Locus 4054

Sequence ID	3L_DroMel_CAF1
Location	11,827,539 – 11,827,742
Length	203
Max. P	0.999790

overview

Window 6

Location	11,827,539 – 11,827,646
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.52
Mean single sequence MFE	-35.77
Consensus MFE	-10.14
Energy contribution	-10.00
Covariance contribution	-0.14
Combinations/Pair	1.08
Mean z-score	-2.71
Structure conservation index	0.28
SVM decision value	1.47
SVM RNA-class probability	0.956635
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11827539 107 - 23771897
CCGCGCGAGGCAAUAAAAAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAACCGGCU----GGAU-GC-----CCCAGGGUAAGCAGCCAACCUGUC--U-GCAGUUCGCCCUUC
....((((((((.........)))).........((((((...........(....).((((----(..(-((-----(....))))..)))))........--)-)))))))))..... ( -33.00)
>DroVir_CAF1 20276 99 - 1
C--CA-----CGGGCAAGAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAACAGCCA--CCGCGUGGC-----UGCAGGGCAAACGGCCAACCUUAU----UCAGCU---UCCAG
.--..-----..((...((((((............(((((..........((....))((((--(...)))))-----)))))(((.....)))........----.)))))---))).. ( -28.30)
>DroPse_CAF1 4848 104 - 1
CCCUGCGCGGCAAUAAAAAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAGCCGGUC----GUGU-GC-----CACGGGGCAAGCAGCCAACCUGUC--U-GCCCCG---CCCAC
...((.((((((.......((((((((..((((............)))))))))))).....----...)-))-----)..((((((..(((.....)))..--)-))))))---).)). ( -39.26)
>DroMoj_CAF1 19805 105 - 1
C--CA-----CGAUGCAGAGAUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAACAGCCAAACAGUGCGGC-----GGCAGGGCAAACAGCCAACCUGGCCCUGCCAGCU---GCCAG
.--..-----...(((((((((.......))))..)))))........((((((....))))))..(.(((((-----((((((((...(((.....))))))))))).)))---))).. ( -39.60)
>DroAna_CAF1 3383 109 - 1
UCCGGGGCGGCAAUAAAAAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAAGCGGCU----GUAG-GGACCCCUUCAGGGCAAGCAGCCAACCUGUC--U-GCUACU---CCCUC
...((((..(((.......((((((((..((((............))))))))).)))((((----((..-.(.(((.....))))..))))))........--)-))..))---))... ( -35.20)
>DroPer_CAF1 4877 104 - 1
CCCUGCGCGGCAAUAAAAAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAGCCGGUC----GUGU-GC-----CACGGGGCAAGCAGCCAACCUGUC--U-GCCCCG---CCCAC
...((.((((((.......((((((((..((((............)))))))))))).....----...)-))-----)..((((((..(((.....)))..--)-))))))---).)). ( -39.26)
>consensus
CCCCGCGCGGCAAUAAAAAGCUGCCAACAAUUUGACUGCAAAAUAAAAUUUGGCAACCGGCA____GUGU_GC_____CACAGGGCAAGCAGCCAACCUGUC__U_GCAGCU___CCCAC
.....................((((((..((((............))))))))))............................(((.....))).......................... (-10.14 = -10.00 +  -0.14)

alignment

secondary structure

dotplot

Window 7

Location	11,827,646 – 11,827,742
Length	96
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	77.30
Mean single sequence MFE	-40.48
Consensus MFE	-27.99
Energy contribution	-28.43
Covariance contribution	0.44
Combinations/Pair	1.10
Mean z-score	-3.18
Structure conservation index	0.69
SVM decision value	4.09
SVM RNA-class probability	0.999790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11827646 96 + 23771897
GAGGUGUUGGGUAUAUAGUGGAGUUCAUGCAAAGUGGGCGGCUGUUUGGAUGGCCAUCGGUGGGCGUGGCAGCUGGCUAUAGUUGCCAUGUUUUGU-----------------
..(.((.(((.(((..((..(.((((((.....))))))..)..))...))).))).)).)((((((((((((((....))))))))))))))...----------------- ( -32.90)
>DroSim_CAF1 3959 96 + 1
GAGCUGGUGGGUAUAUAGUGGAGUUCAUGCAAAGUGGGCGGCUGUUUGGAUGGCCAUCGGUGGGCGUGGCAGCUGGCUAUAGUUGCCAUGUUUUGU-----------------
..((((((((.(((..((..(.((((((.....))))))..)..))...))).))))))))((((((((((((((....))))))))))))))...----------------- ( -41.00)
>DroEre_CAF1 3828 104 + 1
GAAU---------UAUAGUGGCGGUCAUGCAAAGUGGGCAGCUGUUUGGAUGCCCACCGGUGGGCGUGGCAGCUGGCUAUAGCUGCCAUGUUUUGGCCAGCACUCGAAUGCAU
(.((---------(..((((..(((((.((...(((((((.((....)).)))))))..))((((((((((((((....)))))))))))))))))))..))))..))).).. ( -45.40)
>DroYak_CAF1 4341 104 + 1
GACG---------CAUAGUGGAGGUCAUGCAAAGUGGGCGGCUGUUUGGAUGGCCAUCGGUGGGCGUGGCAGCUGGCUAUGGUUACCAUGUUUUGGCCAGCACUCGAGUGCAU
...(---------(((..(.((((((((((..(.(((..((((((....)))))).))).)..))))))).(((((((((((...)))).....))))))).))).))))).. ( -42.60)
>consensus
GAGG_________UAUAGUGGAGGUCAUGCAAAGUGGGCGGCUGUUUGGAUGGCCAUCGGUGGGCGUGGCAGCUGGCUAUAGUUGCCAUGUUUUGG_________________
...............((.(((.((((((.((((.(((....))))))).)))))).))).))(((((((((((((....)))))))))))))..................... (-27.99 = -28.43 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:28 2006