Locus 6120

Sequence ID	3R_DroMel_CAF1
Location	16,044,347 – 16,044,561
Length	214
Max. P	0.758575

overview

Window 4

Location	16,044,347 – 16,044,442
Length	95
Sequences	4
Columns	95
Reading direction	reverse
Mean pairwise identity	96.84
Mean single sequence MFE	-28.98
Consensus MFE	-28.04
Energy contribution	-27.85
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.65
Structure conservation index	0.97
SVM decision value	0.41
SVM RNA-class probability	0.724121
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16044347 95 - 27905053
UUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUACUCAUGUAAAGUAGAAGGAUGGGCGCUACUAUGCU
....((((((.................((((((.......))))))((((((..(..((((....))))..)..))))))..))))))....... ( -28.10)
>DroSec_CAF1 1858 95 - 1
UUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUAGAAGGAUGGGCGCUACUAUGCU
....((((((.................((((((.......))))))((((((..(..((((....))))..)..))))))..))))))....... ( -28.10)
>DroSim_CAF1 1847 95 - 1
UUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUAGAAGGAUGGGCGCUACUAUGCU
....((((((.................((((((.......))))))((((((..(..((((....))))..)..))))))..))))))....... ( -28.10)
>DroYak_CAF1 9088 95 - 1
CUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUUGAAGGAUGGGCGCUACUAUACG
....((((((.................((((((.......))))))((((((.((((((((....)).))))))))))))..))))))....... ( -31.60)
>consensus
UUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUAGAAGGAUGGGCGCUACUAUGCU
....((((((.................((((((.......))))))((((((..(..((((....))))..)..))))))..))))))....... (-28.04 = -27.85 +  -0.19)

alignment

secondary structure

dotplot

Window 5

Location	16,044,369 – 16,044,466
Length	97
Sequences	4
Columns	97
Reading direction	forward
Mean pairwise identity	97.94
Mean single sequence MFE	-24.95
Consensus MFE	-24.60
Energy contribution	-24.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.99
SVM decision value	0.35
SVM RNA-class probability	0.699582
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16044369 97 + 27905053
UACUUUACAUGAGUAAGUUGAAAGGAUUCCGCCGUGGAGUGGCGGACACAGUUUUCAUUCGAUACGCCAGGAAACUGAAAUCGAAAUCAAAUAAUGU
(((((.....)))))...((((((...(((((((.....))))))).....))))))((((((....(((....)))..))))))............ ( -26.00)
>DroSec_CAF1 1880 97 + 1
UACUUUACAUAAGCAAGUUGAAAGGAUUCCGCCGUGGAGUGGCGGACACAGUUUUCAUUCGAUACGCCAGGAAACUGAAAUCGAAAUCAAAUAAUGU
......((((........((((((...(((((((.....))))))).....))))))((((((....(((....)))..))))))........)))) ( -24.60)
>DroSim_CAF1 1869 97 + 1
UACUUUACAUAAGCAAGUUGAAAGGAUUCCGCCGUGGAGUGGCGGACACAGUUUUCAUUCGAUACGCCAGGAAACUGAAAUCGAAAUCAAAUAAUGU
......((((........((((((...(((((((.....))))))).....))))))((((((....(((....)))..))))))........)))) ( -24.60)
>DroYak_CAF1 9110 97 + 1
AACUUUACAUAAGCAAGUUGAAAGGAUUCCGCCGUGGAGUGGCGGACACAGUUUUCAUUCGAUACGCCAGGAGACUGAAAUCGAAAUCAAAUAAUGU
......((((........((((((...(((((((.....))))))).....))))))((((((....(((....)))..))))))........)))) ( -24.60)
>consensus
UACUUUACAUAAGCAAGUUGAAAGGAUUCCGCCGUGGAGUGGCGGACACAGUUUUCAUUCGAUACGCCAGGAAACUGAAAUCGAAAUCAAAUAAUGU
......((((........((((((...(((((((.....))))))).....))))))((((((....(((....)))..))))))........)))) (-24.60 = -24.60 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	16,044,369 – 16,044,466
Length	97
Sequences	4
Columns	97
Reading direction	reverse
Mean pairwise identity	97.94
Mean single sequence MFE	-23.28
Consensus MFE	-22.74
Energy contribution	-22.55
Covariance contribution	-0.19
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.98
SVM decision value	0.50
SVM RNA-class probability	0.758575
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16044369 97 - 27905053
ACAUUAUUUGAUUUCGAUUUCAGUUUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUACUCAUGUAAAGUA
((.((((.(((.((((((.((((....))))...))))))(((((......((((((.......))))))....)))))......))).)))).)). ( -24.00)
>DroSec_CAF1 1880 97 - 1
ACAUUAUUUGAUUUCGAUUUCAGUUUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUA
.(((..(((...((((((.((((....))))...))))))...)))..)))((((((.......)))))).........((((((....)).)))). ( -22.70)
>DroSim_CAF1 1869 97 - 1
ACAUUAUUUGAUUUCGAUUUCAGUUUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUA
.(((..(((...((((((.((((....))))...))))))...)))..)))((((((.......)))))).........((((((....)).)))). ( -22.70)
>DroYak_CAF1 9110 97 - 1
ACAUUAUUUGAUUUCGAUUUCAGUCUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUU
.(((..(((...((((((....(((....)))..))))))...)))..)))((((((.......))))))........(((((((....)).))))) ( -23.70)
>consensus
ACAUUAUUUGAUUUCGAUUUCAGUUUCCUGGCGUAUCGAAUGAAAACUGUGUCCGCCACUCCACGGCGGAAUCCUUUCAACUUGCUUAUGUAAAGUA
.(((..(((...((((((.((((....))))...))))))...)))..)))((((((.......)))))).........((((((....)).)))). (-22.74 = -22.55 +  -0.19)

alignment

secondary structure

dotplot

Window 7

Location	16,044,466 – 16,044,561
Length	95
Sequences	4
Columns	108
Reading direction	reverse
Mean pairwise identity	87.85
Mean single sequence MFE	-30.61
Consensus MFE	-22.05
Energy contribution	-22.67
Covariance contribution	0.63
Combinations/Pair	1.12
Mean z-score	-1.59
Structure conservation index	0.72
SVM decision value	0.13
SVM RNA-class probability	0.599805
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16044466 95 - 27905053
CGAGCUAUA-------------UAUUUGCGUACACGUGUAUUUGGGCACAUAUGAGUGUCAGCUGCGUUUGUGUGCGGGAGAUCCUUUUGUGCCAGGUCCCCCAACAA
...((....-------------.....))(((((((((((....(((((......)))))...))))..)))))))(((.((.(((........))))).)))..... ( -26.50)
>DroSec_CAF1 1977 95 - 1
CGAGCAAUA-------------UAUUUGCGUACAAGUGUAUUUGGGAACAUAUGAGUGUCAGCUGCGCUUGUGUGCGGGAGAUCCUUUUGUGCCAGCUCCCCCAACAA
.((((((((-------------((((((....))))))))))(((..(((...(((..((..((((((....))))))..))..))).))).)))))))......... ( -30.80)
>DroSim_CAF1 1966 95 - 1
CGAGCAAUA-------------UAUUUGCGUACAAGUGUAUUUGGGCACAUAUGAGUGUCAGCUGCGCUUGUGUGCGGGAGAUCCUUUUGUGCCAGCUCCCCCAACAA
.((((((((-------------((((((....))))))))))..((((((...(((..((..((((((....))))))..))..))).)))))).))))......... ( -37.00)
>DroYak_CAF1 9207 108 - 1
CGAUCUAUAUACUAUGUAUGUAUAUUCGCGUACAAGUGUAUUUGGGCAUAUAUGAGUGCCAGCUGCGUUUGUGUUCGGGAGAUCCUUUUGUGCCAGCUACCCCAACAA
......(((((((.(((((((......))))))))))))))((((((((......)))))(((((.((........(((....))).....)))))))....)))... ( -28.12)
>consensus
CGAGCAAUA_____________UAUUUGCGUACAAGUGUAUUUGGGCACAUAUGAGUGUCAGCUGCGCUUGUGUGCGGGAGAUCCUUUUGUGCCAGCUCCCCCAACAA
...........................(((((((((((((....(((((......)))))...)))))))))))))(((((...(......)....)))))....... (-22.05 = -22.67 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:10 2006