Locus 3413

Sequence ID	3R_DroMel_CAF1
Location	9,257,876 – 9,258,022
Length	146
Max. P	0.747647

overview

Window 7

Location	9,257,876 – 9,257,982
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	84.34
Mean single sequence MFE	-42.30
Consensus MFE	-34.98
Energy contribution	-35.23
Covariance contribution	0.26
Combinations/Pair	1.26
Mean z-score	-1.85
Structure conservation index	0.83
SVM decision value	0.43
SVM RNA-class probability	0.733064
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9257876 106 - 27905053
GGCGGUGUCGGCUGUGGCCUCGGUUAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCCGCAUCCCAAUCGCCUGCACCGGCUACUCCCUUAGUAUCUUCCCAA
((.((((.((((((((((((((((....)).))))..(((((....))))).))))))))))))))))....(((......)))((((.....))))......... ( -45.10)
>DroVir_CAF1 30439 99 - 1
GGCAGCCUCUGCCGUUGCCACGGUCAAUGCACGUGCAGCUGCCGCUGCAGCUGCAGCCGCCGCAGCUCAAGUGUC---GUCAGCGGCAUCUGUUGUUCCUUC----
(((((...)))))(((((..((((.........(((((((((....)))))))))))))..))))).((..((((---(....)))))..))..........---- ( -41.70)
>DroSec_CAF1 28767 106 - 1
GGCGGUGUCGGCGGUGGCCUCCGUUAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCUGCAUCUCAAUCGCCUGCACCGGCUACUCCCUUAGUAUCUUCCCAA
((((((((.(((((..((.((.((....))..))))..)(((.(((((((...))))))).))).......)))).))))))((((......))))......)).. ( -43.00)
>DroSim_CAF1 28842 106 - 1
GGCGGUGUCGGCGGUAGCCUCGGUUAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCUGCAUCUCAAUCGCCUGCACCGGCUACUCCCUUAGUAUCUUCCCAA
((((((((.(((((((((.(((((....)).))))))))(((.(((((((...))))))).))).......)))).))))))((((......))))......)).. ( -48.00)
>DroEre_CAF1 29293 106 - 1
AGCGGUGUCGGCUGUGGCCUCGGUUAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCUGCAUCCCAAUCACCUGCGCCAGCUACUCCCUUAAUAUCUUCCCAA
((((((((.((..(..((.(((((....)).)))))..)(((.(((((((...))))))).))).........)).))))).)))..................... ( -38.10)
>DroYak_CAF1 28730 106 - 1
GGCGGUGUCGGCUGUGGCCUCGGUCAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCUGCAACCCAAUCACCUGCACCAGCUACUCCCUUAGUAUCUUCCCAA
((((((((.((..(..((.(((((....)).)))))..)(((.(((((((...))))))).))).........)).))))).)))..................... ( -37.90)
>consensus
GGCGGUGUCGGCUGUGGCCUCGGUUAAUGCUCGAGCUGCUGCCGCUGCGGCUGCCGCAGCUGCAUCCCAAUCGCCUGCACCAGCUACUCCCUUAGUAUCUUCCCAA
((((((((.(((.(((((.(((((....)).))))))))(((.(((((((...))))))).)))........))).))))).)))..................... (-34.98 = -35.23 +   0.26)

alignment

secondary structure

dotplot

Window 8

Location	9,257,914 – 9,258,022
Length	108
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	74.01
Mean single sequence MFE	-48.57
Consensus MFE	-24.80
Energy contribution	-24.67
Covariance contribution	-0.14
Combinations/Pair	1.33
Mean z-score	-1.77
Structure conservation index	0.51
SVM decision value	0.47
SVM RNA-class probability	0.747647
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9257914 108 - 27905053
CGCACCUGUUGCGCGAACGUCAAAAGGCUUCCCAGGAGGCGGCGGUGUCGGCUGUGGCCUCGGUUAAUGCUCGAGCUGCUGC---CGCUGCGGCUGCCGCAGCCGCAUCC---C
.((.(((.(((.(.(((.(((....)))))))))).)))..))((((.((((((((((((((((....)).))))..(((((---....))))).)))))))))))))).---. ( -50.10)
>DroVir_CAF1 30470 108 - 1
CGCAUUUAUUGCGCGAACGCCAGAAGGCUUCGCAGGAAUCGGCAGCCUCUGCCGUUGCCACGGUCAAUGCACGUGCAGCUGC---CGCUGCAGCUGCAGCCGCCGCAGCU---C
.(((((.((((.(((((.(((....)))))))).((...((((((...))))))...)).)))).)))))...((((((...---.))))))(((((.......))))).---. ( -49.40)
>DroPse_CAF1 27305 111 - 1
CCCAUCUUCUGCGAGAGCGGCAAAAAGCCUCCCAAGAGUCGGCCGCUUCAGCCGUGGCCUCGGUCAAUGCUCGGGCUGCUGCAGCCGCCGCCGCUGCUGCAGCUGCCUCA---C
..............(((((((.....)))......((.(.((((((.......))))))..).))...))))((((.((((((((.((....)).)))))))).))))..---. ( -47.60)
>DroMoj_CAF1 29854 99 - 1
CGCACUUGUUGCGCGAGCGUCAAAAG---------GAGUCGGCCGCAGCUGCCGUAGCUACGGUCAAUGCACGAGCAGCAGC---CGCUGCAGCUGCAGCAGCCGCAGGU---C
.....(((.(((....))).)))...---------.....((((((.(((((.((((((.((((....)).)).(((((...---.))))))))))).))))).)).)))---) ( -42.20)
>DroAna_CAF1 28474 111 - 1
CGCACCUGUUGCGGGAACGCCAAAAGGCCUCCCAGGAAUCGGCUGCCUCCGCUGUGGCUUCAGUUAAUGCCAGAGCUGCCGC---UGCUGCGGCGGCAGCUGCUGCUUCCUCAC
.(((.....)))((((..(((....))).))))(((((.((((((((...(((.((((..........)))).))).(((((---....)))))))))))))....)))))... ( -54.30)
>DroPer_CAF1 29866 111 - 1
CCCAUCUUCUGCGAGAGCGGCAAAAGGCCUCCCAAGAGUCGGCCGCUUCAGCCGUGGCCUCGGUCAAUGCUCGGGCUGCUGCAGCCGCCGCCGCUGCUGCAGCUGCCUCA---C
...........((((((((((....(((((....)).))).)))))))..((..((((....))))..)))))(((.((((((((.((....)).)))))))).)))...---. ( -47.80)
>consensus
CGCACCUGUUGCGCGAACGCCAAAAGGCCUCCCAGGAGUCGGCCGCCUCAGCCGUGGCCUCGGUCAAUGCUCGAGCUGCUGC___CGCUGCAGCUGCAGCAGCCGCAUCA___C
....(((.(((((....)).))).)))............((((.((..((((.(((((....((....((....))....))....))))).))))..)).))))......... (-24.80 = -24.67 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:23 2006