Locus 3901

Sequence ID	2R_DroMel_CAF1
Location	12,869,183 – 12,869,327
Length	144
Max. P	0.998907

overview

Window 7

Location	12,869,183 – 12,869,291
Length	108
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	93.93
Mean single sequence MFE	-29.23
Consensus MFE	-27.97
Energy contribution	-28.47
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.99
Structure conservation index	0.96
SVM decision value	3.28
SVM RNA-class probability	0.998907
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12869183 108 + 20766785
ACCCCUGCCGCUACUUCCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUAUACUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))......... ( -30.00)
>DroVir_CAF1 3519 107 + 1
ACCCCUGCCGCUACUUUCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))....-.... ( -30.00)
>DroPse_CAF1 1737 94 + 1
AACCCUGCCGCUACUUUCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGU--------------
....((((.(((.............((((......))))...........(((((....(((.(((....))))))....)))))))).)))).-------------- ( -25.40)
>DroGri_CAF1 3531 107 + 1
ACCCCUGCCGCUACUUUCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))....-.... ( -30.00)
>DroMoj_CAF1 4134 107 + 1
ACCCCUGCCGCUACUUUCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))....-.... ( -30.00)
>DroAna_CAF1 3152 108 + 1
ACCCCUGCCGCUACUUCCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUAUACUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))......... ( -30.00)
>consensus
ACCCCUGCCGCUACUUUCAUCCCCCCCUGCACCUACAGGCACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU_UCUA
......((((((.............((((......))))..........))))))..........((((((((.((.((....)).)).)))))..)))......... (-27.97 = -28.47 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	12,869,183 – 12,869,291
Length	108
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	93.93
Mean single sequence MFE	-37.80
Consensus MFE	-36.92
Energy contribution	-37.20
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-0.83
Structure conservation index	0.98
SVM decision value	0.37
SVM RNA-class probability	0.707379
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12869183 108 - 20766785
UAGUAUAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGGAAGUAGCGGCAGGGGU
..........(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... ( -38.20)
>DroVir_CAF1 3519 107 - 1
UAGA-AAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGAAAGUAGCGGCAGGGGU
....-.....(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... ( -38.60)
>DroPse_CAF1 1737 94 - 1
--------------ACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGAAAGUAGCGGCAGGGUU
--------------.((...(((((.((.((....)).))(((.((....)).)))(((((((.((.(.(((((....))))).).)).))))))).))))).))... ( -34.60)
>DroGri_CAF1 3531 107 - 1
UAGA-AAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGAAAGUAGCGGCAGGGGU
....-.....(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... ( -38.60)
>DroMoj_CAF1 4134 107 - 1
UAGA-AAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGAAAGUAGCGGCAGGGGU
....-.....(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... ( -38.60)
>DroAna_CAF1 3152 108 - 1
UAGUAUAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGGAAGUAGCGGCAGGGGU
..........(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... ( -38.20)
>consensus
UAGA_AAUAGCCAUACCGCAGCUGCAGCAGCGACAGCGGUGGCGCGUGUUUGGGCCGCUUUUAAUUGUGCCUGUAGGUGCAGGGGGGGAUGAAAGUAGCGGCAGGGGU
..........(((.(((((.((..(....((....)).)..))))).)).)))((((((((((.((.(.(((((....))))).).)).))))...))))))...... (-36.92 = -37.20 +   0.28)

alignment

secondary structure

dotplot

Window 9

Location	12,869,223 – 12,869,327
Length	104
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	87.22
Mean single sequence MFE	-20.77
Consensus MFE	-20.70
Energy contribution	-20.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.08
Structure conservation index	1.00
SVM decision value	0.38
SVM RNA-class probability	0.712762
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12869223 104 + 20766785
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUAUACUAUAUAUUUUU-CUAUACUUUUCGAACCUUCUCUUU--GCG
..........(((.........)))((((((((.((.((....)).)).)))))..)))..................-........................--... ( -20.70)
>DroVir_CAF1 3559 93 + 1
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUAUAUUUACUU-UUAUACUU---------UCUCUUU--C-U
.....((((((((.........)))((((((((.((.((....)).)).)))))..)))....-...........))-))).....---------.......--.-. ( -20.80)
>DroGri_CAF1 3571 93 + 1
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUAUAUUUACUU-UUAUACUU---------UCUCUUA--C-U
.....((((((((.........)))((((((((.((.((....)).)).)))))..)))....-...........))-))).....---------.......--.-. ( -20.80)
>DroEre_CAF1 2638 104 + 1
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUAUACUAUAUAUUUUU-CUAUACUUUUCGAACCUUCUCCUU--GCG
..........(((.........)))((((((((.((.((....)).)).)))))..)))..................-........................--... ( -20.70)
>DroMoj_CAF1 4174 94 + 1
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUU-UCUAUAUUUACUUUUUAUACUU---------UCUCUUU--C-U
.....((((((((.........)))((((((((.((.((....)).)).)))))..)))....-............))))).....---------.......--.-. ( -20.90)
>DroAna_CAF1 3192 106 + 1
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUAUACUAUAUAUUUUU-CUAUACUUUUCGAACCUUCUCUUUUUCAG
..........(((.........)))((((((((.((.((....)).)).)))))..)))..................-............................. ( -20.70)
>consensus
ACAAUUAAAAGCGGCCCAAACACGCGCCACCGCUGUCGCUGCUGCAGCUGCGGUAUGGCUAUA_ACUAUAUAUACUU_CUAUACUU_________UCUCUUU__C_G
..........(((.........)))((((((((.((.((....)).)).)))))..)))................................................ (-20.70 = -20.70 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:50 2006