Locus 1374

Sequence ID 3L_DroMel_CAF1
Location 3,998,163 – 3,998,256
Length 93
Max. P 0.562029
window2138 window2139

overview

Window 8

Location 3,998,163 – 3,998,256
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.94
Mean single sequence MFE -28.10
Consensus MFE -19.03
Energy contribution -19.23
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -1.17
Structure conservation index 0.68
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3998163 93 + 23771897
GGAG----UU---------GUCAGGAUGU----------UGCC--ACUGCCUG-UAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUGGAGAUUUGACAGCUGCUUUAUGCC-G
((((----(.---------(.(((....)----------))).--))).))((-((((.....))))))........((((..((((((((........))))))))..)))).....-. ( -25.00)
>DroVir_CAF1 64273 93 + 1
GGAU----GU---------GGCAGGAUGU----------UGCCUUGUUGCC-G-CAUUUUAAUAAUACAUCGAAAUGAAAGUGGCUGUCAACUAGAGAUUUGACAUCUGCUUUGU-GG-C
((((----((---------(((((.(...----------.....).)))))-)-)))))..................((((..(.((((((........)))))).)..))))..-..-. ( -25.90)
>DroGri_CAF1 80378 111 + 1
GGAG----GUGGGUACUUUGCCAGGAUGU--UGCCUUGUUGCCUUGUUGCC-GUUAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUGGAGAUUUGACAUCUGCUUUGU-CG-C
.(((----((.(((.....))).((((((--(.((..((((.(..((..(.-.((((((..((.....))..))))))..)..)).).)))).))......))))))))))))..-..-. ( -25.60)
>DroMoj_CAF1 73015 99 + 1
GGAU----GU---------GCCAGGAUGUGUUGC----UUGCCUUGUUGCC-G-CAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUAGAGAUUUGACAGCUGCUUUGU-CG-C
((..----..---------((.(((..(.....)----...))).))..))-(-((((.....)))))..(((....((((..((((((((........))))))))..)))).)-))-. ( -30.50)
>DroAna_CAF1 80015 100 + 1
GGAG----GUG---UCGGUGUCAGGAUGU----------UGCC--AGUGCCUG-UAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUGGAGAUUUGACAGCUGCUUUAGCCAAC
...(----((.---(((((((((((.((.----------...)--)...))))-............)))))))....((((..((((((((........))))))))..)))).)))... ( -33.30)
>DroPer_CAF1 72353 95 + 1
GGAGGAUGGU---------GUCUGGAUGU----------UGCC--GCUGCC-G-UAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUGGAGAUUUGACAGCUGCUUUA-GCU-U
((.((.((((---------(.(.....).----------))))--))).))-(-((((.....))))).........((((..((((((((........))))))))..)))).-...-. ( -28.30)
>consensus
GGAG____GU_________GUCAGGAUGU__________UGCC__GUUGCC_G_UAUUUUAAUAAUGCAUCGAAAUGAAAGUGGCUGUCAACUGGAGAUUUGACAGCUGCUUUAU_CG_C
........................(((((...........((......))................)))))......((((..((((((((........))))))))..))))....... (-19.03 = -19.23 +   0.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,998,163 – 3,998,256
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.94
Mean single sequence MFE -21.15
Consensus MFE -12.26
Energy contribution -12.23
Covariance contribution -0.03
Combinations/Pair 1.12
Mean z-score -1.71
Structure conservation index 0.58
SVM decision value 0.06
SVM RNA-class probability 0.562029
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3998163 93 - 23771897
C-GGCAUAAAGCAGCUGUCAAAUCUCCAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUA-CAGGCAGU--GGCA----------ACAUCCUGAC---------AA----CUCC
.-.((((((((..((((((((........))))))))..)))).......))))............-((((..((--(...----------.)))))))..---------..----.... ( -24.11)
>DroVir_CAF1 64273 93 - 1
G-CC-ACAAAGCAGAUGUCAAAUCUCUAGUUGACAGCCACUUUCAUUUCGAUGUAUUAUUAAAAUG-C-GGCAACAAGGCA----------ACAUCCUGCC---------AC----AUCC
(-((-..((((....((((((........))))))....)))).........(((((.....))))-)-))).....((((----------......))))---------..----.... ( -20.00)
>DroGri_CAF1 80378 111 - 1
G-CG-ACAAAGCAGAUGUCAAAUCUCCAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUAAC-GGCAACAAGGCAACAAGGCA--ACAUCCUGGCAAAGUACCCAC----CUCC
(-(.-.....))...((((((........))))))((((...((.....))(((..............-(....)..(....)...)))--......))))...........----.... ( -17.40)
>DroMoj_CAF1 73015 99 - 1
G-CG-ACAAAGCAGCUGUCAAAUCUCUAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUG-C-GGCAACAAGGCAA----GCAACACAUCCUGGC---------AC----AUCC
.-((-(.((((..((((((((........))))))))..))))....))).((((((.....))))-)-)((....(((...----.........))).))---------..----.... ( -21.10)
>DroAna_CAF1 80015 100 - 1
GUUGGCUAAAGCAGCUGUCAAAUCUCCAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUA-CAGGCACU--GGCA----------ACAUCCUGACACCGA---CAC----CUCC
(((((.....(((((((((((........)))))))).....((.....)))))............-((((...(--(...----------.)).))))...))))---)..----.... ( -26.20)
>DroPer_CAF1 72353 95 - 1
A-AGC-UAAAGCAGCUGUCAAAUCUCCAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUA-C-GGCAGC--GGCA----------ACAUCCAGAC---------ACCAUCCUCC
.-.((-.((((..((((((((........))))))))..)))).....((.(((..(((....)))-.-.))).)--))).----------..........---------.......... ( -18.10)
>consensus
G_CG_ACAAAGCAGCUGUCAAAUCUCCAGUUGACAGCCACUUUCAUUUCGAUGCAUUAUUAAAAUA_C_GGCAAC__GGCA__________ACAUCCUGAC_________AC____CUCC
..........((.((((((((........))))))))..............(((..(((....)))....))).....))........................................ (-12.26 = -12.23 +  -0.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:56 2006