Locus 7790

Sequence ID	3R_DroMel_CAF1
Location	20,870,494 – 20,870,619
Length	125
Max. P	0.999522

overview

Window 8

Location	20,870,494 – 20,870,598
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	94.80
Mean single sequence MFE	-27.08
Consensus MFE	-24.04
Energy contribution	-23.88
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-1.38
Structure conservation index	0.89
SVM decision value	0.72
SVM RNA-class probability	0.832756
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20870494 104 + 27905053
AAAUUCGAUUAUCGGCGGGCGCUGAAUGUGCUGAAUACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAU
....(((.....))).((((.((((((...((((...((((.....))))....)))))))))(((((((((....)))))))))...).)))).......... ( -28.00)
>DroSec_CAF1 9095 104 + 1
AAAUUCGAUUAUCGGCGGGCGCUGAAUGUACUGAAUACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAU
....(((.....))).((((.((((((...((((...((((.....))))....)))))))))(((((((((....)))))))))...).)))).......... ( -28.00)
>DroSim_CAF1 10118 104 + 1
AAAUUCGAUUAUCGACGGGCGCUGAAUGUGCUGAAUACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAU
....(((.....))).((((.((((((...((((...((((.....))))....)))))))))(((((((((....)))))))))...).)))).......... ( -28.90)
>DroEre_CAF1 11426 103 + 1
AAAUUCGAUUAUCGGCGGGCGUU-AAUGUGCUGAAUACCAAUUUGUUUGGGGACUCGGAUUCGGAUACACAUAUCAAUGUAUGUCAGUGAGUCCAUACAUAAAU
...........((((((.(....-..).))))))...((((.....))))(((((((......((((.((((....)))).))))..))))))).......... ( -25.00)
>DroYak_CAF1 10564 103 + 1
AAAUUCGAUUAUCGGCGGGCGCU-AAUGUGCUGAAUACCAAUUUGUUUGGGAGCUCGGAUUCGGUUAUACAUAUCUAUGUAUGUCAGUGGGUCCAUACAUAAAU
.............(((.(((((.-...))))).....((((.....))))..))).(((((((.((((((((....)))))))..).))))))).......... ( -25.50)
>consensus
AAAUUCGAUUAUCGGCGGGCGCUGAAUGUGCUGAAUACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAU
....(((.....))).((((.(........((((...((((.....))))....)))).....(((((((((....)))))))))...).)))).......... (-24.04 = -23.88 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	20,870,529 – 20,870,619
Length	90
Sequences	5
Columns	90
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-25.24
Consensus MFE	-22.42
Energy contribution	-22.82
Covariance contribution	0.40
Combinations/Pair	1.07
Mean z-score	-2.58
Structure conservation index	0.89
SVM decision value	3.46
SVM RNA-class probability	0.999244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20870529 90 + 27905053
UACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
........(((.((((..(((((.....(((((((((....))))))))).))))))))).)))....((((((((......)))))))) ( -26.00)
>DroSec_CAF1 9130 90 + 1
UACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
........(((.((((..(((((.....(((((((((....))))))))).))))))))).)))....((((((((......)))))))) ( -26.00)
>DroSim_CAF1 10153 90 + 1
UACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
........(((.((((..(((((.....(((((((((....))))))))).))))))))).)))....((((((((......)))))))) ( -26.00)
>DroEre_CAF1 11460 90 + 1
UACCAAUUUGUUUGGGGACUCGGAUUCGGAUACACAUAUCAAUGUAUGUCAGUGAGUCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
..((((.....))))(((((((......((((.((((....)))).))))..))))))).(((((....(((((.....))))).))))) ( -25.20)
>DroYak_CAF1 10598 90 + 1
UACCAAUUUGUUUGGGAGCUCGGAUUCGGUUAUACAUAUCUAUGUAUGUCAGUGGGUCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
..((((.....))))......(((((((.((((((((....)))))))..).))))))).(((((....(((((.....))))).))))) ( -23.00)
>consensus
UACCAAUUUGUUUGGGAACUCGGAUUCGGAUAUACAUAUCUAUGUAUGUCACUGGGCCCAUACAUAAAUAUGCGAUUUACGCAUCGUGUA
........(((.((((..(((((.....(((((((((....))))))))).))))))))).)))....((((((((......)))))))) (-22.42 = -22.82 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	20,870,529 – 20,870,619
Length	90
Sequences	5
Columns	90
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-21.48
Consensus MFE	-20.52
Energy contribution	-20.72
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.96
SVM decision value	3.68
SVM RNA-class probability	0.999522
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20870529 90 - 27905053
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUUCCCAAACAAAUUGGUA
.....(((......)))(((((((((((((((..........)))))))))))))))......((((....))))((((.....)))).. ( -21.40)
>DroSec_CAF1 9130 90 - 1
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUUCCCAAACAAAUUGGUA
.....(((......)))(((((((((((((((..........)))))))))))))))......((((....))))((((.....)))).. ( -21.40)
>DroSim_CAF1 10153 90 - 1
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUUCCCAAACAAAUUGGUA
.....(((......)))(((((((((((((((..........)))))))))))))))......((((....))))((((.....)))).. ( -21.40)
>DroEre_CAF1 11460 90 - 1
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGACUCACUGACAUACAUUGAUAUGUGUAUCCGAAUCCGAGUCCCCAAACAAAUUGGUA
((((..(((((.....))))).....)))).((((((...((.((((((....)))))).)).(....)))))))((((.....)))).. ( -21.50)
>DroYak_CAF1 10598 90 - 1
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGACCCACUGACAUACAUAGAUAUGUAUAACCGAAUCCGAGCUCCCAAACAAAUUGGUA
.....((.((.......(((((((((((((((..........))))))))))))))).....((....)).))))((((.....)))).. ( -21.70)
>consensus
UACACGAUGCGUAAAUCGCAUAUUUAUGUAUGGGCCCAGUGACAUACAUAGAUAUGUAUAUCCGAAUCCGAGUUCCCAAACAAAUUGGUA
.....(((.((......(((((((((((((((..........))))))))))))))).....)).))).......((((.....)))).. (-20.52 = -20.72 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:42 2006