Locus 4158

Sequence ID	3R_DroMel_CAF1
Location	11,324,326 – 11,324,479
Length	153
Max. P	0.999967

overview

Window 3

Location	11,324,326 – 11,324,440
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.85
Mean single sequence MFE	-27.90
Consensus MFE	-25.66
Energy contribution	-26.10
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.43
Structure conservation index	0.92
SVM decision value	1.21
SVM RNA-class probability	0.931222
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11324326 114 + 27905053
------GGGGCAGGAGGAGUCCCUGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCGCCGGAAAAUAAUCAAAAUAAAAUAUGGAUUUUUCUUUG
------(((((.((((.(((.....)))........)))))))))(((((((((((.((((....))...(((((....)))..))....................))))))))))))). ( -28.50)
>DroSec_CAF1 63558 114 + 1
------GGGGCAGGGGGAAUCCCUGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCGCCGGAAAAUAAUCAAAAUAAAAUAUGGAUUUUUCUUUG
------(((((.((((....))))((............)))))))(((((((((((.((((....))...(((((....)))..))....................))))))))))))). ( -29.30)
>DroSim_CAF1 59839 114 + 1
------GGGGCAGGGGGAAUCCCUGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCGCCGGAAAAUAAUCAAAAUAAAAUAUGGAUUUUUCUUUG
------(((((.((((....))))((............)))))))(((((((((((.((((....))...(((((....)))..))....................))))))))))))). ( -29.30)
>DroEre_CAF1 58915 119 + 1
GGGCAGGGGGCAGGGAAAAUCCCAGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCGCCGGAAAAUAAUCAAAAUAAAAUAUGGAUU-UUCUUUG
.((((((((((.(((.....))).((............)))))))..............((....))....)))))........(((((((..(((..........))))))-))))... ( -26.20)
>DroYak_CAF1 60602 114 + 1
------GGGACAGGGGAAAUCCCAGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCACCGGAAAAUAAUCAAAAUAAAAUAUGGAUUUUUCUUUG
------((.....(((....))).(((.((((...)))).)))))(((((((((((.((((....))...(((((....)))..))....................))))))))))))). ( -26.20)
>consensus
______GGGGCAGGGGGAAUCCCUGGCUAAAUUUAAUUUCGCCCCAAAGAAAAAUCACACGAAAUCGACACCUGCCGUGGCGCCGGAAAAUAAUCAAAAUAAAAUAUGGAUUUUUCUUUG
......(((((.(((.....))).((............)))))))(((((((((((.((((....))...(((((....)))..))....................))))))))))))). (-25.66 = -26.10 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	11,324,326 – 11,324,440
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.85
Mean single sequence MFE	-34.72
Consensus MFE	-32.86
Energy contribution	-32.58
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-2.83
Structure conservation index	0.95
SVM decision value	5.00
SVM RNA-class probability	0.999967
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11324326 114 - 27905053
CAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCAGGGACUCCUCCUGCCCC------
(((((((((((((((..........((......))(((((((......))))))).....))).))))))))))))(((((((......))).....((((....)))))))).------ ( -34.10)
>DroSec_CAF1 63558 114 - 1
CAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCAGGGAUUCCCCCUGCCCC------
(((((((((((((((..........((......))(((((((......))))))).....))).))))))))))))(((((((......)))....((((.....)))))))).------ ( -36.30)
>DroSim_CAF1 59839 114 - 1
CAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCAGGGAUUCCCCCUGCCCC------
(((((((((((((((..........((......))(((((((......))))))).....))).))))))))))))(((((((......)))....((((.....)))))))).------ ( -36.30)
>DroEre_CAF1 58915 119 - 1
CAAAGAA-AAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCUGGGAUUUUCCCUGCCCCCUGCCC
(((((((-((..(((((........((......))(((((((......))))))).....)))))..)))))))))(((((((......))).((..(((.....))).)).....)))) ( -33.80)
>DroYak_CAF1 60602 114 - 1
CAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGUGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCUGGGAUUUCCCCUGUCCC------
(((((((((((((((..........((......))(((..((......))..))).....))).))))))))))))((((.((((...)))).))))(((((.......)))))------ ( -33.10)
>consensus
CAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGCGAAAUUAAAUUUAGCCAGGGAUUCCCCCUGCCCC______
(((((((((((((((..........((......))(((((((......))))))).....))).))))))))))))(((((((......))).....(((.....))).))))....... (-32.86 = -32.58 +  -0.28)

alignment

secondary structure

dotplot

Window 5

Location	11,324,360 – 11,324,479
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.99
Mean single sequence MFE	-36.44
Consensus MFE	-32.44
Energy contribution	-32.68
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.99
Structure conservation index	0.89
SVM decision value	1.83
SVM RNA-class probability	0.979159
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11324360 119 - 27905053
UCACCGUCUCUAACUC-GAUUCGCCUUCGGGUGCGUGGAACAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
...((.........((-.((.((((....)))).)).)).(((((((((((((((..........((......))(((((((......))))))).....))).)))))))))))))).. ( -38.90)
>DroSec_CAF1 63592 119 - 1
UCACCGUCUCUAACUC-GAUUCGCCUUCGGGUGCGUGGAACAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
...((.........((-.((.((((....)))).)).)).(((((((((((((((..........((......))(((((((......))))))).....))).)))))))))))))).. ( -38.90)
>DroSim_CAF1 59873 119 - 1
UCACCGUCUCUAACUC-GAUUCGCCUUCGGGUGCGUGGAACAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
...((.........((-.((.((((....)))).)).)).(((((((((((((((..........((......))(((((((......))))))).....))).)))))))))))))).. ( -38.90)
>DroEre_CAF1 58955 119 - 1
UCACCGUCUCUAACUGGGAUUCGCCUUCGGGUGCGUGGAACAAAGAA-AAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
((((.(((((.....))))).((((....)))).))))..(((((((-((..(((((........((......))(((((((......))))))).....)))))..))))))))).... ( -36.60)
>DroYak_CAF1 60636 119 - 1
UCAGCGUCUCUAACUC-GAUUCGCCUUCGGCUGCGUGGAACAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGUGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
...(((..((......-))..))).(((.((...)).)))(((((((((((((((..........((......))(((..((......))..))).....))).)))))))))))).... ( -28.90)
>consensus
UCACCGUCUCUAACUC_GAUUCGCCUUCGGGUGCGUGGAACAAAGAAAAAUCCAUAUUUUAUUUUGAUUAUUUUCCGGCGCCACGGCAGGUGUCGAUUUCGUGUGAUUUUUCUUUGGGGC
.....((((.........((.((((....)))).))....(((((((((((((((..........((......))(((((((......))))))).....))).)))))))))))))))) (-32.44 = -32.68 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:19:44 2006