Locus 2066

Sequence ID	2R_DroMel_CAF1
Location	7,758,758 – 7,758,899
Length	141
Max. P	0.927972

overview

Window 4

Location	7,758,758 – 7,758,878
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.77
Mean single sequence MFE	-33.33
Consensus MFE	-22.72
Energy contribution	-23.75
Covariance contribution	1.03
Combinations/Pair	1.13
Mean z-score	-1.05
Structure conservation index	0.68
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7758758 120 + 20766785
UCCACACGCAGGUGUCGUCGGUUCAGGAACAGAUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAGCUGAAUGCAAAAAGAUACAAAAGUAUCUUAGAAAUA
....((((.(((((((....(((....))).)))))))).((((((((.((.......))....)))))))).))).(((((.....)))))...(((((((....)))))))....... ( -33.70)
>DroPse_CAF1 15181 90 + 1
AGGACACGCCGGUGCCACCGGUUCAAGAACCGCUGCCUAAUGGAGCGAGCCAAUUGCCGGACAAGUGUCUCGAGUGAGUCUCAA-G-----GAAUA------------------------
.((((((.((((((((...((((....))))(((.((....)))))).)).....)))))....)))))).(((.....)))..-.-----.....------------------------ ( -29.30)
>DroSec_CAF1 10738 113 + 1
UCCACACGCAGGUGUCGUCGGUUUAGGAACAGGUGCCUCUUGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAG-------CAAUAAGAUACAAAAGUAUCUUAGAAAUA
...((((.((((..((.((.......))...))..)).((((((((((.((.......))....)))))))))))).))))...-------...((((((((....))))))))...... ( -34.10)
>DroSim_CAF1 11526 113 + 1
UCCACACGCAGGUGUCGUCGGUUUAGGAACAGGUGCCUCUUGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAG-------CAAUAAGAUACAAAAGUAUCUUAGAAAUA
...((((.((((..((.((.......))...))..)).((((((((((.((.......))....)))))))))))).))))...-------...((((((((....))))))))...... ( -34.10)
>DroEre_CAF1 14239 120 + 1
UCCACUCGCAGGUGUCAACGGUUCAAGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUAGGCUGAAUCCAAUGAGAUACAAAAGUAUCUCAGAUAUG
...(((((((((..((....(((....))).))..)))..((((((((.((.......))....)))))))).))))))...((......))..((((((((....))))))))...... ( -37.70)
>DroYak_CAF1 12719 120 + 1
UCCAGUCGCAGGUGUCAUCGGUUCAAGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUGGCUGAAUCCCAUUAGAUACAAAAGUAUCUUAGAAAUG
..((((((((..(((..((.......)))))..)))((((((((((((.((.......))....))))))))..))))....))))).........((((((....))))))........ ( -31.10)
>consensus
UCCACACGCAGGUGUCAUCGGUUCAAGAACAGGUGCCUCAUGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAG_U_____CAAUAAGAUACAAAAGUAUCUUAGAAAUA
...((.(((.((..((....(((....))).))..))...((((((((.((.......))....)))))))).))).))...............((((((((....))))))))...... (-22.72 = -23.75 +   1.03)

alignment

secondary structure

dotplot

Window 5

Location	7,758,798 – 7,758,899
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	64.26
Mean single sequence MFE	-25.63
Consensus MFE	-13.32
Energy contribution	-14.66
Covariance contribution	1.33
Combinations/Pair	1.30
Mean z-score	-1.75
Structure conservation index	0.52
SVM decision value	1.19
SVM RNA-class probability	0.927972
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7758798 101 + 20766785
UGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAGCUGAAUGCAAAAAGAUACAAAAGUAUCUUAGAAAUACAAGACCA-UUUAUAUGAUU------UC------------
((((((((.((.......))....)))))))).....(((((.((.....))...(((((((....)))))))...))))).......-...........------..------------ ( -23.20)
>DroSec_CAF1 10778 101 + 1
UGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAG-------CAAUAAGAUACAAAAGUAUCUUAGAAAUACAAGAC------AUAUGCUG------UUUGACUUUUUUAC
((((((((.((.......))....)))))))).(((((((((..-------...((((((((....))))))))..))))).((((------(.....))------))).......)))) ( -24.40)
>DroSim_CAF1 11566 104 + 1
UGGAGCGGGCCAACUGCCGGACGACCGUUUCAAGUGAGUGUUAG-------CAAUAAGAUACAAAAGUAUCUUAGAAAUACAAGACCA-UUUAUAUGAUU------UUUGAGA--CUUAC
((((((((.((.......))....)))))))).((((((.((((-------...((((((((....))))))))............((-(....)))...------.)))).)--))))) ( -27.30)
>DroEre_CAF1 14279 102 + 1
UGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUAGGCUGAAUCCAAUGAGAUACAAAAGUAUCUCAGAUAUGCCAGAA----------------CGUAUCUCAGA--CUAGC
((((((((.((.......))....))))))))........(((.((((......((((((((....))))))))((((((......----------------)))))))))).--))).. ( -32.60)
>DroYak_CAF1 12759 117 + 1
UGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUGGCUGAAUCCCAUUAGAUACAAAAGUAUCUUAGAAAUGCCAGAAUA-CUUGUCUGAAUUACAUAUCUGAGA--CUAGC
((((((((.((.......))....))))))))...((((((((((....((.....((((((....))))))..))...))))..)))-)))((((.(..........).)))--).... ( -28.50)
>DroAna_CAF1 10523 83 + 1
UGGAACGAACCAAUUGCAAUGCAAGUGGAUCAAGUGAGUCUCAA-------AAAUAGUCUAUA----------AGGGUUAUGAGACCAAGUUAUAUAAUA--------------------
...(((((.(((.((((...)))).))).))...((.((((((.-------...((..((...----------.))..)))))))))).)))........-------------------- ( -17.80)
>consensus
UGGAGCGGGCCAACUGCCGGACAACCGUUUCAAGUGAGUAUUAG_______CAAUAAGAUACAAAAGUAUCUUAGAAAUACAAGACCA__UUAUAUGAUU______UCUGAGA__CU__C
((((((((.((.......))....)))))))).....(((((............((((((((....))))))))..)))))....................................... (-13.32 = -14.66 +   1.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:23 2006