Locus 4601

Sequence ID	3L_DroMel_CAF1
Location	13,138,786 – 13,138,918
Length	132
Max. P	0.999920

overview

Window 3

Location	13,138,786 – 13,138,906
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-31.04
Consensus MFE	-29.42
Energy contribution	-29.26
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-2.48
Structure conservation index	0.95
SVM decision value	3.57
SVM RNA-class probability	0.999397
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13138786 120 + 23771897
CACCCAGCGAUUGGCGCCACACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGG
...(((((((..((((...(.(((.(((.........(((((((....)))))))((.....)).........))).))))...))))((((((.....))))))........))))))) ( -30.90)
>DroSec_CAF1 126529 120 + 1
CACCCAGCGAUUGGCGCCAUACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGUUUGUGCAACAACUGCACAUUAUUUAUUCGCUGG
...(((((((.(((.(((...(((.(((.........(((((((....)))))))((.....)).........))).)))))).....((((((.....))))))....))).))))))) ( -30.30)
>DroSim_CAF1 126484 120 + 1
CACCCAGCGAUUGGCGCCACACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGG
...(((((((..((((...(.(((.(((.........(((((((....)))))))((.....)).........))).))))...))))((((((.....))))))........))))))) ( -30.90)
>DroEre_CAF1 123415 120 + 1
CACCCAGCGAUUGGCGCCACACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACCCUCGUGCAACAACUGCACAUUAUUUAUUCGCUGG
...(((((((..((.(((...(((.(((.........(((((((....)))))))((.....)).........))).)))))).))...(((((.....))))).........))))))) ( -32.20)
>DroYak_CAF1 127769 120 + 1
CACCCAGCGAUUGGCGCCACACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUCGUGCAACAACUGCAUAUUAUUUAUUCGCUGG
...(((((((...(((.........)))................(((((((((((((.............(((.....)))((((....)))).......)))))))))))))))))))) ( -30.90)
>consensus
CACCCAGCGAUUGGCGCCACACAUAUGCAACUAAUUGAUAUUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGG
...(((((((.(((.(((...(((.(((.........(((((((....)))))))((.....)).........))).))))))......(((((.....))))).....))).))))))) (-29.42 = -29.26 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	13,138,786 – 13,138,906
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-37.95
Consensus MFE	-37.01
Energy contribution	-36.97
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-3.12
Structure conservation index	0.98
SVM decision value	4.56
SVM RNA-class probability	0.999920
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13138786 120 - 23771897
CCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUGUGGCGCCAAUCGCUGGGUG
(((((((........(((((((...))))))).(.((((((((((((.(((((((.(((((.................))))).)))).))))))))))...))))))..)))))))... ( -38.33)
>DroSec_CAF1 126529 120 - 1
CCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAACGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUAUGGCGCCAAUCGCUGGGUG
(((((((........(((((((...)))))))...((((((((((((.(((((((.(((((.................))))).)))).))))))))))...)))))...)))))))... ( -38.03)
>DroSim_CAF1 126484 120 - 1
CCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUGUGGCGCCAAUCGCUGGGUG
(((((((........(((((((...))))))).(.((((((((((((.(((((((.(((((.................))))).)))).))))))))))...))))))..)))))))... ( -38.33)
>DroEre_CAF1 123415 120 - 1
CCAGCGAAUAAAUAAUGUGCAGUUGUUGCACGAGGGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUGUGGCGCCAAUCGCUGGGUG
(((((((........(((((((...)))))))..(((((((((((((.(((((((.(((((.................))))).)))).))))))))))...))))))..)))))))... ( -41.23)
>DroYak_CAF1 127769 120 - 1
CCAGCGAAUAAAUAAUAUGCAGUUGUUGCACGAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUGUGGCGCCAAUCGCUGGGUG
(((((((...........(((..((..((((....)))).))..)))((((((((.(((((.................))))).)))).((..((....))..)))))).)))))))... ( -33.83)
>consensus
CCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAAUAUCAAUUAGUUGCAUAUGUGUGGCGCCAAUCGCUGGGUG
(((((((........(((((((...)))))))...((((((((((((.(((((((.(((((.................))))).)))).))))))))))...)))))...)))))))... (-37.01 = -36.97 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	13,138,826 – 13,138,918
Length	92
Sequences	5
Columns	92
Reading direction	forward
Mean pairwise identity	98.04
Mean single sequence MFE	-21.60
Consensus MFE	-21.30
Energy contribution	-20.74
Covariance contribution	-0.56
Combinations/Pair	1.18
Mean z-score	-2.51
Structure conservation index	0.99
SVM decision value	4.08
SVM RNA-class probability	0.999787
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13138826 92 + 23771897
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((....(((....)))(((((.....)))))...........)))))))...))..... ( -21.00)
>DroSec_CAF1 126569 92 + 1
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGUUUGUGCAACAACUGCACAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((..(((....))).((((((.....))))))..........)))))))...))..... ( -21.40)
>DroSim_CAF1 126524 92 + 1
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((....(((....)))(((((.....)))))...........)))))))...))..... ( -21.00)
>DroEre_CAF1 123455 92 + 1
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACCCUCGUGCAACAACUGCACAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((....((....))..(((((.....)))))...........)))))))...))..... ( -23.30)
>DroYak_CAF1 127809 92 + 1
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUCGUGCAACAACUGCAUAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((....(((....)))(((((.....)))))...........)))))))...))..... ( -21.30)
>consensus
UUAUAUGAAUGAUAUGUUAAAUACAAAUUGCCAGCACAUGGGCACGCUUGUGCAACAACUGCACAUUAUUUAUUCGCUGGCAUAAUGAAAAA
.......................((...(((((((....(((....)))(((((.....)))))...........)))))))...))..... (-21.30 = -20.74 +  -0.56)

alignment

secondary structure

dotplot

Window 6

Location	13,138,826 – 13,138,918
Length	92
Sequences	5
Columns	92
Reading direction	reverse
Mean pairwise identity	98.04
Mean single sequence MFE	-22.02
Consensus MFE	-20.56
Energy contribution	-20.56
Covariance contribution	0.00
Combinations/Pair	1.11
Mean z-score	-2.17
Structure conservation index	0.93
SVM decision value	2.86
SVM RNA-class probability	0.997417
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13138826 92 - 23771897
UUUUUCAUUAUGCCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........(((((((..........(((((((...))))))).((((....)))))))))))............................ ( -22.40)
>DroSec_CAF1 126569 92 - 1
UUUUUCAUUAUGCCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAACGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........(((((((..........(((((((...))))))).((((....)))))))))))............................ ( -22.10)
>DroSim_CAF1 126524 92 - 1
UUUUUCAUUAUGCCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........(((((((..........(((((((...))))))).((((....)))))))))))............................ ( -22.40)
>DroEre_CAF1 123455 92 - 1
UUUUUCAUUAUGCCAGCGAAUAAAUAAUGUGCAGUUGUUGCACGAGGGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........((((((((.........(((((((...))))))).((....))...))))))))............................ ( -23.00)
>DroYak_CAF1 127809 92 - 1
UUUUUCAUUAUGCCAGCGAAUAAAUAAUAUGCAGUUGUUGCACGAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........((((((((....((((((.....))))))((((....)))).....))))))))............................ ( -20.20)
>consensus
UUUUUCAUUAUGCCAGCGAAUAAAUAAUGUGCAGUUGUUGCACAAGCGUGCCCAUGUGCUGGCAAUUUGUAUUUAACAUAUCAUUCAUAUAA
..........(((((((..........(((((((...))))))).((((....)))))))))))............................ (-20.56 = -20.56 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:06 2006