Locus 6009

Sequence ID	X_DroMel_CAF1
Location	15,427,209 – 15,427,320
Length	111
Max. P	0.901383

overview

Window 1

Location	15,427,209 – 15,427,320
Length	111
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	93.81
Mean single sequence MFE	-28.22
Consensus MFE	-23.72
Energy contribution	-24.22
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.77
Structure conservation index	0.84
SVM decision value	0.38
SVM RNA-class probability	0.714548
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15427209 111 + 22224390
AAUUCGGCAAGCAGACAACAACACAACACGCUGUUUUAAUUAUUAUUAGCCCUCGCUGUUGUUGUCCCUGCCUAUUUGCUUUU-UUU--UUCGCUGGUUACGACGAUAAGUUCG
.....((((....((((((((((......((((.............))))......))))))))))..)))).....((((..-...--.(((.((....)).))).))))... ( -23.62)
>DroSec_CAF1 17358 112 + 1
AAUUCGGCGAGCAGACAACAACACAGCACGCUGUUUUAAUUAUUAUUAGCCCUCGUUGUUGUUGUCACUGCCUAUUUGCUUUUUUUU--UUCGCUGGUUACGACGAUAAGUUCG
...((((((((..((((((((((......((((.............))))......))))))))))...((......))........--))))))))......(((.....))) ( -26.92)
>DroEre_CAF1 16123 111 + 1
AAUUCGGCGAGCAGACAACAACACAACACGCUGUU-UAAUUAUUAUUAGCCCUCGCUGUUGUUGUCACUGCCUAUUUGCUGUUUUUU--GUCGCUGGUUACGACGAUAAGUUCG
....(((((((((((((((((((......((((..-..........))))......))))))))))..)))....))))))...(((--((((.((....)).))))))).... ( -29.10)
>DroYak_CAF1 15955 114 + 1
AAUUCGGCGAGCAGACAACAACACAACACGCUGUUUUAAUUAUUAUUAGCCUUUGCUGUUGUUGUCACUGCUUAUUUGGUUUUUUUUUGUUCGCUGGUUACGACGAUAAGUUCG
...(((((((((((((((((((((((...((((.............))))..))).))))))))))...(((.....))).......))))))))))......(((.....))) ( -33.22)
>consensus
AAUUCGGCGAGCAGACAACAACACAACACGCUGUUUUAAUUAUUAUUAGCCCUCGCUGUUGUUGUCACUGCCUAUUUGCUUUUUUUU__UUCGCUGGUUACGACGAUAAGUUCG
...(((((((...((((((((((......((((.............))))......))))))))))...((......))...........)))))))......(((.....))) (-23.72 = -24.22 +   0.50)

alignment

secondary structure

dotplot

Window 2

Location	15,427,209 – 15,427,320
Length	111
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	93.81
Mean single sequence MFE	-28.70
Consensus MFE	-24.05
Energy contribution	-24.36
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.29
Structure conservation index	0.84
SVM decision value	1.02
SVM RNA-class probability	0.901383
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15427209 111 - 22224390
CGAACUUAUCGUCGUAACCAGCGAA--AAA-AAAAGCAAAUAGGCAGGGACAACAACAGCGAGGGCUAAUAAUAAUUAAAACAGCGUGUUGUGUUGUUGUCUGCUUGCCGAAUU
........((.((((.....)))).--...-...........((((((((((((((((.(((.((((...............))).).)))))))))))))..))))))))... ( -29.46)
>DroSec_CAF1 17358 112 - 1
CGAACUUAUCGUCGUAACCAGCGAA--AAAAAAAAGCAAAUAGGCAGUGACAACAACAACGAGGGCUAAUAAUAAUUAAAACAGCGUGCUGUGUUGUUGUCUGCUCGCCGAAUU
........((.((((.....)))).--...............((((((((((((((((....(.(((...............))).)....)))))))))).))).)))))... ( -27.66)
>DroEre_CAF1 16123 111 - 1
CGAACUUAUCGUCGUAACCAGCGAC--AAAAAACAGCAAAUAGGCAGUGACAACAACAGCGAGGGCUAAUAAUAAUUA-AACAGCGUGUUGUGUUGUUGUCUGCUCGCCGAAUU
........(((((((.....)))))--...............(((((((((((((((((((..(..((((....))))-..)..)))....)))))))))).))).)))))... ( -32.20)
>DroYak_CAF1 15955 114 - 1
CGAACUUAUCGUCGUAACCAGCGAACAAAAAAAAACCAAAUAAGCAGUGACAACAACAGCAAAGGCUAAUAAUAAUUAAAACAGCGUGUUGUGUUGUUGUCUGCUCGCCGAAUU
........(((((((.....))))..................(((((((((((((.(((((...(((...............))).))))))))))))).)))))...)))... ( -25.46)
>consensus
CGAACUUAUCGUCGUAACCAGCGAA__AAAAAAAAGCAAAUAGGCAGUGACAACAACAGCGAGGGCUAAUAAUAAUUAAAACAGCGUGUUGUGUUGUUGUCUGCUCGCCGAAUU
........((.((((.....))))..................((((((((((((((((....(.(((...............))).)....)))))))))).))).)))))... (-24.05 = -24.36 +   0.31)

alignment

secondary structure

dotplot

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