Locus 1546

Sequence ID	X_DroMel_CAF1
Location	4,455,127 – 4,455,316
Length	189
Max. P	0.938328

overview

Window 1

Location	4,455,127 – 4,455,247
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.48
Mean single sequence MFE	-27.66
Consensus MFE	-25.34
Energy contribution	-25.70
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.48
Structure conservation index	0.92
SVM decision value	1.29
SVM RNA-class probability	0.938328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4455127 120 - 22224390
UUUCCAGAGUGUUGUUUUCCCAGCGACAACACAGACAUCUCUCGAUCGCACCAUCAUCAUCUUCAUUAUUGUCAUCAUGGUAAACGAUGAUCGUCAUCGAUGUCGACCCAAACCUGACGG
....(((.((((((((........)))))))).((((((...((((((((((((...((..........)).....)))))....).)))))).....)))))).........))).... ( -27.70)
>DroSec_CAF1 56524 116 - 1
UUUCCAGAGUGUUGUUUUCCCAGCGACAACACAGACAUCUCUCGAUCGCACCAU---CAUCUUCAUUAUUGUCAUCGUGGUAACCGAUGAUCGUCAUCGAUGUCGACCCA-ACCUGACGA
....(((.((((((((........)))))))).((((((...((((((((((((---.((...((....))..)).)))))....).)))))).....))))))......-..))).... ( -29.30)
>DroSim_CAF1 57857 119 - 1
UUUCCAGAGUGUUGUUUUCCCAGCGACAACACAGACAUCUCUCGAUCGCACCAUCAUCAUCUUCAUUAUUGUCAUCGUGGUAACCGAUGAUCGUCAUCGAUGUCGACCCA-ACCUGACGG
....(((.((((((((........)))))))).((((((....(((......)))...............(((((((.(....)))))))).......))))))......-..))).... ( -28.90)
>DroEre_CAF1 58526 119 - 1
UUUCCACAGUGUUGUUUUCCCAGCGACAACACAGACAUCUCUCGAUCGCACCAUCAUCAUCUUCAUUAUUGUCAUCAUGGUAACCGAUGAUCGUCAUCGAUGUCGACCCA-ACCUGACGG
...((...((((((((........)))))))).((((((...((((((((((((...((..........)).....)))))....).)))))).....))))))......-.......)) ( -26.10)
>DroYak_CAF1 57203 119 - 1
UUUCCAGAGUUGUGUUUUCCCAGCGACAACACAGACAUCUCCCGAUCGCACCAUCAUCAUCUUCAUUAUUGUCAUCAUGGUAACCGAUGAUCGUCAUCGAUGUCGACCCA-ACCUGCUGG
...((((((.((((((.((.....)).))))))((((((..........(((((...((..........)).....)))))....((((.....))))))))))......-..)).)))) ( -26.30)
>consensus
UUUCCAGAGUGUUGUUUUCCCAGCGACAACACAGACAUCUCUCGAUCGCACCAUCAUCAUCUUCAUUAUUGUCAUCAUGGUAACCGAUGAUCGUCAUCGAUGUCGACCCA_ACCUGACGG
....(((.((((((((........)))))))).((((((...((((((((((((...((..........)).....)))))....).)))))).....)))))).........))).... (-25.34 = -25.70 +   0.36)

alignment

secondary structure

dotplot

Window 2

Location	4,455,207 – 4,455,316
Length	109
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	91.17
Mean single sequence MFE	-26.62
Consensus MFE	-21.11
Energy contribution	-21.42
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-2.18
Structure conservation index	0.79
SVM decision value	0.87
SVM RNA-class probability	0.871869
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4455207 109 + 22224390
AGAUGUCUGUGUUGUCGCUGGGAAAACAACACUCUGGAAACAAGAAAAAGUGACGAGACAAGGCGCGGCGAGACGGGACGGCAUCGAGAUGCAAUAAUCGAUAAUAGGA
.(((((((((.(((((((((((.........)))((....))......)))))))).))).(.(.((......)).).)))))))..(((......))).......... ( -28.50)
>DroSec_CAF1 56600 99 + 1
AGAUGUCUGUGUUGUCGCUGGGAAAACAACACUCUGGAAACAAGAAAAAGUGACGAGACAA----------GACGGGACGGCAACGAGAUGCAAUAAUCGAUAAUAGGA
...(((((((.(((((((((((.........)))((....))......)))))))).)).)----------))))...((....)).(((......))).......... ( -25.30)
>DroSim_CAF1 57936 98 + 1
AGAUGUCUGUGUUGUCGCUGGGAAAACAACACUCUGGAAACAAGAA-AAGUGACGAGACAA----------GACGGGACGGCAACGAGAUGCAAUAAUCGAUAAUAGGA
...(((((((.(((((((((((.........)))((....))....-.)))))))).)).)----------))))...((....)).(((......))).......... ( -25.30)
>DroYak_CAF1 57282 103 + 1
AGAUGUCUGUGUUGUCGCUGGGAAAACACAACUCUGGAAACAAGA-AAAGUGACGAGACGAGUC-----GGGACGGGACGGCAUCGAGAUGCAAUAAUCGAUAAUAGGA
.(((((((((.(((((((((((.........)))((....))...-..)))))))).))).(((-----.......)))))))))..(((......))).......... ( -27.40)
>consensus
AGAUGUCUGUGUUGUCGCUGGGAAAACAACACUCUGGAAACAAGAAAAAGUGACGAGACAA__________GACGGGACGGCAACGAGAUGCAAUAAUCGAUAAUAGGA
.(((((((((.(((((((((((.........)))((....))......)))))))).)))...........(......)))))))..(((......))).......... (-21.11 = -21.42 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:02 2006