Locus 6385

Sequence ID	2R_DroMel_CAF1
Location	19,975,258 – 19,975,377
Length	119
Max. P	0.999981

overview

Window 2

Location	19,975,258 – 19,975,377
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-36.90
Consensus MFE	-33.60
Energy contribution	-35.04
Covariance contribution	1.44
Combinations/Pair	1.08
Mean z-score	-3.33
Structure conservation index	0.91
SVM decision value	4.27
SVM RNA-class probability	0.999856
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19975258 119 + 20766785
GACGAGACUCAAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUCUGAAAGG-GGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGGA
..((((((..........((((((.......))))))...((((....))-)).))))))....((((((((.(((((((((((....))))))))....))).))))))))........ ( -34.80)
>DroSec_CAF1 16326 119 + 1
GACGAGACUCAAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUCUGAAAGG-GGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGGA
..((((((..........((((((.......))))))...((((....))-)).))))))....((((((((.(((((((((((....))))))))....))).))))))))........ ( -34.80)
>DroSim_CAF1 16956 120 + 1
GACGAGACUCAAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUCUGAAAGGGGGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGGA
..((((((..........((((((.......))))))..(((((....))))).))))))....((((((((.(((((((((((....))))))))....))).))))))))........ ( -37.90)
>DroEre_CAF1 16380 119 + 1
GACGGGACUUGAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUCUGGAAGGGGGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGG-
......(((((((((...((((((.......))))))..(((((....))))).))))))))).((((((((.(((((((((((....))))))))....))).)))))))).......- ( -37.60)
>DroYak_CAF1 16972 120 + 1
GACGGGGCUCGAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUUUGAAAGGGGGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGGA
......(((((((((...((((((.......))))))..(((((....))))).))))))))).((((((((.(((((((((((....))))))))....))).))))))))........ ( -39.40)
>consensus
GACGAGACUCAAAAUAGUUGUCCUGUCUAAAAGGACAUUCCUCUGAAAGGGGGCGUUUCGAGUGCAAAGUGUGUGUAAAUAAAUCAAAGUUUAUUUAGUGACAGACACUUUGAGAUGGGA
..((((((..........((((((.......))))))..(((((....))))).))))))....((((((((.(((((((((((....))))))))....))).))))))))........ (-33.60 = -35.04 +   1.44)

alignment

secondary structure

dotplot

Window 3

Location	19,975,258 – 19,975,377
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-26.64
Consensus MFE	-26.46
Energy contribution	-26.46
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-3.07
Structure conservation index	0.99
SVM decision value	5.26
SVM RNA-class probability	0.999981
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19975258 119 - 20766785
UCCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCC-CCUUUCAGAGGAAUGUCCUUUUAGACAGGACAACUAUUUUGAGUCUCGUC
........((((((((.(((....(((((((......)))))))))).)))))))).((((((((....-((((...))))..((((((.......))))))....))))))))...... ( -27.30)
>DroSec_CAF1 16326 119 - 1
UCCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCC-CCUUUCAGAGGAAUGUCCUUUUAGACAGGACAACUAUUUUGAGUCUCGUC
........((((((((.(((....(((((((......)))))))))).)))))))).((((((((....-((((...))))..((((((.......))))))....))))))))...... ( -27.30)
>DroSim_CAF1 16956 120 - 1
UCCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCCCCCUUUCAGAGGAAUGUCCUUUUAGACAGGACAACUAUUUUGAGUCUCGUC
........((((((((.(((....(((((((......)))))))))).)))))))).((((((((.....((((...))))..((((((.......))))))....))))))))...... ( -27.30)
>DroEre_CAF1 16380 119 - 1
-CCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCCCCCUUCCAGAGGAAUGUCCUUUUAGACAGGACAACUAUUUCAAGUCCCGUC
-.......((((((((.(((....(((((((......)))))))))).)))))))).(((.((((.....((((...))))..((((((.......))))))....)))).)))...... ( -23.50)
>DroYak_CAF1 16972 120 - 1
UCCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCCCCCUUUCAAAGGAAUGUCCUUUUAGACAGGACAACUAUUUCGAGCCCCGUC
........((((((((.(((....(((((((......)))))))))).))))))))..(((((((.....(((.....)))..((((((.......))))))....)))))))....... ( -27.80)
>consensus
UCCCAUCUCAAAGUGUCUGUCACUAAAUAAACUUUGAUUUAUUUACACACACUUUGCACUCGAAACGCCCCCUUUCAGAGGAAUGUCCUUUUAGACAGGACAACUAUUUUGAGUCUCGUC
........((((((((.(((....(((((((......)))))))))).)))))))).((((((((.....((((...))))..((((((.......))))))....))))))))...... (-26.46 = -26.46 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:09:43 2006