Locus 6630

Sequence ID	3R_DroMel_CAF1
Location	17,432,843 – 17,432,989
Length	146
Max. P	0.997143

overview

Window 3

Location	17,432,843 – 17,432,949
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	96.62
Mean single sequence MFE	-20.15
Consensus MFE	-19.34
Energy contribution	-19.22
Covariance contribution	-0.12
Combinations/Pair	1.04
Mean z-score	-1.87
Structure conservation index	0.96
SVM decision value	2.81
SVM RNA-class probability	0.997143
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17432843 106 - 27905053
UU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACUGGAACUACGUCCGCAGUUUUACAACUUUACAAC
..-((((((((...(((((....)))))(((.....))).............)))((((((.(((((...............))))).))))))....))))).... ( -20.66)
>DroSec_CAF1 36833 106 - 1
UU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACUGGAACUACGUCCGCAGUUUUACAACUUUACAAC
..-((((((((...(((((....)))))(((.....))).............)))((((((.(((((...............))))).))))))....))))).... ( -20.66)
>DroSim_CAF1 33973 106 - 1
UU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACUGGAACUACGUCCGCAGUUUUACAACUUUACAAC
..-((((((((...(((((....)))))(((.....))).............)))((((((.(((((...............))))).))))))....))))).... ( -20.66)
>DroEre_CAF1 36530 106 - 1
UA-UAAAGCAGAGGGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACUGGAACUACGUCCGCAGUUUUACAACUUUACAAC
..-(((((.((.(((((((....)))))(((.....)))....)).)).......((((((.(((((...............))))).))))))....))))).... ( -20.56)
>DroYak_CAF1 36944 106 - 1
UUUUAAAGCAGAGGGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACA-ACUACAACUAGAACUACGUCUGCAGUUUUACAACUUUACAAC
.......(((((.((((((....)))))...............(((.......)))........-................).)))))................... ( -18.20)
>consensus
UU_UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACUGGAACUACGUCCGCAGUUUUACAACUUUACAAC
...((((((((...(((((....)))))(((.....))).............)))((((((.(((((...............))))).))))))....))))).... (-19.34 = -19.22 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	17,432,876 – 17,432,989
Length	113
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	93.30
Mean single sequence MFE	-26.25
Consensus MFE	-22.30
Energy contribution	-22.02
Covariance contribution	-0.28
Combinations/Pair	1.11
Mean z-score	-1.61
Structure conservation index	0.85
SVM decision value	1.03
SVM RNA-class probability	0.902811
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17432876 113 - 27905053
CAUUUUGUUGUGGUUGGAUAAUAUGCCUUUGAUGUCCCGGUU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACU
......((((((((((((((.((......)).))))).((((-(((........(((((....))))).........))).))))....((...(....)..))))))))))). ( -26.73)
>DroSec_CAF1 36866 113 - 1
CAUUUUGUUGUAGUUGGAUAAUAUGUCUUUGAUGUCCAGAUU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACU
......(((((((((((......((.((((((.........)-)))))))....(((((....)))))...............))....((...(....)..))))))))))). ( -26.10)
>DroSim_CAF1 34006 113 - 1
CAUUUUGUUGUGGUUGGAUAAUAUAUCUUUGAUGUCCCGAUU-UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACU
....((((.(((((((((((...))))((((.((((.(....-....)..))))(((((....))))).....))))...))))))).))))(((.......)))......... ( -25.20)
>DroEre_CAF1 36563 112 - 1
CAAUUUGUUGUGGUUGGAUAAUAUGC-UCUGAUGUUCCGAUA-UAAAGCAGAGGGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACU
....((((.(((((((.........(-((((.(((......)-))...))))).(((((....)))))............))))))).))))(((.......)))......... ( -28.10)
>DroYak_CAF1 36977 113 - 1
CAAUUUGUUGUGGUAGGAUAAUGUGCCUUUGAUGUCCCGAUUUUAAAGCAGAGGGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACA-ACUACAACU
......((((((((.((........((((((.................))))))(((((....)))))...............)))))))))).(....)....-......... ( -25.13)
>consensus
CAUUUUGUUGUGGUUGGAUAAUAUGCCUUUGAUGUCCCGAUU_UAAAGCAGACAGAGUGUAAACACUCGAUUACAAAUUACAACCACUACGACUGGAAACUACGGACUACAACU
......((((((((((((((.((......)).)))))..........(.((...(((((....)))))...............(((.......)))...)).).))))))))). (-22.30 = -22.02 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:26:20 2006