Locus 7411

Sequence ID	3R_DroMel_CAF1
Location	19,720,056 – 19,720,231
Length	175
Max. P	0.994255

overview

Window 9

Location	19,720,056 – 19,720,176
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.00
Mean single sequence MFE	-24.68
Consensus MFE	-24.44
Energy contribution	-24.52
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.80
Structure conservation index	0.99
SVM decision value	2.46
SVM RNA-class probability	0.994255
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720056 120 + 27905053
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCUUGACAAGGCAAAUGUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).)))))....(((((((((....)))))))))... ( -25.40)
>DroSec_CAF1 33661 120 + 1
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCCUGACAAGGCAAAUUUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).))))).....((((((((....)))))))).... ( -25.20)
>DroSim_CAF1 39037 120 + 1
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCCUGACAAGGCAAAUUUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).))))).....((((((((....)))))))).... ( -25.20)
>DroEre_CAF1 34542 120 + 1
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGCUUUUGAUUUGAUAUUAUUUGCUUGACAAGGCAAAUGUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).)))))....(((((((((....)))))))))... ( -23.80)
>DroYak_CAF1 34497 120 + 1
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGCUUUUGAUUUGAUAUUAUUUGCUUGACAAGGCAAAUGUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).)))))....(((((((((....)))))))))... ( -23.80)
>consensus
UGUGUUUGACAUAAAUAAUUUGUUCUUCUAGAGUUUAAAAAACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCUUGACAAGGCAAAUGUAA
((((.(((.(((((((..((((..(((...)))..)))).....)))))))))).)))).(((((.((((.(((...))).)))).)))))....(((((((((....)))))))))... (-24.44 = -24.52 +   0.08)

alignment

secondary structure

dotplot

Window 0

Location	19,720,056 – 19,720,176
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-19.52
Consensus MFE	-17.36
Energy contribution	-17.36
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.57
Structure conservation index	0.89
SVM decision value	0.76
SVM RNA-class probability	0.843146
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720056 120 - 27905053
UUACAUUUGCCUUGUCAAGCAAAUGAUAUCAAAUCAAAAACAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
...(((((((........))))))).....((((.((((.(((...))).)))).))))..((((.(((((.((((((((((((........))))))))....)))).)).))).)))) ( -19.80)
>DroSec_CAF1 33661 120 - 1
UUAAAUUUGCCUUGUCAGGCAAAUGAUAUCAAAUCAAAAACAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
....((((((((....))))))))(((((.((((.((((.(((...))).)))).)))).(((((....))))).(((((((((........))))))))).......)))))....... ( -22.30)
>DroSim_CAF1 39037 120 - 1
UUAAAUUUGCCUUGUCAGGCAAAUGAUAUCAAAUCAAAAACAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
....((((((((....))))))))(((((.((((.((((.(((...))).)))).)))).(((((....))))).(((((((((........))))))))).......)))))....... ( -22.30)
>DroEre_CAF1 34542 120 - 1
UUACAUUUGCCUUGUCAAGCAAAUAAUAUCAAAUCAAAAGCAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
....((((((........))))))......((((.((((.(((...))).)))).))))..((((.(((((.((((((((((((........))))))))....)))).)).))).)))) ( -16.60)
>DroYak_CAF1 34497 120 - 1
UUACAUUUGCCUUGUCAAGCAAAUAAUAUCAAAUCAAAAGCAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
....((((((........))))))......((((.((((.(((...))).)))).))))..((((.(((((.((((((((((((........))))))))....)))).)).))).)))) ( -16.60)
>consensus
UUACAUUUGCCUUGUCAAGCAAAUGAUAUCAAAUCAAAAACAGCUACUGAUUUUCAUUUAUUGUGAUUGCACAAAUUGUUUUUUAAACUCUAGAAGAACAAAUUAUUUAUGUCAAACACA
....((((((........))))))......((((.((((.(((...))).)))).))))..((((.(((((.((((((((((((........))))))))....)))).)).))).)))) (-17.36 = -17.36 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	19,720,096 – 19,720,212
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.90
Mean single sequence MFE	-24.50
Consensus MFE	-19.74
Energy contribution	-20.32
Covariance contribution	0.58
Combinations/Pair	1.06
Mean z-score	-1.47
Structure conservation index	0.81
SVM decision value	0.22
SVM RNA-class probability	0.641645
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720096 116 + 27905053
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCUUGACAAGGCAAAUGUAAUUGUU----GUGGAUGUUCUUUAAACUUAGUGGCUAAGUA
........(.(((.(((((((((....(((((((.........))))))).....(((((((((....)))))))))...)))))----)))).))).).....((((((...)))))). ( -27.40)
>DroSec_CAF1 33701 120 + 1
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCCUGACAAGGCAAAUUUAAUUGUUGUUUGUGGAUGUUCUUUAAACUUAGUGGCUAAGUA
........(.(((.(((((((((((.((((.(((...))).)))).))))).....((((((((....))))))))...........)))))).))).).....((((((...)))))). ( -25.50)
>DroSim_CAF1 39077 120 + 1
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCCUGACAAGGCAAAUUUAAUUGUUGUUUGUGGAUGUUCUUUAAACUUAGUGGCUAAGUA
........(.(((.(((((((((((.((((.(((...))).)))).))))).....((((((((....))))))))...........)))))).))).).....((((((...)))))). ( -25.50)
>DroEre_CAF1 34582 99 + 1
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGCUUUUGAUUUGAUAUUAUUUGCUUGACAAGGCAAAUGUAAUUGUU----GUGGAUGUUCUUUA-----------------
........(.(((.(((((((((....(((((((.........))))))).....(((((((((....)))))))))...)))))----)))).))).)....----------------- ( -22.50)
>DroYak_CAF1 34537 116 + 1
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGCUUUUGAUUUGAUAUUAUUUGCUUGACAAGGCAAAUGUAAUUGUU----UUGGAUGUUCUUUAAACUUAGUGGCUAAGUA
......(((((....)))))..............((((..((((..(..((((..(((((((((....)))))))))..))))..----)..)).(((.....)))..))..)))).... ( -21.60)
>consensus
AACAAUUUGUGCAAUCACAAUAAAUGAAAAUCAGUAGCUGUUUUUGAUUUGAUAUCAUUUGCUUGACAAGGCAAAUGUAAUUGUU____GUGGAUGUUCUUUAAACUUAGUGGCUAAGUA
........(.(((.((((..(((((.((((.(((...))).)))).)))))....(((((((((....)))))))))............)))).))).).....((((((...)))))). (-19.74 = -20.32 +   0.58)

alignment

secondary structure

dotplot

Window 2

Location	19,720,136 – 19,720,231
Length	95
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	94.41
Mean single sequence MFE	-13.75
Consensus MFE	-12.00
Energy contribution	-12.50
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.88
Structure conservation index	0.87
SVM decision value	0.69
SVM RNA-class probability	0.823018
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19720136 95 - 27905053
AAUAGGUAACCUAAGCUGAUACUUAGCCACUAAGUUUAAAGAACAUCCAC----AACAAUUACAUUUGCCUUGUCAAGCAAAUGAUAUCAAAUCAAAAA
..((((...))))...((((((((((...)))))................----........(((((((........))))))).)))))......... ( -13.90)
>DroSec_CAF1 33741 99 - 1
AAUAGGUAACCUAAGCUGAUACUUAGCCACUAAGUUUAAAGAACAUCCACAAACAACAAUUAAAUUUGCCUUGUCAGGCAAAUGAUAUCAAAUCAAAAA
..((((...))))...((((((((((...))))).............................((((((((....))))))))..)))))......... ( -15.20)
>DroSim_CAF1 39117 99 - 1
AAUAGGUAACCUAAGCUGAUACUUAGCCACUAAGUUUAAAGAACAUCCACAAACAACAAUUAAAUUUGCCUUGUCAGGCAAAUGAUAUCAAAUCAAAAA
..((((...))))...((((((((((...))))).............................((((((((....))))))))..)))))......... ( -15.20)
>DroYak_CAF1 34577 95 - 1
AAUAGGUAACCUAAGCUGAUACUUAGCCACUAAGUUUAAAGAACAUCCAA----AACAAUUACAUUUGCCUUGUCAAGCAAAUAAUAUCAAAUCAAAAG
..((((...))))...((((((((((...)))))................----.........((((((........))))))..)))))......... ( -10.70)
>consensus
AAUAGGUAACCUAAGCUGAUACUUAGCCACUAAGUUUAAAGAACAUCCAC____AACAAUUAAAUUUGCCUUGUCAAGCAAAUGAUAUCAAAUCAAAAA
..((((...))))...((((((((((...))))).............................((((((((....))))))))..)))))......... (-12.00 = -12.50 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:19 2006