....)))...))))))))).))).........((((.......))))......(((((((((((((....)))..))))))))))... (-27.12 = -27.93 +   0.81)

alignment

secondary structure

dotplot

Window 4

Location	22,638,561 – 22,638,661
Length	100
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	79.41
Mean single sequence MFE	-19.15
Consensus MFE	-13.50
Energy contribution	-13.75
Covariance contribution	0.25
Combinations/Pair	1.12
Mean z-score	-1.24
Structure conservation index	0.70
SVM decision value	0.21
SVM RNA-class probability	0.634662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22638561 100 + 27905053
UUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCGGGCGAAAUGAUGUGUAAUACGUAUACGUAUAA--AUGUAUGUAUAUACUAU
..........(((((............)))))....(((((((((.(((....)))...)))))))))...((((((((((..--..))))))))))..... ( -24.40)
>DroSec_CAF1 86457 102 + 1
UUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUACGUACAAGUAUAUGUAUAUAUGUAUAUACUGU
..........(((((............)))))....(((((((((.(((....)))...)))))))))........((((((((........)))))))).. ( -21.60)
>DroSim_CAF1 88277 96 + 1
UUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUACGU------AUAUGUAUAUAUGUAUAUACUGU
..........(((((............))))).....((((((((.(((....)))...))))))))((((((------(((....)))))))))....... ( -21.80)
>DroEre_CAF1 94698 82 + 1
UUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCACAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUAUG--------------------UUUAUACUAU
......((((((...((((.......))))..))))))(((((((.(((....)))...)))))))......--------------------.......... ( -17.00)
>DroYak_CAF1 90087 88 + 1
UUCCCCAAAUUGCCUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCUGGCGAAAUGAUGUGUAAUAUGUA--------------UAUGUAUAUACUAU
..........(((.(((.........))))))....(((((((((.(((....)))...)))))))))...(((--------------((....)))))... ( -17.50)
>DroAna_CAF1 88006 89 + 1
UUCCACAAAU-GCCUUUCUUGUCCUUGGACCAUAAUUCACGCAUCGACGCAGGCCAAAUGAUGUGAGAUAUACACAC--------AAAUAUGCACACA----
..........-((((.....(((....)))..........((......)))))).......((((..((((......--------..)))).))))..---- ( -12.60)
>consensus
UUCCCCAAAUUGCUUCUCUUGUCUUUAGAGCAUAAUUUACGCAUCGUCGCAGGCGAAAUGAUGUGUAAUACGUA___________AUAUAUGUAUAUACUAU
...............((((.......))))......(((((((((((((....)))..)))))))))).................................. (-13.50 = -13.75 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:12:31 2006