Locus 10123

Sequence ID	3R_DroMel_CAF1
Location	27,149,838 – 27,149,970
Length	132
Max. P	0.973236

overview

Window 4

Location	27,149,838 – 27,149,931
Length	93
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	78.50
Mean single sequence MFE	-24.50
Consensus MFE	-14.14
Energy contribution	-16.86
Covariance contribution	2.72
Combinations/Pair	1.09
Mean z-score	-2.41
Structure conservation index	0.58
SVM decision value	1.71
SVM RNA-class probability	0.973236
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27149838 93 + 27905053
CUGGGC-------UUUCUCCAGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAACGUUAACUU
..((((-------........((((.((.......)).))))...(((((((((.((((......)))))))))))))..))))................ ( -26.00)
>DroSec_CAF1 51456 93 + 1
GCGGGC-------UUUCUCCAGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAAUGUUAGCUC
((((((-------........((((.((.......)).))))...(((((((((.((((......)))))))))))))..)))).((.....))..)).. ( -26.50)
>DroSim_CAF1 54264 93 + 1
GCGGGC-------UUUCUCCAGGGCUUGCUUAUUUCACGUUCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAAUGUUAACUC
((((((-------((......)))))))).........(..(((.(((((((((.((((......))))))))))))))))..)................ ( -24.90)
>DroEre_CAF1 52268 91 + 1
GUGGGCUUUCGGCUUUCUCCAGGGCUAACUAAUUUCGCGUCCAUCAGUCGUGAUUGCCAGCAGUAAAUCUUCAC---------CUAUAAAACGUAGACCU
((.(((....(((((......)))))........(((((.(.....).)))))..))).)).............---------((((.....)))).... ( -16.20)
>DroYak_CAF1 54464 90 + 1
GUGGCC-------UUUCUCCAGGGCUUGAUAAUUUCACUUCCAUUGGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCUGUAAGA---AAAUCA
......-------(((((.((((((.(((.....))).......((((((((((.((((......)))))))))))))).))))))..)))---)).... ( -28.90)
>consensus
GUGGGC_______UUUCUCCAGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAACGUUAACUC
..((((...............((((.((.......)).))))...(((((((((.((((......)))))))))))))..))))................ (-14.14 = -16.86 +   2.72)

alignment

secondary structure

dotplot

Window 5

Location	27,149,851 – 27,149,970
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.92
Mean single sequence MFE	-27.26
Consensus MFE	-13.14
Energy contribution	-15.62
Covariance contribution	2.48
Combinations/Pair	1.21
Mean z-score	-2.16
Structure conservation index	0.48
SVM decision value	1.42
SVM RNA-class probability	0.951875
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27149851 119 + 27905053
AGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAACGUUAACUUUUACCAUUCUAAAGAGUUUGC-AUUGCCGUAUAAGUUAUA
..(((.(((.........(..(((.(((((((((.((((......))))))))))))))))..)...........(((((((.........))))))).))-)..)))............ ( -25.50)
>DroSec_CAF1 51469 117 + 1
AGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAAUGUUAGCUCUUGCCAUUCUAAAGAGUUCGC-AUUGCCAUAUAAGUAA--
..(((.............(..(((.(((((((((.((((......))))))))))))))))..).....(((((.(((((((.........))))))).))-))))))..........-- ( -31.10)
>DroSim_CAF1 54277 119 + 1
AGGGCUUGCUUAUUUCACGUUCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAAUGUUAACUCUUACCAUUCUAAAGAGUUCGC-AUUGCCAUAUAAGUAAGA
....(((((((((.....(..(((.(((((((((.((((......))))))))))))))))..).....(((((.(((((((.........))))))).))-))).....))))))))). ( -33.60)
>DroEre_CAF1 52288 110 + 1
AGGGCUAACUAAUUUCGCGUCCAUCAGUCGUGAUUGCCAGCAGUAAAUCUUCAC---------CUAUAAAACGUAGACCUUUACAAUUCCAAAGAGUUCGC-AUUGCCGCAUAAGUGAGG
..(((.........(((((.(.....).)))))..)))..........((((((---------.(((..((.(..(((((((........)))).)))..)-.)).....))).)))))) ( -18.00)
>DroYak_CAF1 54477 104 + 1
AGGGCUUGAUAAUUUCACUUCCAUUGGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCUGUAAGA---AAAUCAUAAUACUCCAGGAGAGUUUGUUAUUUU-------------
(((((.(((.....))).......((((((((((.((((......)))))))))))))).))))).....(---((((.((((.((((.....)))))))).)))))------------- ( -28.10)
>consensus
AGGGCUUGCUAAUUUCACGUCCAUCAGUCGUGAUUGAUUGAAAUAAAUCAUCACGAUUAUGCCCCACAAAACGUUAACUCUUACCAUUCUAAAGAGUUCGC_AUUGCCAUAUAAGUAA__
.((((.((.......)).))))...(((((((((.((((......)))))))))))))..............((.(((((((.........))))))).))................... (-13.14 = -15.62 +   2.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:49:24 2006