Locus 1896

Sequence ID	3R_DroMel_CAF1
Location	5,421,776 – 5,421,886
Length	110
Max. P	0.999225

overview

Window 0

Location	5,421,776 – 5,421,866
Length	90
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	83.75
Mean single sequence MFE	-25.88
Consensus MFE	-20.19
Energy contribution	-20.00
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-2.92
Structure conservation index	0.78
SVM decision value	2.41
SVM RNA-class probability	0.993618
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421776 90 + 27905053
CCUGAAAGGUAAACAAUGUCGGGAGACACAUGUAUCUGAG-CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAUACAUACAUGUAGGUACG
((((............((((....))))(((((((.....-...(((((((((((.(.....).))))))))))).))))))))))).... ( -26.70)
>DroSec_CAF1 8465 77 + 1
CCUGAAAGGUAAACAAUGUCGGGAGACACAUGUAUC--------UAUCUGGUGACCCAAUUUGAGUCAUCAGAUACAU------GGGCACG
((((..(((((.....((((....))))....))))--------)((((((((((.(.....).)))))))))).)).------))..... ( -24.00)
>DroEre_CAF1 8979 76 + 1
CCUGAAAGGUAAACAAUGUCGGGAGACAUAU----CUGAG-CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU----------GGGUACG
..((..(((((.....((((....)))))))----))...-))((((((((((((.(.....).))))))))))----------))..... ( -25.60)
>DroYak_CAF1 9195 77 + 1
CCUGAAAGGUAAACAAUGUCGGGAGACAUAU----CUGAGCCACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU----------GGGUACG
.......(((.....(((((....)))))..----....))).((((((((((((.(.....).))))))))))----------))..... ( -27.20)
>consensus
CCUGAAAGGUAAACAAUGUCGGGAGACACAU____CUGAG_CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU__________GGGUACG
(((.............((((....)))).................((((((((((.(.....).))))))))))..........))).... (-20.19 = -20.00 +  -0.19)

alignment

secondary structure

dotplot

Window 1

Location	5,421,776 – 5,421,866
Length	90
Sequences	4
Columns	91
Reading direction	reverse
Mean pairwise identity	83.75
Mean single sequence MFE	-22.55
Consensus MFE	-17.51
Energy contribution	-17.07
Covariance contribution	-0.44
Combinations/Pair	1.11
Mean z-score	-2.47
Structure conservation index	0.78
SVM decision value	1.75
SVM RNA-class probability	0.975489
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421776 90 - 27905053
CGUACCUACAUGUAUGUAUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG-CUCAGAUACAUGUGUCUCCCGACAUUGUUUACCUUUCAGG
....(((((((((((.((((((.((((((.....)))))).))))))(..-..)..))))))))(((....)))..............))) ( -25.10)
>DroSec_CAF1 8465 77 - 1
CGUGCCC------AUGUAUCUGAUGACUCAAAUUGGGUCACCAGAUA--------GAUACAUGUGUCUCCCGACAUUGUUUACCUUUCAGG
.....((------((.((((((.((((((.....)))))).))))))--------.))(((.(((((....))))))))..........)) ( -22.10)
>DroEre_CAF1 8979 76 - 1
CGUACCC----------AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG-CUCAG----AUAUGUCUCCCGACAUUGUUUACCUUUCAGG
.((((..----------(((((.((((((.....)))))).))))).)))-)..((----(((((((....)))).))))).......... ( -22.40)
>DroYak_CAF1 9195 77 - 1
CGUACCC----------AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUGGCUCAG----AUAUGUCUCCCGACAUUGUUUACCUUUCAGG
.(..(((----------(((((.((((((.....)))))).))))).).))..)((----(((((((....)))).))))).......... ( -20.60)
>consensus
CGUACCC__________AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG_CUCAG____AUAUGUCUCCCGACAUUGUUUACCUUUCAGG
.(((.............(((((.((((((.....)))))).)))))................(((((....)))))....)))........ (-17.51 = -17.07 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	5,421,793 – 5,421,886
Length	93
Sequences	4
Columns	94
Reading direction	forward
Mean pairwise identity	82.43
Mean single sequence MFE	-33.23
Consensus MFE	-26.75
Energy contribution	-26.38
Covariance contribution	-0.38
Combinations/Pair	1.10
Mean z-score	-4.45
Structure conservation index	0.80
SVM decision value	3.45
SVM RNA-class probability	0.999225
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421793 93 + 27905053
GUCGGGAGACACAUGUAUCUGAG-CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAUACAUACAUGUAGGUACGACAAUUGCAUCCCGGCUAAU
(((((((..((..((((((((..-...(((((((((((.(.....).)))))))))))........)))))))).....))..))))))).... ( -33.82)
>DroSec_CAF1 8482 80 + 1
GUCGGGAGACACAUGUAUC--------UAUCUGGUGACCCAAUUUGAGUCAUCAGAUACAU------GGGCACGACAAUUGCAUCCCGGCGAAU
(((((((....((((((..--------..(((((((((.(.....).))))))))))))))------).(((.......))).))))))).... ( -32.70)
>DroEre_CAF1 8996 79 + 1
GUCGGGAGACAUAU----CUGAG-CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU----------GGGUACGACAAUUGCAUCCCGACGAAA
(((((((..((...----.((.(-(.((((((((((((.(.....).))))))))))----------)))).)).....))..))))))).... ( -34.20)
>DroYak_CAF1 9212 80 + 1
GUCGGGAGACAUAU----CUGAGCCACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU----------GGGUACGACAAUUGCAUCCCGGCGAAA
(((((((..((...----........((((((((((((.(.....).))))))))))----------))..........))..))))))).... ( -32.20)
>consensus
GUCGGGAGACACAU____CUGAG_CACUAUCUGGUGACCCAAUUUGAGUCAUCAGAU__________GGGUACGACAAUUGCAUCCCGGCGAAA
(((((((.....................((((((((((.(.....).))))))))))............(((.......))).))))))).... (-26.75 = -26.38 +  -0.38)

alignment

secondary structure

dotplot

Window 3

Location	5,421,793 – 5,421,886
Length	93
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	82.43
Mean single sequence MFE	-30.55
Consensus MFE	-22.17
Energy contribution	-22.18
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.78
Structure conservation index	0.73
SVM decision value	3.26
SVM RNA-class probability	0.998866
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5421793 93 - 27905053
AUUAGCCGGGAUGCAAUUGUCGUACCUACAUGUAUGUAUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG-CUCAGAUACAUGUGUCUCCCGAC
......(((((.(((..((((((....))..((((.((((((.((((((.....)))))).)))))))))-)...))))....))).))))).. ( -30.90)
>DroSec_CAF1 8482 80 - 1
AUUCGCCGGGAUGCAAUUGUCGUGCCC------AUGUAUCUGAUGACUCAAAUUGGGUCACCAGAUA--------GAUACAUGUGUCUCCCGAC
......(((((.(((.....((((...------((.((((((.((((((.....)))))).))))))--------.)).))))))).))))).. ( -28.60)
>DroEre_CAF1 8996 79 - 1
UUUCGUCGGGAUGCAAUUGUCGUACCC----------AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG-CUCAG----AUAUGUCUCCCGAC
....(((((((.((((((...((((..----------(((((.((((((.....)))))).))))).)))-)...)----)).))).))))))) ( -33.40)
>DroYak_CAF1 9212 80 - 1
UUUCGCCGGGAUGCAAUUGUCGUACCC----------AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUGGCUCAG----AUAUGUCUCCCGAC
......(((((.(((..(((((..(((----------(((((.((((((.....)))))).))))).).))..).)----)))))).))))).. ( -29.30)
>consensus
AUUCGCCGGGAUGCAAUUGUCGUACCC__________AUCUGAUGACUCAAAUUGGGUCACCAGAUAGUG_CUCAG____AUAUGUCUCCCGAC
......(((((.(((...(.....)............(((((.((((((.....)))))).))))).................))).))))).. (-22.17 = -22.18 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:10 2006