Locus 4525

Sequence ID	3L_DroMel_CAF1
Location	13,038,478 – 13,038,569
Length	91
Max. P	0.729437

overview

Window 8

Location	13,038,478 – 13,038,569
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	77.49
Mean single sequence MFE	-21.40
Consensus MFE	-11.08
Energy contribution	-12.75
Covariance contribution	1.67
Combinations/Pair	1.06
Mean z-score	-1.90
Structure conservation index	0.52
SVM decision value	0.31
SVM RNA-class probability	0.683545
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13038478 91 + 23771897
CAAAUGUCUGCGCUGUAAUUAAUACGCA--UAAUACGCGUAUUAUGCUAAUGCCAAUGUCAUAAUGACUCGAGGAAACCCGAAA---------UG-AAAGAC---G
.....(((((((..(((..((((((((.--......)))))))))))...)))....(((.....)))(((.(....).)))..---------..-..))))---. ( -21.80)
>DroVir_CAF1 25365 95 + 1
CAAAUGUCGGCGCUGUAAUUAAUACGCA--UAAUACGCGUAUUAUGCUAAUGCCAAUGCUUUAAUGACUUGG-----CCCAAAACUUCGUCGUGG-AAAGAC---A
....((((((((..(((..((((((((.--......)))))))))))...)))).....(((.(((((..((-----.......))..))))).)-)).)))---) ( -23.90)
>DroPse_CAF1 19622 83 + 1
CAAAUGUCUGCGCUGUAAUUAAUACGCAUAUAAUACGCGUAUUAUGCUAAUGCCAAUGUCAUAAUGACUUGGGGAAACCG--------------------AA---C
.........(((..(((..((((((((.........)))))))))))...)))(((.(((.....))))))((....)).--------------------..---. ( -19.20)
>DroGri_CAF1 43491 96 + 1
CAAAUGUCUGCGCUGUAAUUAAUACGCA--UAAUACGCGUAUUAUGCAAAUGCCAUUGUAAUAAUGACUUGG-----CCCAAAACUUGCCCUUGGGUAAGAC---A
.............((((..((((((((.--......))))))))))))...((((..((.......)).)))-----)......((((((....))))))..---. ( -23.60)
>DroAna_CAF1 21909 96 + 1
CAAAUGUCUGCGCUGUAAUUAAUACGCA--UAAUACGCGUAUUAUGCUAAUACCAAUGUCAUAAUGACUUGAGGAAACCCAAAAAC-------UG-GAAGAGACUC
.....((((.....(((..((((((((.--......))))))))))).....(((..(((.....)))(((.(....).)))....-------))-)...)))).. ( -20.70)
>DroPer_CAF1 19579 83 + 1
CAAAUGUCUGCGCUGUAAUUAAUACGCAUAUAAUACGCGUAUUAUGCUAAUGCCAAUGUCAUAAUGACUUGGGGAAACCG--------------------AA---C
.........(((..(((..((((((((.........)))))))))))...)))(((.(((.....))))))((....)).--------------------..---. ( -19.20)
>consensus
CAAAUGUCUGCGCUGUAAUUAAUACGCA__UAAUACGCGUAUUAUGCUAAUGCCAAUGUCAUAAUGACUUGGGGAAACCCAAAA__________G__AAGAC___C
.....(((...........((((((((.........)))))))).((....))............)))(((((....)))))........................ (-11.08 = -12.75 +   1.67)

alignment

secondary structure

dotplot

Window 9

Location	13,038,478 – 13,038,569
Length	91
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	77.49
Mean single sequence MFE	-22.10
Consensus MFE	-13.49
Energy contribution	-13.35
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-1.58
Structure conservation index	0.61
SVM decision value	0.42
SVM RNA-class probability	0.729437
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13038478 91 - 23771897
C---GUCUUU-CA---------UUUCGGGUUUCCUCGAGUCAUUAUGACAUUGGCAUUAGCAUAAUACGCGUAUUA--UGCGUAUUAAUUACAGCGCAGACAUUUG
.---((((..-..---------..(((((....)))))(((.....)))....((....((((((((....)))))--)))(((.....)))...))))))..... ( -23.10)
>DroVir_CAF1 25365 95 - 1
U---GUCUUU-CCACGACGAAGUUUUGGG-----CCAAGUCAUUAAAGCAUUGGCAUUAGCAUAAUACGCGUAUUA--UGCGUAUUAAUUACAGCGCCGACAUUUG
.---(((...-....))).((((.(((((-----((((((.......)).))))).......((((((((((...)--))))))))).........)))).)))). ( -22.80)
>DroPse_CAF1 19622 83 - 1
G---UU--------------------CGGUUUCCCCAAGUCAUUAUGACAUUGGCAUUAGCAUAAUACGCGUAUUAUAUGCGUAUUAAUUACAGCGCAGACAUUUG
(---((--------------------(((((...(((((((.....))).))))....))).(((((((((((...))))))))))).......))..)))..... ( -19.80)
>DroGri_CAF1 43491 96 - 1
U---GUCUUACCCAAGGGCAAGUUUUGGG-----CCAAGUCAUUAUUACAAUGGCAUUUGCAUAAUACGCGUAUUA--UGCGUAUUAAUUACAGCGCAGACAUUUG
(---((((..(((((((.....)))))))-----....((((((.....)))))).......((((((((((...)--)))))))))..........))))).... ( -24.60)
>DroAna_CAF1 21909 96 - 1
GAGUCUCUUC-CA-------GUUUUUGGGUUUCCUCAAGUCAUUAUGACAUUGGUAUUAGCAUAAUACGCGUAUUA--UGCGUAUUAAUUACAGCGCAGACAUUUG
..(((((..(-((-------((..(((((....)))))(((.....))))))))........((((((((((...)--)))))))))........).))))..... ( -22.50)
>DroPer_CAF1 19579 83 - 1
G---UU--------------------CGGUUUCCCCAAGUCAUUAUGACAUUGGCAUUAGCAUAAUACGCGUAUUAUAUGCGUAUUAAUUACAGCGCAGACAUUUG
(---((--------------------(((((...(((((((.....))).))))....))).(((((((((((...))))))))))).......))..)))..... ( -19.80)
>consensus
G___GUCUU__C__________UUUUGGGUUUCCCCAAGUCAUUAUGACAUUGGCAUUAGCAUAAUACGCGUAUUA__UGCGUAUUAAUUACAGCGCAGACAUUUG
......................................(((............((....)).(((((((((.......)))))))))...........)))..... (-13.49 = -13.35 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:43 2006