Locus 3212

Sequence ID	3R_DroMel_CAF1
Location	8,562,439 – 8,562,545
Length	106
Max. P	0.896044

overview

Window 9

Location	8,562,439 – 8,562,545
Length	106
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.89
Mean single sequence MFE	-27.27
Consensus MFE	-14.62
Energy contribution	-15.18
Covariance contribution	0.56
Combinations/Pair	1.11
Mean z-score	-1.90
Structure conservation index	0.54
SVM decision value	0.99
SVM RNA-class probability	0.896044
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8562439 106 + 27905053
GU--------UCAGUGGACGAUAAACGGACGCGAUUAAAUGAGCAAAUCGUUUAAUUAUAAGUCCACUUAAUGCCCAGCGUAAAGCCAAAGGCUUUAUGGGCGACAUAUC--CUGG----
((--------(.(((((((......((....))(((((((((.....))))))))).....))))))).)))(((((...(((((((...))))))))))))........--....---- ( -33.80)
>DroVir_CAF1 38077 104 + 1
----------------GACGAUAAACACACCCGAUUAAAUGGGCAGAGCGUUUAAUUAUAAGUUCACUUAAUGUCAAGCAUAAAGCCAAAGGCUUUACGGCCAACAACUCUCGUUAAAAC
----------------(((((........((((......))))..(((..........((((....)))).(((...((.(((((((...)))))))..))..))).))))))))..... ( -19.90)
>DroGri_CAF1 33702 120 + 1
GUUGCCGUUCUCAUUGGUCGAUAAGCAUAUCGGAUUAAAUGGGAAAAUCGUUUAAUUAUAAGUUCAUUUAGUGCCGAGGAUAAAGCCAAAGGCUUUAUGACCACAAACUCUCGUUAAAAC
.(((.((.......(((((..........((((((((((((((...................)))))))))).))))..((((((((...)))))))))))))........)).)))... ( -25.97)
>DroAna_CAF1 23657 107 + 1
GU--------CCAUCGAACGAUAAACAGACGCGAUUAAAUGAGCAAAUCGUUUAAUUAUAAGUCCACUUAAUGCCAAGCGUAAAGCCAAAGGCUUUAUGAGCGCUCUUUU--GUGAA---
..--------..........(((((.((((((((((((((((.....)))))))))).((((....))))........(((((((((...))))))))).))).))))))--))...--- ( -26.60)
>DroPer_CAF1 39648 106 + 1
-U--------GCAGUGGCCGAUAAACAGGCGCGAUUAAAUGAGAAAAUCGUUUAAUUAUAAUUCCACUUAAUGCCAGGCGUAAAGCCGAAGGCUUUAUAGACGACAUUUG--CUGCA---
-.--------(((((.(((........)))..((((((((((.....)))))))))).........(((((.(((.(((.....)))...))).))).)).........)--)))).--- ( -30.10)
>consensus
GU________UCAGUGGACGAUAAACAGACGCGAUUAAAUGAGCAAAUCGUUUAAUUAUAAGUCCACUUAAUGCCAAGCGUAAAGCCAAAGGCUUUAUGGCCGACAUCUC__GUGAA___
................................((((((((((.....)))))))))).....................(((((((((...)))))))))..................... (-14.62 = -15.18 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	8,562,439 – 8,562,545
Length	106
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	72.89
Mean single sequence MFE	-27.40
Consensus MFE	-8.91
Energy contribution	-9.39
Covariance contribution	0.48
Combinations/Pair	1.20
Mean z-score	-1.79
Structure conservation index	0.33
SVM decision value	0.38
SVM RNA-class probability	0.712562
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8562439 106 - 27905053
----CCAG--GAUAUGUCGCCCAUAAAGCCUUUGGCUUUACGCUGGGCAUUAAGUGGACUUAUAAUUAAACGAUUUGCUCAUUUAAUCGCGUCCGUUUAUCGUCCACUGA--------AC
----....--........((((((((((((...)))))))...)))))....(((((((.......((((((...(((..........)))..))))))..)))))))..--------.. ( -31.10)
>DroVir_CAF1 38077 104 - 1
GUUUUAACGAGAGUUGUUGGCCGUAAAGCCUUUGGCUUUAUGCUUGACAUUAAGUGAACUUAUAAUUAAACGCUCUGCCCAUUUAAUCGGGUGUGUUUAUCGUC----------------
......((((....(((..(.(((((((((...))))))))).)..))).((((....))))....(((((((...((((........))))))))))))))).---------------- ( -31.10)
>DroGri_CAF1 33702 120 - 1
GUUUUAACGAGAGUUUGUGGUCAUAAAGCCUUUGGCUUUAUCCUCGGCACUAAAUGAACUUAUAAUUAAACGAUUUUCCCAUUUAAUCCGAUAUGCUUAUCGACCAAUGAGAACGGCAAC
((((((((....)))..(((((((((((((...))))))))..((((...((((((.......................))))))..))))..........)))))...)))))...... ( -25.00)
>DroAna_CAF1 23657 107 - 1
---UUCAC--AAAAGAGCGCUCAUAAAGCCUUUGGCUUUACGCUUGGCAUUAAGUGGACUUAUAAUUAAACGAUUUGCUCAUUUAAUCGCGUCUGUUUAUCGUUCGAUGG--------AC
---.....--....(((((....(((((((...)))))))))))).((((((((((..(....((((....)))).)..)))))))).))....(((((((....)))))--------)) ( -25.30)
>DroPer_CAF1 39648 106 - 1
---UGCAG--CAAAUGUCGUCUAUAAAGCCUUCGGCUUUACGCCUGGCAUUAAGUGGAAUUAUAAUUAAACGAUUUUCUCAUUUAAUCGCGCCUGUUUAUCGGCCACUGC--------A-
---....(--(.(((((((....(((((((...)))))))....))))))).((((..............(((((.........))))).(((........)))))))))--------.- ( -24.50)
>consensus
___UUCAC__GAAAUGUCGCCCAUAAAGCCUUUGGCUUUACGCUUGGCAUUAAGUGGACUUAUAAUUAAACGAUUUGCUCAUUUAAUCGCGUCUGUUUAUCGUCCAAUGA________AC
..................((...(((((((...))))))).))...((((((((((..(.................)..)))))))).)).............................. ( -8.91 =  -9.39 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:49 2006