Locus 613

Sequence ID	3L_DroMel_CAF1
Location	1,781,971 – 1,782,063
Length	92
Max. P	0.910221

overview

Window 2

Location	1,781,971 – 1,782,063
Length	92
Sequences	6
Columns	92
Reading direction	forward
Mean pairwise identity	74.86
Mean single sequence MFE	-26.54
Consensus MFE	-10.57
Energy contribution	-10.33
Covariance contribution	-0.25
Combinations/Pair	1.31
Mean z-score	-2.37
Structure conservation index	0.40
SVM decision value	1.07
SVM RNA-class probability	0.910221
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1781971 92 + 23771897
CAUAUGAAGCAUAUCACUCGCGAAUUCUUCCGCGAAUUCCGCAAGCUCGAAAUAGAAUUGGAGGAGGAGGAGGAACGUAACAUGGUUUGAUG
.........((.((((...(((..((((((((((.....)))...(((.((......)).)))..)))))))...)))....)))).))... ( -21.00)
>DroPse_CAF1 2748 92 + 1
ACAAUGAAAAGCAUGACGCGUGAGUUCUUCCGCGAGUUCCACAAGUUGGAAGUGGAACUCGAGGAGGAGGAAAAACAGAAAAUGCUUUAGUA
.......(((((((...((....))((((((.((((((((((.........)))))))))).)))))).............))))))).... ( -35.40)
>DroGri_CAF1 2685 91 + 1
GGCAUGAAAGCCAUGACACGUGAAUUCUUCGGCGAAUUCCGCAAGUCGGAGCUGGAAUUGGAGCGGGAGGAGAAGAAACAAAUGCAGUAAA-
(((......))).......((...((((((.((.((((((((........)).))))))...)).))))))......))............- ( -22.30)
>DroSim_CAF1 2751 92 + 1
CAUAUGAAGCAUAUCACUCGCGAAUUCUUCCGCGAAUUCCGCAAGCUCGAAAUAGAGCUGGAGGAGGAGGAGGAACGUAACAUGGUUUGAUG
..(((.((((...((.(((.(...((((((((((.....))).(((((......))))))))))))..)))))).(((...))))))).))) ( -27.00)
>DroYak_CAF1 2697 92 + 1
AAUAUGAAGCAUAUCACACGCCAAUUUUUCCGCGAAUUCCGCAAGCUCGAAGUCGAACUGGAGGAGGAGGAAGAACGUAACAUGGUUUGAUG
..(((.((((.......(((....(((((((.....((((...((.(((....))).))...))))..))))))))))......)))).))) ( -19.22)
>DroPer_CAF1 3204 92 + 1
ACAAUGAAAAGCAUGACGCGUGAGUUCUUCCGCGAGUUCCACAAGUUGGAAGUGGAACUCGAAGAGGAGGAAAAACAGAAGAUGCUUUAGAA
.......(((((((...((....))((((((.((((((((((.........))))))))))....))))))..........))))))).... ( -34.30)
>consensus
AAUAUGAAACACAUCACACGCGAAUUCUUCCGCGAAUUCCGCAAGCUCGAAGUGGAACUGGAGGAGGAGGAAAAACAUAACAUGCUUUAAUG
........................(((((((.(.(((((...............))))).)....))))))).................... (-10.57 = -10.33 +  -0.25)

alignment

secondary structure

dotplot

Window 3

Location	1,781,971 – 1,782,063
Length	92
Sequences	6
Columns	92
Reading direction	reverse
Mean pairwise identity	74.86
Mean single sequence MFE	-24.35
Consensus MFE	-6.21
Energy contribution	-6.49
Covariance contribution	0.28
Combinations/Pair	1.33
Mean z-score	-2.90
Structure conservation index	0.25
SVM decision value	1.01
SVM RNA-class probability	0.900655
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1781971 92 - 23771897
CAUCAAACCAUGUUACGUUCCUCCUCCUCCUCCAAUUCUAUUUCGAGCUUGCGGAAUUCGCGGAAGAAUUCGCGAGUGAUAUGCUUCAUAUG
........(((((((((((((.(...(((...............)))...).)))))(((((((....)))))))))))))))......... ( -21.06)
>DroPse_CAF1 2748 92 - 1
UACUAAAGCAUUUUCUGUUUUUCCUCCUCCUCGAGUUCCACUUCCAACUUGUGGAACUCGCGGAAGAACUCACGCGUCAUGCUUUUCAUUGU
....(((((((....(((......((.(((.((((((((((.........)))))))))).))).))......)))..)))))))....... ( -28.30)
>DroGri_CAF1 2685 91 - 1
-UUUACUGCAUUUGUUUCUUCUCCUCCCGCUCCAAUUCCAGCUCCGACUUGCGGAAUUCGCCGAAGAAUUCACGUGUCAUGGCUUUCAUGCC
-......((((.((.((((((.......(((........)))((((.....)))).......))))))..)).))))...(((......))) ( -18.80)
>DroSim_CAF1 2751 92 - 1
CAUCAAACCAUGUUACGUUCCUCCUCCUCCUCCAGCUCUAUUUCGAGCUUGCGGAAUUCGCGGAAGAAUUCGCGAGUGAUAUGCUUCAUAUG
........((((((((...........(((.(.(((((......))))).).)))..(((((((....)))))))))))))))......... ( -27.70)
>DroYak_CAF1 2697 92 - 1
CAUCAAACCAUGUUACGUUCUUCCUCCUCCUCCAGUUCGACUUCGAGCUUGCGGAAUUCGCGGAAAAAUUGGCGUGUGAUAUGCUUCAUAUU
........(((((((((..........(((.(.((((((....)))))).).)))...(((.((....)).))))))))))))......... ( -22.90)
>DroPer_CAF1 3204 92 - 1
UUCUAAAGCAUCUUCUGUUUUUCCUCCUCUUCGAGUUCCACUUCCAACUUGUGGAACUCGCGGAAGAACUCACGCGUCAUGCUUUUCAUUGU
....(((((((.....((((((((.......((((((((((.........)))))))))).)))))))).........)))))))....... ( -27.34)
>consensus
CAUCAAACCAUGUUACGUUCCUCCUCCUCCUCCAGUUCCACUUCCAACUUGCGGAAUUCGCGGAAGAAUUCACGAGUCAUAUGCUUCAUAUU
........................((.(((.(.((((((.............)))))).).))).))......................... ( -6.21 =  -6.49 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:45 2006