Locus 10095

Sequence ID	3R_DroMel_CAF1
Location	27,052,887 – 27,052,986
Length	99
Max. P	0.989325

overview

Window 3

Location	27,052,887 – 27,052,986
Length	99
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.46
Mean single sequence MFE	-36.75
Consensus MFE	-21.36
Energy contribution	-21.03
Covariance contribution	-0.33
Combinations/Pair	1.25
Mean z-score	-3.25
Structure conservation index	0.58
SVM decision value	2.16
SVM RNA-class probability	0.989325
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27052887 99 + 27905053
GCAAUCUGAUGGCUGCUAAUGCCACAGCCAGCAAGAUACUCAAGCUGGCCACCAAUGUGGCCAAUGGUG-----GCUCCUCU----------AUGGACAUUGUGCAGCAGCAAC
((.((((..((((((.........))))))...))))......(((((((((((.((....)).)))))-----))(((...----------..))).......)))).))... ( -36.70)
>DroEre_CAF1 107429 99 + 1
GUAAUCUGAUGGCUGCCAAUGCCACAGCCAGCAAGAUACUCAAGCUGGCCACCAAUGUGGCCAAUGGUG-----GCUCCACU----------AUGGACAUUGUGCAGCAGCAAC
......((...(((((((((((((((((((((..(.....)..))))))......)))))(((.(((((-----....))))----------)))).))))).)))))..)).. ( -39.00)
>DroWil_CAF1 108613 114 + 1
GCAAUUUAAUGGCUGCCAAUGCAACGGCCAAUAAGAUCCUCAAAUUGGCCACCAAUGUGGCAAAUGGCGUUGUCGCUGCUCCACCGCAUGUGGUGGAUAUUGUUCAGCAGCACA
...........(((((....(((..(((((((..(.....)..)))))))......(((((((......))))))))))(((((((....))))))).........)))))... ( -40.00)
>DroYak_CAF1 103424 99 + 1
GCAAUCUGAUGGCUGCCAAUGCUACAGCCAGCAAGAUACUCAAGCUGGCCACCAAUGUGGCCAACGGUG-----GCUCCUCU----------AUGGACAUUGUGCAGCAGCAAC
......((...((((((((((.....((((.(..(.....)..(.(((((((....))))))).)).))-----))(((...----------..)))))))).)))))..)).. ( -37.00)
>DroMoj_CAF1 133198 88 + 1
--AAUUUAAUAGCCGCCAAUGCCACGGCCAACAAAAUACUCAAGUUGGCCACCAAUGUGGCAAACGGCG------------------------UGGACAUUGCACAGCAACACA
--.........((((....(((((((((((((...........)))))))......))))))..))))(------------------------((....((((...))))))). ( -29.00)
>DroAna_CAF1 110498 99 + 1
GCAAUCUUAUGGCUGCCAAUGCAACGGCCAGCAAGAUUCUCAAGCUGGCCACCAAUGUGGCCAACGGCG-----GCUCCGCC----------GUCGACAUCGUACAGCACCAGC
((((((((.((((((.........))))))..)))))).....(((((((((....))))))..(((((-----((...)))----------)))).........)))....)) ( -38.80)
>consensus
GCAAUCUGAUGGCUGCCAAUGCCACAGCCAGCAAGAUACUCAAGCUGGCCACCAAUGUGGCCAACGGCG_____GCUCCUCU__________AUGGACAUUGUGCAGCAGCAAC
...........(((((((((((((..((((((...........))))))(((....)))((.....)).........................))).)))))....)))))... (-21.36 = -21.03 +  -0.33)

alignment

secondary structure

dotplot

Window 4

Location	27,052,887 – 27,052,986
Length	99
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.46
Mean single sequence MFE	-42.38
Consensus MFE	-31.49
Energy contribution	-30.43
Covariance contribution	-1.05
Combinations/Pair	1.39
Mean z-score	-3.59
Structure conservation index	0.74
SVM decision value	1.86
SVM RNA-class probability	0.980544
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27052887 99 - 27905053
GUUGCUGCUGCACAAUGUCCAU----------AGAGGAGC-----CACCAUUGGCCACAUUGGUGGCCAGCUUGAGUAUCUUGCUGGCUGUGGCAUUAGCAGCCAUCAGAUUGC
...(((((((....(((.((((----------((....((-----(((((.((....)).)))))))((((..(.....)..)))).))))))))))))))))........... ( -40.90)
>DroEre_CAF1 107429 99 - 1
GUUGCUGCUGCACAAUGUCCAU----------AGUGGAGC-----CACCAUUGGCCACAUUGGUGGCCAGCUUGAGUAUCUUGCUGGCUGUGGCAUUGGCAGCCAUCAGAUUAC
.(((..(((((.(((((.((((----------(((...((-----(((((.((....)).)))))))((((..(.....)..)))))))))))))))))))))...)))..... ( -46.80)
>DroWil_CAF1 108613 114 - 1
UGUGCUGCUGAACAAUAUCCACCACAUGCGGUGGAGCAGCGACAACGCCAUUUGCCACAUUGGUGGCCAAUUUGAGGAUCUUAUUGGCCGUUGCAUUGGCAGCCAUUAAAUUGC
((.(((((..(......((((((......))))))((((((....(((((..........)))))((((((..(.....)..)))))))))))).)..)))))))......... ( -45.40)
>DroYak_CAF1 103424 99 - 1
GUUGCUGCUGCACAAUGUCCAU----------AGAGGAGC-----CACCGUUGGCCACAUUGGUGGCCAGCUUGAGUAUCUUGCUGGCUGUAGCAUUGGCAGCCAUCAGAUUGC
.(((..(((((.((((((((..----------...))(((-----(...(((((((((....)))))))))...(((.....)))))))...)))))))))))...)))..... ( -39.20)
>DroMoj_CAF1 133198 88 - 1
UGUGUUGCUGUGCAAUGUCCA------------------------CGCCGUUUGCCACAUUGGUGGCCAACUUGAGUAUUUUGUUGGCCGUGGCAUUGGCGGCUAUUAAAUU--
......(((((.(((((.(((------------------------(.......(((.....)))(((((((...........))))))))))))))))))))).........-- ( -33.80)
>DroAna_CAF1 110498 99 - 1
GCUGGUGCUGUACGAUGUCGAC----------GGCGGAGC-----CGCCGUUGGCCACAUUGGUGGCCAGCUUGAGAAUCUUGCUGGCCGUUGCAUUGGCAGCCAUAAGAUUGC
((..((((....((((((((((----------((((....-----))))))))...))))))..(((((((..(.....)..)))))))...))))..)).............. ( -48.20)
>consensus
GUUGCUGCUGCACAAUGUCCAU__________AGAGGAGC_____CACCAUUGGCCACAUUGGUGGCCAGCUUGAGUAUCUUGCUGGCCGUGGCAUUGGCAGCCAUCAGAUUGC
......(((((.(((((.((((........................((((.((....)).))))(((((((..(.....)..)))))))))))))))))))))........... (-31.49 = -30.43 +  -1.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:48:47 2006