Locus 4845

Sequence ID	2L_DroMel_CAF1
Location	13,770,077 – 13,770,282
Length	205
Max. P	0.975040

overview

Window 6

Location	13,770,077 – 13,770,186
Length	109
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	77.78
Mean single sequence MFE	-30.36
Consensus MFE	-11.26
Energy contribution	-12.02
Covariance contribution	0.76
Combinations/Pair	1.14
Mean z-score	-2.29
Structure conservation index	0.37
SVM decision value	1.17
SVM RNA-class probability	0.925664
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13770077 109 + 22407834
GCUGCGUCUGCUU----ACAUA----UGUGCACCCAAGUGGGGCCUCAUAGAUACGUAUCCUUAUAUGUACAUAUCUUUAUGUGGGCUGGGAUCCCCAGUCGGACAUUUUAUCUCAC
.....((((...(----(((((----((.((.(((....)))))..)).(((((.((((........)))).))))).))))))(((((((...)))))))))))............ ( -31.20)
>DroSec_CAF1 32643 105 + 1
ACUGCGUCUGCUU----ACAUA----UGUGCACCCAAGUGGGGCCUUAUAGAUACGUAUCUUUAUAUGU----AUCUUUAUGUGGGCAGGGUUCCCCAUUCGGACAUUUUAUCUCAC
.....((((((((----(((((----...((.(((....))))).....((((((((((....))))))----)))).))))))))).(((...)))....))))............ ( -33.50)
>DroSim_CAF1 35674 97 + 1
ACUGCGUCUGCUU----ACAUAUGUAUGUGCACCCAAGUUGUGCCUUAUAGAUACGUAUC----------------UUUAUGUGGGCAGGGUUCCCCAUUCGGACAUUUUAUCUCAC
.....((((((((----(((((.((((((((((.......)))).........)))))).----------------..))))))))).(((...)))....))))............ ( -24.40)
>DroEre_CAF1 34679 89 + 1
ACUGGGUGU--------ACUUA----UGUGCACCCAAGUGGGGCCUUAAAGAUAUGUAUC----------------UUUUUGUGGGCAGGGUUCCCCUGUCGAACAUUUUAUCCGGC
..(((((((--------((...----.))))))))).((.(((....((((((....)))----------------))).(((.(((((((...)))))))..))).....))).)) ( -33.90)
>DroYak_CAF1 35753 95 + 1
GCUGCGUGUCCCUACAUACAUA----UGUGCACCCAAGUGGGGCCUUAUAGAUACGUAUC----------------UUUAUGUGGG--GGGUUCCCCUGUCAGACAUUUUAUCUGAC
..((((((((...((((....)----)))((.(((....)))))......))))))))..----------------.......(((--(....)))).((((((.......)))))) ( -28.80)
>consensus
ACUGCGUCUGCUU____ACAUA____UGUGCACCCAAGUGGGGCCUUAUAGAUACGUAUC________________UUUAUGUGGGCAGGGUUCCCCAGUCGGACAUUUUAUCUCAC
.....(((((......................(((....)))((((((((((........................)))))).)))).(((...)))...)))))............ (-11.26 = -12.02 +   0.76)

alignment

secondary structure

dotplot

Window 7

Location	13,770,186 – 13,770,282
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.10
Mean single sequence MFE	-23.25
Consensus MFE	-21.44
Energy contribution	-21.33
Covariance contribution	-0.11
Combinations/Pair	1.06
Mean z-score	-1.92
Structure conservation index	0.92
SVM decision value	1.74
SVM RNA-class probability	0.975040
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13770186 96 + 22407834
CGAGCGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC------------------------
...(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))------------------------ ( -23.00)
>DroSec_CAF1 32748 95 + 1
-GAGCGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC------------------------
-..(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))------------------------ ( -23.00)
>DroAna_CAF1 53492 120 + 1
CGAACGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAAUGUUUAUGUUUAUUUGUCUGUGUUUAAGCAUUAAUGUUUAUCGUUAUGUUGAUCCUGAGAAUGGUAUCCUUGUUUCGCUUGU
...((((((.(((((((((.(((......(((((((((((((.(((((((..(......)..))))))).))))))))).))))...)))..))))....((...)).))))).)))))) ( -24.50)
>DroSim_CAF1 35771 96 + 1
CGAGCGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC------------------------
...(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))------------------------ ( -23.00)
>DroEre_CAF1 34768 96 + 1
CGAGCGGGUCAAGCAUCAGUUCAUUCUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC------------------------
...(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))------------------------ ( -23.00)
>DroYak_CAF1 35848 96 + 1
CGAGCGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC------------------------
...(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))------------------------ ( -23.00)
>consensus
CGAGCGGGUCAAGCAUCAGUUCAUUUUAUUGACAUAAACGUUUAUGUUUAUUUGUCUGCGUUUAAGCAUUACUGUUUAUUGUAUUGUUGAUCCUGC________________________
...(((((((((.(((((((.......))))).(((((((...(((((((..((....))..)))))))...))))))).....)))))).)))))........................ (-21.44 = -21.33 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:10 2006