Locus 4520

Sequence ID	3L_DroMel_CAF1
Location	13,016,868 – 13,016,958
Length	90
Max. P	0.994714

overview

Window 2

Location	13,016,868 – 13,016,958
Length	90
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	73.01
Mean single sequence MFE	-32.23
Consensus MFE	-22.95
Energy contribution	-23.98
Covariance contribution	1.03
Combinations/Pair	1.05
Mean z-score	-2.73
Structure conservation index	0.71
SVM decision value	2.50
SVM RNA-class probability	0.994714
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13016868 90 + 23771897
AA-----AGCAUUAUAUU--GUAAUU------------------C----UGUGGGCUACGUCGAAGACCGAUUUCCGCUUGUUGCCAUGUGUCUAUUGGUUCAAAUCGAAGCCCAAAGC
..-----.(((......)--))....------------------(----(.((((((.((.....(((((((...(((.((....)).)))...))))))).....)).)))))).)). ( -23.60)
>DroSec_CAF1 728 107 + 1
AU-----AGCAUUAUAUU--GUCAUUCCC-UUCAAGAGGGAAAAC----UGUGGGCUUCGUCGAAGACCGAUUUCCGCCGUUUGCCAUGUGUCUAUUGGUUCAAAUCGAAGCCCAAAGC
..-----.(((......)--))..(((((-((...)))))))..(----(.(((((((((.....(((((((...(((..........)))...))))))).....))))))))).)). ( -33.40)
>DroSim_CAF1 729 106 + 1
AU-----AG-AUUACAUU--GUCAUUCCC-UUCAAGAGGGAAAAC----UGUGGGCUUCGUCGAAGACCGAUUUUCGCCUGUUGCCAUGUGUUCAUUGGUUCAAAUCGAAGCCCAAAGC
..-----.(-((......--))).(((((-((...)))))))..(----(.(((((((((.....(((((((...(((.((....)).)))...))))))).....))))))))).)). ( -36.40)
>DroEre_CAF1 918 108 + 1
GU-----AUUAUU----A--GUUAUUCAUAAUUAAUAAGGGAAACUGUUUGUGGGCUUCGUCGAAGACCGAUUUCCGCCUGUUGCCAUGUGUCUAUUGGUUCAAAUCGAAGCCCAAAGC
..-----.(((((----(--((((....))))))))))((....))((((.(((((((((.....(((((((...(((.((....)).)))...))))))).....))))))))))))) ( -34.80)
>DroYak_CAF1 943 112 + 1
UU-----AGUAUUAUUCA--GUUAUUCAGAAUUAAUGGGGUAAACUGUUUGUGGGCUUCGUCGAAGACCGAUUUGCGCCUGUUGCCAUGUGUUUAUUGGUUCAAAUCGAAGCCCAAAGC
.(-----(((.((((((.--((((........)))).))))))))))....(((((((((.....(((((((..((((.((....)).))))..))))))).....))))))))).... ( -36.50)
>DroAna_CAF1 601 106 + 1
UUAAGAGAGACUUGUAUUUGGAAACUCCA----AAAAGCCCAGAU----UCUGGGCUUUGUCGAAGACCGAUUUAC-----UUUUUAUAAGAAUAUUGGUUCAAAACGAAGCCCAAAGC
.....((((.((.((.(((((.....)))----))..))..)).)----)))(((((((((....(((((((...(-----((.....)))...)))))))....)))))))))..... ( -28.70)
>consensus
AU_____AGCAUUAUAUU__GUAAUUCCC__U_AAGAGGGAAAAC____UGUGGGCUUCGUCGAAGACCGAUUUCCGCCUGUUGCCAUGUGUCUAUUGGUUCAAAUCGAAGCCCAAAGC
...................................................(((((((((.....(((((((...(((.((....)).)))...))))))).....))))))))).... (-22.95 = -23.98 +   1.03)

alignment

secondary structure

dotplot

Window 3

Location	13,016,868 – 13,016,958
Length	90
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	73.01
Mean single sequence MFE	-26.99
Consensus MFE	-17.30
Energy contribution	-18.47
Covariance contribution	1.17
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.64
SVM decision value	1.69
SVM RNA-class probability	0.972393
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13016868 90 - 23771897
GCUUUGGGCUUCGAUUUGAACCAAUAGACACAUGGCAACAAGCGGAAAUCGGUCUUCGACGUAGCCCACA----G------------------AAUUAC--AAUAUAAUGCU-----UU
.((.((((((((((...((.((.((...(.(.((....)).).)...)).)))).))))...)))))).)----)------------------......--...........-----.. ( -20.10)
>DroSec_CAF1 728 107 - 1
GCUUUGGGCUUCGAUUUGAACCAAUAGACACAUGGCAAACGGCGGAAAUCGGUCUUCGACGAAGCCCACA----GUUUUCCCUCUUGAA-GGGAAUGAC--AAUAUAAUGCU-----AU
((..(((((((((..((((((((.........))).....(((.(....).)))))))))))))))))..----(((((((((.....)-))))).)))--........)).-----.. ( -31.90)
>DroSim_CAF1 729 106 - 1
GCUUUGGGCUUCGAUUUGAACCAAUGAACACAUGGCAACAGGCGAAAAUCGGUCUUCGACGAAGCCCACA----GUUUUCCCUCUUGAA-GGGAAUGAC--AAUGUAAU-CU-----AU
(((.(((((((((..(((((((.((.......((....)).......)).)))..))))))))))))).)----)).((((((.....)-)))))....--........-..-----.. ( -32.14)
>DroEre_CAF1 918 108 - 1
GCUUUGGGCUUCGAUUUGAACCAAUAGACACAUGGCAACAGGCGGAAAUCGGUCUUCGACGAAGCCCACAAACAGUUUCCCUUAUUAAUUAUGAAUAAC--U----AAUAAU-----AC
....(((((((((..(((((............((....))(((.(....).))))))))))))))))).............((((((.(((....))).--)----))))).-----.. ( -24.50)
>DroYak_CAF1 943 112 - 1
GCUUUGGGCUUCGAUUUGAACCAAUAAACACAUGGCAACAGGCGCAAAUCGGUCUUCGACGAAGCCCACAAACAGUUUACCCCAUUAAUUCUGAAUAAC--UGAAUAAUACU-----AA
....((((((((((((((..((..........((....))))..)))))).(((...)))))))))))....(((((...................)))--)).........-----.. ( -27.01)
>DroAna_CAF1 601 106 - 1
GCUUUGGGCUUCGUUUUGAACCAAUAUUCUUAUAAAAA-----GUAAAUCGGUCUUCGACAAAGCCCAGA----AUCUGGGCUUUU----UGGAGUUUCCAAAUACAAGUCUCUCUUAA
.....((((((.((((((.(((.((...(((.....))-----)...)).)))((((((.(((((((((.----..))))))))))----)))))....)))).))))))))....... ( -26.30)
>consensus
GCUUUGGGCUUCGAUUUGAACCAAUAGACACAUGGCAACAGGCGGAAAUCGGUCUUCGACGAAGCCCACA____GUUUUCCCUAUU_A__GGGAAUAAC__AAUAUAAUACU_____AU
....(((((((((..(((((((.((...(.(.((....)).).)...)).)))..)))))))))))))................................................... (-17.30 = -18.47 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:37 2006