Locus 5781

Sequence ID	3L_DroMel_CAF1
Location	15,663,724 – 15,663,874
Length	150
Max. P	0.982542

overview

Window 4

Location	15,663,724 – 15,663,834
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.50
Mean single sequence MFE	-26.37
Consensus MFE	-16.72
Energy contribution	-17.92
Covariance contribution	1.20
Combinations/Pair	1.24
Mean z-score	-2.89
Structure conservation index	0.63
SVM decision value	1.92
SVM RNA-class probability	0.982542
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15663724 110 - 23771897
GGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUCCAAUCCAACGAAGGCAAAUA-CUAAUAAACAAUUAUUGUUCUUUGUUU-----
((.((..(((((......))))).((((((.((((((........)))))))))))----)...)))).....(((((((((((...-.((((.....))))))).)))))))).----- ( -29.90)
>DroSec_CAF1 23519 114 - 1
GGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAGUCAGUCAACUCCAAUCCAACGAAGGCAAAUA-CUAAUAAACACUUAUUAAUCUUUGUUU-----
(((....(((((......))))).((((((.((((((........))))))))))))..)))...........((((((((..((((-............))))..)))))))).----- ( -29.20)
>DroSim_CAF1 23492 114 - 1
GGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAGUCAGUCAACACCAAUCCAACGAAGGCAAAUA-CUAAUAAACAAUUAUUAAUCUUUGUUU-----
(((....(((((......))))).((((((.((((((........))))))))))))..)))...........((((((((..((((-............))))..)))))))).----- ( -29.20)
>DroEre_CAF1 23322 106 - 1
G----CAGCAAUUGAAAUACUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUUCACUGAAACGAAGGCAAAUA-CUAAUAAGCAAUUAUUGCUCUUUGUUU-----
(----(((...........)))).((((((.((((((........)))))))))))----)...........(((((((((((....-...((((....))))))).))))))))----- ( -30.01)
>DroYak_CAF1 23624 110 - 1
GGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUCCACUCCAACGAAGGCAAAUA-CUAAUAAACAAUUAUUGUUCUUUGUUU-----
((.((..(((((......))))).((((((.((((((........)))))))))))----)...)))).....(((((((((((...-.((((.....))))))).)))))))).----- ( -29.90)
>DroAna_CAF1 82275 96 - 1
----------------AAAUUAAAACUAGGUCGAGGUCUUUAUUAAUCUCACCC-------CACUUCCACCCCUUCCACAAUCAGCACCGAAUAGCUAAU-AAUUCUCUUUGUUUUUUUA
----------------.....(((((..(((.(((((........)))))))).-------......................(((........)))...-..........))))).... ( -10.00)
>consensus
GGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG____UCAACUCCAAUCCAACGAAGGCAAAUA_CUAAUAAACAAUUAUUGAUCUUUGUUU_____
.......(((((......)))))..(((((.((((((........)))))))))))......................(((((((....((((((....))))))...)))))))..... (-16.72 = -17.92 +   1.20)

alignment

secondary structure

dotplot

Window 5

Location	15,663,758 – 15,663,874
Length	116
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.17
Mean single sequence MFE	-28.80
Consensus MFE	-19.01
Energy contribution	-21.65
Covariance contribution	2.64
Combinations/Pair	1.04
Mean z-score	-2.28
Structure conservation index	0.66
SVM decision value	0.53
SVM RNA-class probability	0.770151
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15663758 116 - 23771897
AAUGGAAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGGGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUCCAAUCCAACGAAG
..((((..(((..(((.(((.....(......)...))).)))....(((((......)))))..(((((.((((((........)))))))))))----)))..))))........... ( -34.30)
>DroSec_CAF1 23553 120 - 1
AAUGGCAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGGGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAGUCAGUCAACUCCAAUCCAACGAAG
..((((.......)))).......(((((.......))).(((....(((((......))))).((((((.((((((........))))))))))))..)))....))............ ( -33.30)
>DroSim_CAF1 23526 120 - 1
AAUGGCAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGGGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAGUCAGUCAACACCAAUCCAACGAAG
..((((.......)))).......(((((.......))).(((....(((((......))))).((((((.((((((........))))))))))))..)))....))............ ( -33.70)
>DroEre_CAF1 23356 112 - 1
AAUGGCAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGG----CAGCAAUUGAAAUACUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUUCACUGAAACGAAG
....(((......(((.........)))....(((.(((..----..))).)))......))).((((((.((((((........)))))))))))----)...((((........)))) ( -30.30)
>DroYak_CAF1 23658 116 - 1
AAUGGCAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGGGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG----UCAACUCCACUCCAACGAAG
..((((.......)))).......(((((.......))).((.((..(((((......))))).((((((.((((((........)))))))))))----)...))))...))....... ( -33.00)
>DroAna_CAF1 82314 92 - 1
AAUGACAAUGAAAUCUGGCAAAUAGA--AAAAUAAAC-------------------AAAUUAAAACUAGGUCGAGGUCUUUAUUAAUCUCACCC-------CACUUCCACCCCUUCCACA
.............((((.....))))--.........-------------------............(((.(((((........)))))))).-------................... (  -8.20)
>consensus
AAUGGCAAUGAAAGCCAGCAAAUAGGGCAAAACAAAUGCGGGCAGAAGCAAUUGUAAUAUUGCAACUGGGUCGAGGUCUUCAUUAAUCUCGCCCAG____UCAACUCCAAUCCAACGAAG
....((((((...(((.........)))...((((.(((........))).))))..))))))..(((((.((((((........)))))))))))........................ (-19.01 = -21.65 +   2.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:46 2006