Locus 2043

Sequence ID	3R_DroMel_CAF1
Location	5,794,976 – 5,795,068
Length	92
Max. P	0.913826

overview

Window 7

Location	5,794,976 – 5,795,068
Length	92
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	80.90
Mean single sequence MFE	-22.61
Consensus MFE	-13.34
Energy contribution	-13.06
Covariance contribution	-0.28
Combinations/Pair	1.36
Mean z-score	-2.34
Structure conservation index	0.59
SVM decision value	1.09
SVM RNA-class probability	0.913826
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5794976 92 + 27905053
UCUACCCUCGUGCUGUCUCUUUCGCUCGGCACUGUGUCAUCUCCCUCUAAAGUCCACA-UAUGCCCCCUU-------GAAAAUCCCCUUUAGGUGGGUUU
.........((((((...........))))))(((((...((........))...)))-)).((((.(((-------(((.......)))))).)))).. ( -18.10)
>DroSec_CAF1 86722 92 + 1
UCUACCCUCGUGCUGUCGCUUUCGCUCAGCACUGUGUUAUCUCCCCCUAAAGUCCACA-CAUGCCCCCUU-------GAAAACCCCCUUUAGGUGGGUUU
.........((((((..((....)).))))))(((((...((........))...)))-)).........-------..((((((((....)).)))))) ( -23.70)
>DroSim_CAF1 87455 92 + 1
UCUACCCUCGUGCUGUCUCUUUCGCUCAGCACUGUGUCAUCUCCCUCUAAAGUCCACA-UAUGCCCCCUU-------GAAAACCCCCUUUAGGUGGGUUU
.........((((((...........))))))(((((...((........))...)))-)).........-------..((((((((....)).)))))) ( -19.20)
>DroEre_CAF1 83460 99 + 1
UCUGCCCUCGCGCUGUCUCUUUCACUCAGCAUAUUGUCAUCUCCCUCGAGUGUCAGCA-UACCCCCCGGUCGGUGGGGUAAACCCCUUUUAGGUGGGCUU
...((((.(((((((...........))))....((.((.(((....))))).)))).-((((((((....)).))))))............).)))).. ( -32.60)
>DroYak_CAF1 72317 94 + 1
UCCACCCUCAUGCUGUCUCUUUCACUCAGCAUAUUGCCAUCUCCCGCGAGUGUCAGCAAUAACCCCCCUUCA------AAAACCCCCUUUGGAUGGGUUU
..........(((((.......(((((.((...............))))))).)))))......(((.((((------((.......)))))).)))... ( -19.46)
>consensus
UCUACCCUCGUGCUGUCUCUUUCGCUCAGCACUGUGUCAUCUCCCUCUAAAGUCCACA_UAUGCCCCCUU_______GAAAACCCCCUUUAGGUGGGUUU
.........((((((...........))))))...............................................((((((((....)).)))))) (-13.34 = -13.06 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	5,794,976 – 5,795,068
Length	92
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	80.90
Mean single sequence MFE	-27.90
Consensus MFE	-18.78
Energy contribution	-18.02
Covariance contribution	-0.76
Combinations/Pair	1.36
Mean z-score	-2.01
Structure conservation index	0.67
SVM decision value	0.81
SVM RNA-class probability	0.857560
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5794976 92 - 27905053
AAACCCACCUAAAGGGGAUUUUC-------AAGGGGGCAUA-UGUGGACUUUAGAGGGAGAUGACACAGUGCCGAGCGAAAGAGACAGCACGAGGGUAGA
..((((.(((....)))....((-------.....(((((.-((((..((((....))))....)))))))))..((..........))..))))))... ( -22.00)
>DroSec_CAF1 86722 92 - 1
AAACCCACCUAAAGGGGGUUUUC-------AAGGGGGCAUG-UGUGGACUUUAGGGGGAGAUAACACAGUGCUGAGCGAAAGCGACAGCACGAGGGUAGA
..((((.(((....)))(((((.-------...))))).((-(((...((((....))))...)))))((((((.((....))..))))))..))))... ( -31.90)
>DroSim_CAF1 87455 92 - 1
AAACCCACCUAAAGGGGGUUUUC-------AAGGGGGCAUA-UGUGGACUUUAGAGGGAGAUGACACAGUGCUGAGCGAAAGAGACAGCACGAGGGUAGA
..((((.(((....((((((..(-------(..........-))..))))))..)))...........((((((..(....)...))))))..))))... ( -26.20)
>DroEre_CAF1 83460 99 - 1
AAGCCCACCUAAAAGGGGUUUACCCCACCGACCGGGGGGUA-UGCUGACACUCGAGGGAGAUGACAAUAUGCUGAGUGAAAGAGACAGCGCGAGGGCAGA
..((((((((.....)))).((((((.((....))))))))-(((((.(((((....))).)).))....((((..(....)...))))))).))))... ( -33.80)
>DroYak_CAF1 72317 94 - 1
AAACCCAUCCAAAGGGGGUUUU------UGAAGGGGGGUUAUUGCUGACACUCGCGGGAGAUGGCAAUAUGCUGAGUGAAAGAGACAGCAUGAGGGUGGA
....((((((.......((..(------(...(.(((((((....)))).))).)....))..))..(((((((..(....)...))))))).)))))). ( -25.60)
>consensus
AAACCCACCUAAAGGGGGUUUUC_______AAGGGGGCAUA_UGUGGACUUUAGAGGGAGAUGACACAGUGCUGAGCGAAAGAGACAGCACGAGGGUAGA
..((((.(((....))).........................(((.(.((((....)))).).)))..((((((..(....)...))))))..))))... (-18.78 = -18.02 +  -0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:00 2006