Locus 10323

Sequence ID	3R_DroMel_CAF1
Location	27,723,813 – 27,723,922
Length	109
Max. P	0.959097

overview

Window 2

Location	27,723,813 – 27,723,922
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.18
Mean single sequence MFE	-23.15
Consensus MFE	-17.22
Energy contribution	-17.72
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.68
Structure conservation index	0.74
SVM decision value	0.60
SVM RNA-class probability	0.794849
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27723813 109 + 27905053
GG-AAA-AAAACAUGUUUAAUGCCCCGCCAUUUUUUAUAGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU-UUAGCACAUUAUUUGC--CGGGC------
..-...-..............((((.((..........(((((...........)))))((((((..((.((........)).))..)))-)))...........))--.))))------ ( -16.40)
>DroVir_CAF1 43937 98 + 1
---------AAAAUUUUUAAUGCCACGCCAUUUUUUAUGGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU-UUAGCGCAUUAUUUUU--U----------
---------................((((((.....)))))).........((((((((.(((((..((.((........)).))..)))-))))))))))......--.---------- ( -22.00)
>DroGri_CAF1 44410 98 + 1
---------AAAAUUUUUAAUGCCACGCCAUUUUUUAUGGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU-UUAGCGCAUUAUAUUU--U----------
---------................((((((.....)))))).........((((((((.(((((..((.((........)).))..)))-))))))))))......--.---------- ( -22.00)
>DroMoj_CAF1 44305 108 + 1
---------AAAAUUUUUAAUGCCACGCCAUUUUUUAUGGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU-UUAGCGCAUUAUUUUC--CAGGCAGCGAC
---------...........((((.((((((.....)))))).........((((((((.(((((..((.((........)).))..)))-))))))))))......--..))))..... ( -28.70)
>DroAna_CAF1 38076 109 + 1
GA-AAGGAAAACAU-UUUAAUGCCCCGCCAUUU-UUAUGGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAUUUUAGCGCAUUAUUCGC--CGGGC------
..-...........-......((((((((((..-..)))))).........((((((((.(((((..((.((........)).))..))))).))))))))......--.))))------ ( -29.00)
>DroPer_CAF1 42639 111 + 1
AACAAA--AAAAUCUCUUAAUGCCCCGCCAUUUUUUAUAGCGCUACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU-UUAGCGCAUUAUUUGCGCAGGAC------
......--......((((((((......)))).......((((........((((((((.(((((..((.((........)).))..)))-))))))))))....)))))))).------ ( -20.80)
>consensus
_________AAAAUUUUUAAUGCCACGCCAUUUUUUAUGGCGCCACACUUGAAUGCGCUUAAAUAUUUUAUGUAAUUUUUCGCAAUUUAU_UUAGCGCAUUAUUUGC__CGGGC______
.........................((((((.....)))))).........((((((((...(((..((.((........)).))..)))...))))))))................... (-17.22 = -17.72 +   0.50)

alignment

secondary structure

dotplot

Window 3

Location	27,723,813 – 27,723,922
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.18
Mean single sequence MFE	-28.13
Consensus MFE	-21.93
Energy contribution	-21.57
Covariance contribution	-0.36
Combinations/Pair	1.08
Mean z-score	-3.96
Structure conservation index	0.78
SVM decision value	1.50
SVM RNA-class probability	0.959097
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27723813 109 - 27905053
------GCCCG--GCAAAUAAUGUGCUAA-AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCUAUAAAAAAUGGCGGGGCAUUAAACAUGUUUU-UUU-CC
------((((.--(((...((((((((((-(((...((..(....)..)).....))))).))))))))....)))..((((((.....))))))))))..............-...-.. ( -26.30)
>DroVir_CAF1 43937 98 - 1
----------A--AAAAAUAAUGCGCUAA-AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCCAUAAAAAAUGGCGUGGCAUUAAAAAUUUU---------
----------.--......((((((((((-(((...((..(....)..)).....))))).))))))))..(((((.(((((((.....))))))).))))).........--------- ( -27.80)
>DroGri_CAF1 44410 98 - 1
----------A--AAAUAUAAUGCGCUAA-AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCCAUAAAAAAUGGCGUGGCAUUAAAAAUUUU---------
----------.--......((((((((((-(((...((..(....)..)).....))))).))))))))..(((((.(((((((.....))))))).))))).........--------- ( -27.80)
>DroMoj_CAF1 44305 108 - 1
GUCGCUGCCUG--GAAAAUAAUGCGCUAA-AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCCAUAAAAAAUGGCGUGGCAUUAAAAAUUUU---------
(((((.(((..--......((((((((((-(((...((..(....)..)).....))))).)))))))).......)))(((((.....))))))))))............--------- ( -29.06)
>DroAna_CAF1 38076 109 - 1
------GCCCG--GCGAAUAAUGCGCUAAAAUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCCAUAA-AAAUGGCGGGGCAUUAAA-AUGUUUUCCUU-UC
------((((.--(((...((((((((.(((((...((..(....)..)).....))))).))))))))....)))..((((((..-..))))))))))......-...........-.. ( -30.60)
>DroPer_CAF1 42639 111 - 1
------GUCCUGCGCAAAUAAUGCGCUAA-AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUAGCGCUAUAAAAAAUGGCGGGGCAUUAAGAGAUUUU--UUUGUU
------(((((((((....((((((((((-(((...((..(....)..)).....))))).))))))))...))))).((((((.....)))))))))).............--...... ( -27.20)
>consensus
______GCCCG__GAAAAUAAUGCGCUAA_AUAAAUUGCGAAAAAUUACAUAAAAUAUUUAAGCGCAUUCAAGUGUGGCGCCAUAAAAAAUGGCGGGGCAUUAAAAAUUUU_________
...................((((((((...(((...((..(....)..)).....)))...))))))))..(((((..((((((.....))))))..))))).................. (-21.93 = -21.57 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:54:04 2006