Locus 5343

Sequence ID	3R_DroMel_CAF1
Location	14,020,690 – 14,020,852
Length	162
Max. P	0.804213

overview

Window 8

Location	14,020,690 – 14,020,791
Length	101
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	93.42
Mean single sequence MFE	-34.53
Consensus MFE	-29.89
Energy contribution	-29.95
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.46
Structure conservation index	0.87
SVM decision value	0.19
SVM RNA-class probability	0.626185
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14020690 101 - 27905053
GCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCUUGGGGCCGCCGCCUCCAAUCUGCUCAGUAAUGGCAACAACAAUUUCUGAAGGCGAUG----ACCACAC
(((((.....((((((.......)))))))))))...((.((.((.(((((......(((.((....)))))....((.....)).))))).))----.)).)). ( -33.10)
>DroSec_CAF1 5812 101 - 1
GCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCUUGGGGCCGCCGCCUCCAAUCUGCUCAGCAAUGGCAACAACAAUUUCUGAAGGCGAUG----ACCACAC
(((((.....((((((.......)))))))))))...((.((.((.(((((.((...(((...))).((....))........)).))))).))----.)).)). ( -33.70)
>DroSim_CAF1 5797 101 - 1
GCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCUUGGGGCCGCCGCCUCCAAUCUGCUCAGCAAUGGCAACAACAAUUUCUGAAGGCGAUG----ACCACAC
(((((.....((((((.......)))))))))))...((.((.((.(((((.((...(((...))).((....))........)).))))).))----.)).)). ( -33.70)
>DroEre_CAF1 5795 101 - 1
GCAGCUCCUCGGCCGCUUCUAUUGCGGCUGCUGCUCUUGGGGCCGCCGCGUCCAAUCUGCUCAGCAAUGGCAACAACAAUUUCUGAAGGCAAAG----ACCACAC
(((((.....((((((.......)))))))))))((((...(((...(((.......)))((((.((((....))....)).)))).))).)))----)...... ( -31.00)
>DroYak_CAF1 5765 100 - 1
GCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCACUUGGGGCCGCCGCCUCCAAUCUGCUCAGCAAUGGCAACAACAAUUUCUGA-GGCGAGG----ACCACAC
(((((.....((((((.......)))))))))))...(((..((..((((((.....(((...))).((....)).........))-)))).))----.)))... ( -38.80)
>DroAna_CAF1 5627 105 - 1
GCAGCUCCUCAGCCGCUUCCAUAGCGGCUGCUGCUCUGGGGGCGGCCGCCUCCAAUCUGCUCAGCAAUGGCAACAACAACUUCUGAAUGCGAAACAACACCACGC
(((((.....(((((((.....))))))))))))..(((((((....)))))))...(((.((....)))))................(((...........))) ( -36.90)
>consensus
GCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCUUGGGGCCGCCGCCUCCAAUCUGCUCAGCAAUGGCAACAACAAUUUCUGAAGGCGAUG____ACCACAC
(((((.....((((((.......)))))))))))..(((((((....))).))))..(((((((...((....)).......))))..))).............. (-29.89 = -29.95 +   0.06)

alignment

secondary structure

dotplot

Window 9

Location	14,020,754 – 14,020,852
Length	98
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	81.96
Mean single sequence MFE	-52.58
Consensus MFE	-34.55
Energy contribution	-34.75
Covariance contribution	0.20
Combinations/Pair	1.19
Mean z-score	-2.35
Structure conservation index	0.66
SVM decision value	0.63
SVM RNA-class probability	0.804213
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14020754 98 - 27905053
ACGGUGGCAGCCGCUGUGGCAGCUGUGGUGGCGGCUGCGGCGUCCAACGGA-UCGGCG-----GCGGGCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCU
..((..((((((((.((.((((((((....)))))))).)).......(((-..((((-----(((((......))).)))))))))...))))))))..)).. ( -56.00)
>DroVir_CAF1 6856 104 - 1
ACGGUAGCAGCUGCAGUGGCAGCUGUCGUUGCUGCUGCCGCAUCCAACAGCACCGGUGGAGGGACGAGCAGCUCAACGGCUGCAUCCAUAGCUGCUGCGGCGCU
.(.((((((((((.....((((((((.(..(((((((((.(.((((.(......).))))))).).)))))).).)))))))).....)))))))))).).... ( -49.20)
>DroPse_CAF1 6719 95 - 1
ACGGUGGCAGCCGCUGUGGCAGCUGUUGUGGCAGCAGCUGCAUCCAAUGGC-ACG--------GCGGGCAGCCCCUCGGCGGCAUCCAUAGCAGCGGCAGCCCU
..((.(((.((((((((.((((((((((...)))))))))).....((((.-.((--------.((((......)))).))....)))).)))))))).))))) ( -49.40)
>DroSim_CAF1 5861 98 - 1
ACGGUGGCAGCCGCUGUGGCAGCUGUGGUGGCGGCUGCGGCGUCCAACGGA-UCGGCG-----GCGGGCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCUCU
..((..((((((((.((.((((((((....)))))))).)).......(((-..((((-----(((((......))).)))))))))...))))))))..)).. ( -56.00)
>DroYak_CAF1 5828 98 - 1
ACGGUGGCAGCCGCUGUGGCAGCUGUGGUGGCGGCUGCGGCGUCUAACGGA-UCGGCG-----GUGGGCAGCUCCUCGGCCGCUUCCAUUGCGGCUGCUGCACU
...(..((((((((.((.((((((((....)))))))).)).......(((-.((((.-----(.(((....))).).))))..)))...))))))))..)... ( -55.50)
>DroPer_CAF1 6704 95 - 1
ACGGUGGCAGCCGCUGUGGCAGCUGUUGUGGCAGCAGCUGCAUCCAAUGGC-ACG--------GCGGGCAGCCCCUCGGCGGCAUCCAUAGCAGCGGCAGCCCU
..((.(((.((((((((.((((((((((...)))))))))).....((((.-.((--------.((((......)))).))....)))).)))))))).))))) ( -49.40)
>consensus
ACGGUGGCAGCCGCUGUGGCAGCUGUGGUGGCGGCUGCGGCAUCCAACGGA_UCGGCG_____GCGGGCAGCUCCUCGGCCGCAUCCAUAGCGGCUGCUGCCCU
(((((((...))))))).(((((((((((((.....(((((......((....)).........((((......)))))))))..)))))))))))))...... (-34.55 = -34.75 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:26 2006