Locus 3054

Sequence ID	3R_DroMel_CAF1
Location	8,094,726 – 8,094,829
Length	103
Max. P	0.835911

overview

Window 3

Location	8,094,726 – 8,094,829
Length	103
Sequences	5
Columns	103
Reading direction	forward
Mean pairwise identity	94.35
Mean single sequence MFE	-29.02
Consensus MFE	-25.88
Energy contribution	-25.92
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-1.36
Structure conservation index	0.89
SVM decision value	0.73
SVM RNA-class probability	0.835911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8094726 103 + 27905053
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGCCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUUCGACUAUAUAUGU
.......(((((((((((((..(((.....(......)........((((..(((((......)))))..)))))))..))).))))))).)))......... ( -28.20)
>DroSec_CAF1 46436 101 + 1
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGCCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUUCGGCCAUAUAU--
.(((((((.(((((...((((......)))).........(..((........))..).))).)).))))))).(((.(((.....)))..))).......-- ( -27.70)
>DroSim_CAF1 18457 100 + 1
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGGCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUUCGGCCAUAUA---
.(((((((.(((((...((((......)))).............((.((....).).))))).)).))))))).(((.(((.....)))..)))......--- ( -28.30)
>DroEre_CAF1 21443 102 + 1
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGCCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUU-GGCUAUACUUGU
.......(((((((((((((..(((.....(......)........((((..(((((......)))))..)))))))..))).)))))))-)))......... ( -31.40)
>DroYak_CAF1 14975 100 + 1
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGCCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUU-AGCUAUA--UAC
.(((((((.(((((...((((......)))).........(..((........))..).))).)).))))))).(((.(((.....))).-)))....--... ( -29.50)
>consensus
UCCACCUGUCAGCCAAAUGGACAGCAAUCCGAACACACAAUUAUCUGCCAAAUGACGAGGGCGUGUCAGGUGGCGCUUACCAUUUUGGUUCGGCUAUAUAU__
.(((((((.(((((...((((......)))).........(..((........))..).))).)).))))))).(((.(((.....)))..)))......... (-25.88 = -25.92 +   0.04)

alignment

secondary structure

dotplot

Window 4

Location	8,094,726 – 8,094,829
Length	103
Sequences	5
Columns	103
Reading direction	reverse
Mean pairwise identity	94.35
Mean single sequence MFE	-30.66
Consensus MFE	-28.56
Energy contribution	-28.40
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.14
Structure conservation index	0.93
SVM decision value	0.29
SVM RNA-class probability	0.670899
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8094726 103 - 27905053
ACAUAUAUAGUCGAACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGGCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
(((((((..(((..(((.....)))....((((..((((........))))..)))).)))...)))))))...........((((((((.....)))))))) ( -29.10)
>DroSec_CAF1 46436 101 - 1
--AUAUAUGGCCGAACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGGCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
--.....(((((..(((.....)))..).))))((.(((((((..(((((....))).)).....))))))).)).......((((((((.....)))))))) ( -30.50)
>DroSim_CAF1 18457 100 - 1
---UAUAUGGCCGAACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGCCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
---....(((((..(((.....)))..).))))((.(((((((....(((........)))....))))))).)).......((((((((.....)))))))) ( -30.40)
>DroEre_CAF1 21443 102 - 1
ACAAGUAUAGCC-AACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGGCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
.........((.-.(((.....)))..)).(((((((.((.(((...(((....)))................((((....))))....))))).))))))). ( -30.50)
>DroYak_CAF1 14975 100 - 1
GUA--UAUAGCU-AACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGGCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
...--....(((-.(((.....))).))).(((((((.((.(((...(((....)))................((((....))))....))))).))))))). ( -32.80)
>consensus
__AUAUAUAGCCGAACCAAAAUGGUAAGCGCCACCUGACACGCCCUCGUCAUUUGGCAGAUAAUUGUGUGUUCGGAUUGCUGUCCAUUUGGCUGACAGGUGGA
.........((...(((.....)))..)).(((((((((((((....(((........)))....))))))..((((....))))..........))))))). (-28.56 = -28.40 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:42 2006