Locus 6116

Sequence ID	3R_DroMel_CAF1
Location	16,035,616 – 16,035,720
Length	104
Max. P	0.985956

overview

Window 8

Location	16,035,616 – 16,035,720
Length	104
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	79.06
Mean single sequence MFE	-22.91
Consensus MFE	-12.96
Energy contribution	-13.86
Covariance contribution	0.90
Combinations/Pair	1.17
Mean z-score	-3.26
Structure conservation index	0.57
SVM decision value	2.02
SVM RNA-class probability	0.985956
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16035616 104 + 27905053
UAAUUUAUAUAUACAAAAUGUAUUU--ACAUUUACACAAAAAUGUAAUACAUAUUAGCG--------UAGAAAAAUGUACAGCGAACAUUUUCAAACAAAUUCCCUGUGCAUUC
.................(((((((.--((((((......))))))))))))).......--------......(((((((((.(((..............))).))))))))). ( -18.94)
>DroEre_CAF1 36515 111 + 1
UAACUUACACAUA-AAAAUGUGCUC--ACAUUUAGACAAACAUGUAAUACAUAUUAGUGGAUGUGUAAAGAAAAAUGUACAGGGAACAUUUUCAAACAAACUCCCUGUGCAUUC
....((((((((.-.((((((....--))))))..((.((.(((.....))).)).))..)))))))).....((((((((((((................)))))))))))). ( -28.39)
>DroYak_CAF1 43633 111 + 1
UAAUUUAUAUACA-ACAAUGUACUUGUACAUGUAGACAAACAUGUAAUAAAUAUUAGUGGAUAUGUAAAGA--UAUGUAUAAGGAACAUUUGCAAACAAGCUCCCUGAGCAUUC
.............-..(((((.(((((((((((......((((((.((........))..))))))....)--))))))))))..))))).........((((...)))).... ( -21.40)
>consensus
UAAUUUAUAUAUA_AAAAUGUACUU__ACAUUUAGACAAACAUGUAAUACAUAUUAGUGGAU_UGUAAAGAAAAAUGUACAGGGAACAUUUUCAAACAAACUCCCUGUGCAUUC
.......(((((.....))))).....((((((......))))))............................((((((((((((................)))))))))))). (-12.96 = -13.86 +   0.90)

alignment

secondary structure

dotplot

Window 9

Location	16,035,616 – 16,035,720
Length	104
Sequences	3
Columns	114
Reading direction	reverse
Mean pairwise identity	79.06
Mean single sequence MFE	-22.83
Consensus MFE	-13.30
Energy contribution	-14.87
Covariance contribution	1.57
Combinations/Pair	1.19
Mean z-score	-1.97
Structure conservation index	0.58
SVM decision value	0.10
SVM RNA-class probability	0.583466
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16035616 104 - 27905053
GAAUGCACAGGGAAUUUGUUUGAAAAUGUUCGCUGUACAUUUUUCUA--------CGCUAAUAUGUAUUACAUUUUUGUGUAAAUGU--AAAUACAUUUUGUAUAUAUAAAUUA
(((((.((((.((((............)))).)))).))))).....--------.((....(((((((((((((......))))))--.)))))))...))............ ( -20.60)
>DroEre_CAF1 36515 111 - 1
GAAUGCACAGGGAGUUUGUUUGAAAAUGUUCCCUGUACAUUUUUCUUUACACAUCCACUAAUAUGUAUUACAUGUUUGUCUAAAUGU--GAGCACAUUUU-UAUGUGUAAGUUA
(((((.(((((((((((......))))..))))))).))))).......(((((..((.((((((.....)))))).))....))))--).((((((...-.))))))...... ( -29.00)
>DroYak_CAF1 43633 111 - 1
GAAUGCUCAGGGAGCUUGUUUGCAAAUGUUCCUUAUACAUA--UCUUUACAUAUCCACUAAUAUUUAUUACAUGUUUGUCUACAUGUACAAGUACAUUGU-UGUAUAUAAAUUA
(((((...((((((((((....)))..)))))))...))).--)).................(((((((((((((......)))))))...(((((....-))))))))))).. ( -18.90)
>consensus
GAAUGCACAGGGAGUUUGUUUGAAAAUGUUCCCUGUACAUUUUUCUUUACA_AUCCACUAAUAUGUAUUACAUGUUUGUCUAAAUGU__AAGUACAUUUU_UAUAUAUAAAUUA
(((((.(((((((((............))))))))).)))))....................(((((((((((((......))))))...)))))))................. (-13.30 = -14.87 +   1.57)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:02 2006