Locus 7734

Sequence ID	3L_DroMel_CAF1
Location	20,634,777 – 20,634,879
Length	102
Max. P	0.893878

overview

Window 4

Location	20,634,777 – 20,634,879
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.61
Mean single sequence MFE	-31.14
Consensus MFE	-20.24
Energy contribution	-21.08
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-2.11
Structure conservation index	0.65
SVM decision value	0.40
SVM RNA-class probability	0.722714
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20634777 102 + 23771897
AAAGCGGCGGACAGCGCC---AGUCGUCAACGUCAUCGUUUGC-------UU------UAAGGCUGAGUACAA--AAAGUACUCAGUUAUGCAAAGCGCAUUUAUGCAACGAUAUUCAAC
.....((((.....))))---.(.((....)).)((((((.((-------((------(..((((((((((..--...))))))))))....)))))(((....)))))))))....... ( -33.10)
>DroSec_CAF1 7953 100 + 1
AAAGCGGCGG-CAGCGCC---AGUCGUCAACGUCAUCGUUUGC-------UU------UGAGGUUGAGUACAA---AAGUACUCAGUUAUGCAAAGCGCAUUUAUGCAACGAUAUUCAAC
...(((((((-(...)))---.))))).......((((((.((-------((------((.(..(((((((..---..)))))))..)...))))))(((....)))))))))....... ( -32.50)
>DroSim_CAF1 9634 100 + 1
AAAGCGGCGG-CAGCGCC---AGUCGUCAACGUCAUCGUUUGC-------UU------UGAGGUUGAGUACAA---AAGUACUCAGUUAUGCAAAGCGCAUUUAUGCAACGAUAUUCAAC
...(((((((-(...)))---.))))).......((((((.((-------((------((.(..(((((((..---..)))))))..)...))))))(((....)))))))))....... ( -32.50)
>DroYak_CAF1 187933 103 + 1
AAAGCGGCGG-CAGCGCC---AGUCGUCAACGUCAUCGUUUGC-------UU------UAAGGUUGAGUACAAAAAAAGUACUCAGUUAUGCAAAGCGCAUUUAUGCAACGAUAUUCACC
...(((((((-(...)))---.))))).......((((((.((-------((------(.(..((((((((.......))))))))...)..)))))(((....)))))))))....... ( -28.20)
>DroAna_CAF1 7779 110 + 1
AAAGCGGCAC-CAGCGCCGUCCGCCGUCAACGUCAUCGUUUGACUUUAGCUUUGGCCAUAAGGUUCAGGCCAG--AAAGUACUCAGUUAUGCAAAACGCAUUUGUGCAACGAU-------
...(((((..-....)))))..((.(((((((....)).)))))....))(((((((..........))))))--)..((((......((((.....))))..))))......------- ( -29.40)
>consensus
AAAGCGGCGG_CAGCGCC___AGUCGUCAACGUCAUCGUUUGC_______UU______UAAGGUUGAGUACAA__AAAGUACUCAGUUAUGCAAAGCGCAUUUAUGCAACGAUAUUCAAC
.....((((.....))))....(.((....)).)((((((.((..................((((((((((.......))))))))))((((.....))))....))))))))....... (-20.24 = -21.08 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	20,634,777 – 20,634,879
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	84.61
Mean single sequence MFE	-32.38
Consensus MFE	-22.64
Energy contribution	-23.48
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.31
Structure conservation index	0.70
SVM decision value	0.98
SVM RNA-class probability	0.893878
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20634777 102 - 23771897
GUUGAAUAUCGUUGCAUAAAUGCGCUUUGCAUAACUGAGUACUUU--UUGUACUCAGCCUUA------AA-------GCAAACGAUGACGUUGACGACU---GGCGCUGUCCGCCGCUUU
((..(.((((((((((....)))((((((.....((((((((...--..))))))))...))------))-------)).)))))))...)..))....---((((.....))))..... ( -34.60)
>DroSec_CAF1 7953 100 - 1
GUUGAAUAUCGUUGCAUAAAUGCGCUUUGCAUAACUGAGUACUU---UUGUACUCAACCUCA------AA-------GCAAACGAUGACGUUGACGACU---GGCGCUG-CCGCCGCUUU
((..(.((((((((((....)))((((((......(((((((..---..)))))))....))------))-------)).)))))))...)..))....---((((...-.))))..... ( -33.40)
>DroSim_CAF1 9634 100 - 1
GUUGAAUAUCGUUGCAUAAAUGCGCUUUGCAUAACUGAGUACUU---UUGUACUCAACCUCA------AA-------GCAAACGAUGACGUUGACGACU---GGCGCUG-CCGCCGCUUU
((..(.((((((((((....)))((((((......(((((((..---..)))))))....))------))-------)).)))))))...)..))....---((((...-.))))..... ( -33.40)
>DroYak_CAF1 187933 103 - 1
GGUGAAUAUCGUUGCAUAAAUGCGCUUUGCAUAACUGAGUACUUUUUUUGUACUCAACCUUA------AA-------GCAAACGAUGACGUUGACGACU---GGCGCUG-CCGCCGCUUU
.((.((..((((((((....)))((((((......(((((((.......)))))))....))------))-------))....)))))..)).))....---((((...-.))))..... ( -29.10)
>DroAna_CAF1 7779 110 - 1
-------AUCGUUGCACAAAUGCGUUUUGCAUAACUGAGUACUUU--CUGGCCUGAACCUUAUGGCCAAAGCUAAAGUCAAACGAUGACGUUGACGGCGGACGGCGCUG-GUGCCGCUUU
-------...((.((((....(((((((((...............--.(((((..........)))))........(((((.((....))))))).)))))..))))..-)))).))... ( -31.40)
>consensus
GUUGAAUAUCGUUGCAUAAAUGCGCUUUGCAUAACUGAGUACUUU__UUGUACUCAACCUUA______AA_______GCAAACGAUGACGUUGACGACU___GGCGCUG_CCGCCGCUUU
......(((((((((....((((.....))))...(((((((.......))))))).....................)).))))))).((....))......((((.....))))..... (-22.64 = -23.48 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:29 2006