Locus 2671

Sequence ID	3R_DroMel_CAF1
Location	7,173,970 – 7,174,164
Length	194
Max. P	0.994217

overview

Window 3

Location	7,173,970 – 7,174,090
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-40.08
Consensus MFE	-36.00
Energy contribution	-34.88
Covariance contribution	-1.12
Combinations/Pair	1.30
Mean z-score	-1.96
Structure conservation index	0.90
SVM decision value	2.46
SVM RNA-class probability	0.994217
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7173970 120 + 27905053
AGAAGGGGGCGUGGCGGUAGUGGAUAUCGAUGUAUUGGGACCGGGAUCGUUCUCCUUGUCGGUCGUUUUGUUUGUGUUUGCUGCCGUCAUUUCUGGUAGGAUUAAUUUAUCUAAAUCCCA
....(((((.((((((((((..(((((.((((....(.((((((((......)))....))))).)..)))).)))))..)))))))))).)).....((((......))))....))). ( -41.60)
>DroSec_CAF1 14891 120 + 1
AGAAGAAGGCGUGGCGGUAGUGGAUAUCGAUGUAUGGGGACCGGGAUCGUUCUCCUUGUCGGUCGUUUUGUCUGUGUUUGCUGCCGUCAUUUCUGGUAGGAUUAAUUUAUUUAAAUCCCA
......(((.((((((((((..(((((.((((...((.((((((((......)))....))))).)).)))).)))))..)))))))))).)))....(((((..........))))).. ( -41.40)
>DroSim_CAF1 14861 120 + 1
AGAAGGGGGCGUGGCGGUAGUGGAUACCGAUGUAUGGGGACCGGGAUCGUUCUCCUUGUCGGUCGUUUUGUCUGUGUUUGCUGCCGUCAUUUCUGGUAGGAUUAAUUUAUCUAAAUCCCA
....(((((.((((((((((..(((((.((((...((.((((((((......)))....))))).)).)))).)))))..)))))))))).)).....((((......))))....))). ( -45.60)
>DroEre_CAF1 20113 120 + 1
AGGAGGGGGCGUGGCGGUAGAGGGUUUCGAUGUAUGGGGAUGGGGAUCGUUCUCCUUGUCGGACGUUUUGUCAGUGUUUGCUACCGUCAUUUCUGGUAGGAUUAGUUUUUCUAAAUCUCA
..(((((((.((((((((((..((..(.((((.(((..((..((((......))))..))...)))..)))).)..))..)))))))))).)))..(((((.......)))))..)))). ( -35.50)
>DroYak_CAF1 15185 120 + 1
AGGAGGGGACGUGGCUGUGGUGGACUUCGAUGUAUGGGGACCAGGAUCGUUCUCCUUGUCGGACGUUUUGUCUGUGUUUGCUACCGUCAUUUCUGGUAGGAUUAUUUUUUCUAAAUCUCA
..(((((((.(((((.((((..(((..(((((...(((((.(......).))))).)))))(((.....)))...)))..)))).))))).)))..(((((.......)))))..)))). ( -36.30)
>consensus
AGAAGGGGGCGUGGCGGUAGUGGAUAUCGAUGUAUGGGGACCGGGAUCGUUCUCCUUGUCGGUCGUUUUGUCUGUGUUUGCUGCCGUCAUUUCUGGUAGGAUUAAUUUAUCUAAAUCCCA
......(((.((((((((((..(((((.((((.(((..(((.((((......)))).)))...)))..)))).)))))..)))))))))).)))....(((((..........))))).. (-36.00 = -34.88 +  -1.12)

alignment

secondary structure

dotplot

Window 4

Location	7,174,050 – 7,174,164
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.50
Mean single sequence MFE	-29.00
Consensus MFE	-24.10
Energy contribution	-23.78
Covariance contribution	-0.32
Combinations/Pair	1.17
Mean z-score	-1.39
Structure conservation index	0.83
SVM decision value	0.16
SVM RNA-class probability	0.613298
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7174050 114 - 27905053
CCGAGCAUUCUAACGAAAUUAAGUCA------AAACUCAGCAAAUCAGUUUGUCUUACAAGUGUGCGGCGAACGCUUUGCUGGGAUUUAGAUAAAUUAAUCCUACCAGAAAUGACGGCAG
....((.(((....))).....((((------...(((((((((...(((((((.(((....))).)))))))..))))))))).....(((......)))..........)))).)).. ( -31.20)
>DroSec_CAF1 14971 120 - 1
CCGAGCAUUCUAACGAUAUUAAGUCCAUCUACAAACUCAGCAAAUCAGUUUGUCUUACAAGUGUGCGGCGAACGCUUUGCUGGGAUUUAAAUAAAUUAAUCCUACCAGAAAUGACGGCAG
....((..((....))......(((..(((.......(((((((...(((((((.(((....))).)))))))..)))))))(((((..........)))))....)))...))).)).. ( -29.10)
>DroSim_CAF1 14941 120 - 1
CCGAGCAUUCUAACGAUAUUAAGUCCAUCUACAGACUCAGCAAAUCAGUUUGUCUUACAAGUGUGCGGCGAACGCUUUGCUGGGAUUUAGAUAAAUUAAUCCUACCAGAAAUGACGGCAG
(((..((((((......(((((....(((((.((.(((((((((...(((((((.(((....))).)))))))..))))))))).)))))))...)))))......)).)))).)))... ( -31.20)
>DroEre_CAF1 20193 120 - 1
CCGAUCAUUCUAACAAGCUUAAGUCCAUCGGAAAAGUUGACAAAUCAGUUUGCCUUACAAGUGUGCGGCGAACGCUUUGCUGAGAUUUAGAAAAACUAAUCCUACCAGAAAUGACGGUAG
(((.(((((((........((((((..((((.((((((((....)))(((((((.(((....))).)))))))))))).))))))))))((........)).....)).))))))))... ( -28.40)
>DroYak_CAF1 15265 120 - 1
CCGAGCAUUCUAACGAACUUAAGUCCAUGGAAAAAGUCUACAAAUCAGUUUGCCUUACAAGUGUGCGGCGAACGCUUUGCUGAGAUUUAGAAAAAAUAAUCCUACCAGAAAUGACGGUAG
(((((..(((....))))))..(((..(((...((((((.((((...(((((((.(((....))).)))))))..))))...)))))).((........))...))).....)))))... ( -25.10)
>consensus
CCGAGCAUUCUAACGAAAUUAAGUCCAUCGAAAAACUCAGCAAAUCAGUUUGUCUUACAAGUGUGCGGCGAACGCUUUGCUGGGAUUUAGAUAAAUUAAUCCUACCAGAAAUGACGGCAG
(((...............(((((((...........((((((((...(((((((.(((....))).)))))))..)))))))))))))))...............((....)).)))... (-24.10 = -23.78 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:49 2006