Locus 5402

Sequence ID	2L_DroMel_CAF1
Location	15,402,207 – 15,402,313
Length	106
Max. P	0.958620

overview

Window 5

Location	15,402,207 – 15,402,313
Length	106
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	81.70
Mean single sequence MFE	-22.78
Consensus MFE	-18.02
Energy contribution	-18.18
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.79
SVM decision value	0.36
SVM RNA-class probability	0.704906
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15402207 106 + 22407834
GCCUC-CUGG---------ACCGUGUGUUUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAUUCCCC-
.....-..((---------(.....((((((..((.(((((((......))))))).))....((((((((.(((((......)))))....)))))).))))))))....)))..- ( -24.10)
>DroVir_CAF1 173308 101 + 1
GCUCU----------GCUGUUCGGAUGUGUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAU------
..(((----------(.....))))..((((.(((((((((((......))))))).........((((((.(((((......)))))....)))))))))).))))....------ ( -22.60)
>DroGri_CAF1 155998 110 + 1
GCUCUGCUCU-----ACUGUUCGACAGUGUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGACCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAUUCCU--
...(((((((-----((((.....)))))....((.(((((((......))))))).))..))))))............(((..((.........))..))).............-- ( -22.20)
>DroWil_CAF1 254134 116 + 1
UUUCU-CUGUGUUCUACAGUUUGUAUGUUUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAUUCUAUC
.....-(((((...)))))(((((.....(((.((.(((((((......))))))).))..)))(((((((.(((((......)))))....))))))))))))............. ( -23.80)
>DroYak_CAF1 155214 99 + 1
GCCUC-CU----------------GUGUUUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAUUCCUC-
.....-..----------------.((((((..((.(((((((......))))))).))....((((((((.(((((......)))))....)))))).)))))))).........- ( -21.30)
>DroMoj_CAF1 183289 90 + 1
GCUCU----------------CGGA-----GCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAU------
((((.----------------..))-----))(((((((((((......)))))))...(((..(((((((.(((((......)))))....))))))).)))))))....------ ( -22.70)
>consensus
GCUCU_CU___________UUCGGAUGUUUUCUGUUGUAUUUUAUCGCAAAAAUACUACUUGAGUAGCUUUAUGGCCCAUGUUGGCCAAUAAAAAGCUGACAAAACAAUAUUCC___
................................(((((((((((......)))))))...(((..(((((((.(((((......)))))....))))))).))))))).......... (-18.02 = -18.18 +   0.17)

alignment

secondary structure

dotplot

Window 6

Location	15,402,207 – 15,402,313
Length	106
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	81.70
Mean single sequence MFE	-26.63
Consensus MFE	-23.39
Energy contribution	-23.25
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-2.50
Structure conservation index	0.88
SVM decision value	1.49
SVM RNA-class probability	0.958620
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15402207 106 - 22407834
-GGGGAAUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAAAACACACGGU---------CCAG-GAGGC
-..(((....((((((((.((((((....(((((......))))).))))))))....((.(((((((......))))))).))..)))))).....)---------))..-..... ( -28.00)
>DroVir_CAF1 173308 101 - 1
------AUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAACACAUCCGAACAGC----------AGAGC
------....((((((((.((((((....(((((......))))).)))))).........(((((((......))))))).))))))))............----------..... ( -26.20)
>DroGri_CAF1 155998 110 - 1
--AGGAAUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGUCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAACACUGUCGAACAGU-----AGAGCAGAGC
--.........((((((..((((((....(((((......))))).)))))).(((..((.(((((((......))))))).)).....((((.....))))-----.))))))))) ( -26.90)
>DroWil_CAF1 254134 116 - 1
GAUAGAAUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAAAACAUACAAACUGUAGAACACAG-AGAAA
((((((((...))))))))((((((....(((((......))))).)))))).(((..((.(((((((......))))))).))........(((.....))).......)-))... ( -28.60)
>DroYak_CAF1 155214 99 - 1
-GAGGAAUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAAAACAC----------------AG-GAGGC
-.........((((((((.((((((....(((((......))))).))))))))....((.(((((((......))))))).))..)))))).----------------..-..... ( -24.00)
>DroMoj_CAF1 183289 90 - 1
------AUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGC-----UCCG----------------AGAGC
------....(((((((((((((((....(((((......))))).))))))......((((.....))))))))))))).....((-----((..----------------.)))) ( -26.10)
>consensus
___GGAAUAUUGUUUUGUCAGCUUUUUAUUGGCCAACAUGGGCCAUAAAGCUACUCAAGUAGUAUUUUUGCGAUAAAAUACAACAGAAAACAUACGAA___________AG_AGAGC
..........(((((((((((((((....(((((......))))).))))))......((((.....)))))))))))))..................................... (-23.39 = -23.25 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:16 2006