Locus 7088

Sequence ID	3L_DroMel_CAF1
Location	19,146,391 – 19,146,496
Length	105
Max. P	0.827956

overview

Window 8

Location	19,146,391 – 19,146,496
Length	105
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.83
Mean single sequence MFE	-33.90
Consensus MFE	-28.32
Energy contribution	-28.08
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.84
SVM decision value	0.70
SVM RNA-class probability	0.827956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19146391 105 + 23771897
CUCCACAAUUCACACCUUGCCCGGAAAAUAAA-UCGGGC----AGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGCACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.((((((((((........-))))))----)))).).)))....)))))...........((((((((((((...........)))))).)))))). ( -36.10)
>DroSec_CAF1 9296 105 + 1
CUCCACAAUUCACACCUUGCCCGGAAAAUAAA-UCGGGC----AGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGCACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.((((((((((........-))))))----)))).).)))....)))))...........((((((((((((...........)))))).)))))). ( -36.10)
>DroSim_CAF1 8932 105 + 1
CUCCACAAUUCACACCUUGCCCGGAAAAUAAA-UCGGGC----AGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGCACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.((((((((((........-))))))----)))).).)))....)))))...........((((((((((((...........)))))).)))))). ( -36.10)
>DroEre_CAF1 9695 106 + 1
CUCCACAAUUCACACCUUGCCCGGAAAAUAAAAGCGGGC----AGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGUACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.(((((((((...........)))))----)))).).)))....)))))...........((((((((((((...........)))))).)))))). ( -33.20)
>DroYak_CAF1 9762 110 + 1
CUCCACAAUUCACACCUUGCCCGGAAAAUAAAAGCGGGCAGGCAGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGUACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.(((((((((...........))))))....))).).)))....)))))...........((((((((((((...........)))))).)))))). ( -28.00)
>consensus
CUCCACAAUUCACACCUUGCCCGGAAAAUAAA_UCGGGC____AGGGCGGGAAAAUAUGGGGAAUAUGGUUACGGGCACGGUUGUAAAAUGCGCGCACAAUCAGUGCUUC
(((((...(((.(.(((((((((...........)))))....)))).).)))....)))))...........((((((((((((...........)))))).)))))). (-28.32 = -28.08 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	19,146,391 – 19,146,496
Length	105
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.83
Mean single sequence MFE	-32.27
Consensus MFE	-26.26
Energy contribution	-26.66
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.81
Structure conservation index	0.81
SVM decision value	0.45
SVM RNA-class probability	0.742498
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19146391 105 - 23771897
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUGCCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCU----GCCCGA-UUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))((((...........))))...........))).(((((..(((.((((.(----(((((.-.........)))))).)))).))).))))).. ( -34.30)
>DroSec_CAF1 9296 105 - 1
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUGCCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCU----GCCCGA-UUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))((((...........))))...........))).(((((..(((.((((.(----(((((.-.........)))))).)))).))).))))).. ( -34.30)
>DroSim_CAF1 8932 105 - 1
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUGCCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCU----GCCCGA-UUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))((((...........))))...........))).(((((..(((.((((.(----(((((.-.........)))))).)))).))).))))).. ( -34.30)
>DroEre_CAF1 9695 106 - 1
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUACCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCU----GCCCGCUUUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))(((.....(((....)))..))).......))).(((((..(((.((((.(----(((((...........)))))).)))).))).))))).. ( -30.50)
>DroYak_CAF1 9762 110 - 1
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUACCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCUGCCUGCCCGCUUUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))(((.....(((....)))..))).......))).(((((..(((.((((.((((((...............)))))).)))).))).))))).. ( -27.96)
>consensus
GAAGCACUGAUUGUGCGCGCAUUUUACAACCGUGCCCGUAACCAUAUUCCCCAUAUUUUCCCGCCCU____GCCCGA_UUUAUUUUCCGGGCAAGGUGUGAAUUGUGGAG
(((((((.....))))((((...........))))...........))).(((((..(((.((((......(((((...........)))))..)))).))).))))).. (-26.26 = -26.66 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:31 2006