Locus 4812

Sequence ID	3R_DroMel_CAF1
Location	12,576,527 – 12,576,631
Length	104
Max. P	0.998655

overview

Window 9

Location	12,576,527 – 12,576,631
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	71.35
Mean single sequence MFE	-22.20
Consensus MFE	-11.94
Energy contribution	-13.41
Covariance contribution	1.47
Combinations/Pair	1.11
Mean z-score	-2.06
Structure conservation index	0.54
SVM decision value	1.70
SVM RNA-class probability	0.972659
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12576527 104 + 27905053
----UACAGAUUUUAGGAACCAAUUUCCUAAAAACUUGACCCAG--------UUGUAGGAAAUUGUUUCUAAAAUUUCUAGUUUAAUUUUA--GGUUUUGCAGCAAUAACUUUGUAUU--
----...(((((((((((((.(((((((((..((((......))--------)).))))))))))))))))))))))((((.......)))--)........((((.....))))...-- ( -24.90)
>DroSec_CAF1 65197 108 + 1
UACCUUCAGAUUUUAGGAACCAAUUUUCUAAAAACUUAACCCAG--------UUGUAGGAAAUCGCUCCUAAAAUGUCUAGUUUAAUUUUA--GGUUUUGCAGCAAUAACUUUGUGUU--
.......((.(((((((((.....))))))))).)).......(--------((((((((.......((((((((..........))))))--)))))))))))..............-- ( -18.61)
>DroSim_CAF1 65302 108 + 1
UACCCUCAGAUUUUAGGAACCAAUUUCCUAAAAACUUGACCCAG--------UUGUAGGAAAUCGCUCCUAAAAUGUCUAGUUUAAUUUUA--GGUUUUGCAGCAAUAACUUUGUGUU--
.....((((.(((((((((.....))))))))).).)))....(--------((((((((.......((((((((..........))))))--)))))))))))..............-- ( -22.41)
>DroEre_CAF1 63976 107 + 1
UACCUUCAGAUUUAAGGAAACAAUUUCCUAA-AACUUGACCCAC--------UUGUAGGAAAUUGUUCCCAAAAGUUUUAGUUUAAUUUUA--AGUUUUGCAGCAAUAGCUUUGCAUU--
.......((((((..((.((((((((((((.-............--------...)))))))))))).))..))))))..((..(((....--.)))..)).((((.....))))...-- ( -20.69)
>DroYak_CAF1 64304 91 + 1
UGCCUUCAGAUUUUAGGAAACAAUUUCCUAA-AACUUGACCCAC--------UUCUAGGAAAUUGUUUCUAAAAGGUGUAGUUUAAUUUCC--AA----------------UUGUAUU--
...((.((..((((((.(((((((((((((.-............--------...)))))))))))))))))))..)).))..........--..----------------.......-- ( -20.39)
>DroAna_CAF1 63213 118 + 1
UGCCUAUAGGUUUUAGGAAAUAACAUCCCAAAAUA-UUACGAAGCGGCAACCUAUCAGGAAAUUCUUCCUAAAAGAUUUAGGCA-AUCUCUGUCGCUCCGCGACAAAAACUUCAUAAAUA
((((((.(..(((((((((......(((.((....-))..((((.(....))).)).))).....)))))))))..).))))))-.....((((((...))))))............... ( -26.20)
>consensus
UACCUUCAGAUUUUAGGAAACAAUUUCCUAAAAACUUGACCCAG________UUGUAGGAAAUUGUUCCUAAAAGGUCUAGUUUAAUUUUA__GGUUUUGCAGCAAUAACUUUGUAUU__
..........(((((((((.((((((((((.........................))))))))))))))))))).............................................. (-11.94 = -13.41 +   1.47)

alignment

secondary structure

dotplot

Window 0

Location	12,576,527 – 12,576,631
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.35
Mean single sequence MFE	-26.68
Consensus MFE	-14.49
Energy contribution	-14.49
Covariance contribution	0.00
Combinations/Pair	1.32
Mean z-score	-3.09
Structure conservation index	0.54
SVM decision value	3.17
SVM RNA-class probability	0.998655
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12576527 104 - 27905053
--AAUACAAAGUUAUUGCUGCAAAACC--UAAAAUUAAACUAGAAAUUUUAGAAACAAUUUCCUACAA--------CUGGGUCAAGUUUUUAGGAAAUUGGUUCCUAAAAUCUGUA----
--..((((..................(--(((((((........))))))))...((((((((((.((--------((......))))..))))))))))............))))---- ( -19.90)
>DroSec_CAF1 65197 108 - 1
--AACACAAAGUUAUUGCUGCAAAACC--UAAAAUUAAACUAGACAUUUUAGGAGCGAUUUCCUACAA--------CUGGGUUAAGUUUUUAGAAAAUUGGUUCCUAAAAUCUGAAGGUA
--.......(((....))).....(((--(..........((((..(((((((((((((((.(((.((--------((......))))..))).))))).)))))))))))))).)))). ( -19.60)
>DroSim_CAF1 65302 108 - 1
--AACACAAAGUUAUUGCUGCAAAACC--UAAAAUUAAACUAGACAUUUUAGGAGCGAUUUCCUACAA--------CUGGGUCAAGUUUUUAGGAAAUUGGUUCCUAAAAUCUGAGGGUA
--.......(((....)))......((--(..........((((..(((((((((((((((((((.((--------((......))))..))))))))).)))))))))))))))))... ( -26.60)
>DroEre_CAF1 63976 107 - 1
--AAUGCAAAGCUAUUGCUGCAAAACU--UAAAAUUAAACUAAAACUUUUGGGAACAAUUUCCUACAA--------GUGGGUCAAGUU-UUAGGAAAUUGUUUCCUUAAAUCUGAAGGUA
--..((((..((....)))))).....--...............(((((((((((((((((((((.((--------.(......).))-.)))))))))))))))........)))))). ( -26.90)
>DroYak_CAF1 64304 91 - 1
--AAUACAA----------------UU--GGAAAUUAAACUACACCUUUUAGAAACAAUUUCCUAGAA--------GUGGGUCAAGUU-UUAGGAAAUUGUUUCCUAAAAUCUGAAGGCA
--.......----------------..--..........((.((..((((((((((((((((((((((--------.(......).))-)))))))))))))).))))))..)).))... ( -25.60)
>DroAna_CAF1 63213 118 - 1
UAUUUAUGAAGUUUUUGUCGCGGAGCGACAGAGAU-UGCCUAAAUCUUUUAGGAAGAAUUUCCUGAUAGGUUGCCGCUUCGUAA-UAUUUUGGGAUGUUAUUUCCUAAAACCUAUAGGCA
.........((((((((((((...)))))))))))-)(((((....(((((((((((((.(((..(...(((((......))))-)...)..))).))).))))))))))....))))). ( -41.50)
>consensus
__AAUACAAAGUUAUUGCUGCAAAACC__UAAAAUUAAACUAGACAUUUUAGGAACAAUUUCCUACAA________CUGGGUCAAGUUUUUAGGAAAUUGGUUCCUAAAAUCUGAAGGUA
..............................................(((((((((((((((((((.........................)))))))))).))))))))).......... (-14.49 = -14.49 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:28 2006