Locus 7296

Sequence ID	3R_DroMel_CAF1
Location	19,265,212 – 19,265,335
Length	123
Max. P	0.793235

overview

Window 7

Location	19,265,212 – 19,265,305
Length	93
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	81.05
Mean single sequence MFE	-21.05
Consensus MFE	-14.43
Energy contribution	-14.35
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.69
SVM decision value	0.59
SVM RNA-class probability	0.793235
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19265212 93 + 27905053
GUGCAAUUUCUCUAUUAUCGA-------U-GAAAAUUGCGG-AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
..((................(-------(-((..(((.(((-....))))))....))))(((((((((((((............))))))))))))))).. ( -21.50)
>DroPse_CAF1 75854 79 + 1
--------------AGAUCGA---------GAAAAUUGCGAUAGUCGCAAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
--------------.....((---------(....(((((.....)))))..........(((((((((((((............))))))))))))).))) ( -20.40)
>DroSim_CAF1 61215 93 + 1
GUGCAGUUUUUCUAUUAUCGA-------U-GAAAAUUACGG-AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
..((................(-------(-((..(((.(((-....))))))....))))(((((((((((((............))))))))))))))).. ( -21.50)
>DroEre_CAF1 62070 94 + 1
GUGCAGUUUCUCUAUUAUCGA-------UUGAAAAUUGCGG-AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
..(((((((.((.........-------..)))))))))((-....))..(((....)))(((((((((((((............))))))))))))).... ( -20.90)
>DroAna_CAF1 62797 98 + 1
--GGAAGUGCUCCAUUACCAAAGUUUGGA-GAAAAUUGCAA-AUUCCCGAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
--(((.....))).....((..((((((.-(((........-.)))))))))..))....(((((((((((((............))))))))))))).... ( -21.60)
>DroPer_CAF1 75961 79 + 1
--------------AGAUCGA---------GAAAAUUGCGAUAGUCGCAAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
--------------.....((---------(....(((((.....)))))..........(((((((((((((............))))))))))))).))) ( -20.40)
>consensus
__GCA_UUUCUCUAUUAUCGA_______U_GAAAAUUGCGA_AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUC
.....................................((...........(((....)))(((((((((((((............))))))))))))))).. (-14.43 = -14.35 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	19,265,233 – 19,265,335
Length	102
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	82.41
Mean single sequence MFE	-26.75
Consensus MFE	-18.66
Energy contribution	-20.10
Covariance contribution	1.44
Combinations/Pair	1.09
Mean z-score	-2.24
Structure conservation index	0.70
SVM decision value	0.57
SVM RNA-class probability	0.784013
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19265233 102 + 27905053
---U-GAAAAUUGCGG-AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCGCAUGCCAACGGGUAGCUGUGAGAAAAAUU
---(-((..(((.(((-....))))))....))).(((((((((((((............))))))))))))).((((((((((....))))..))))))....... ( -28.80)
>DroPse_CAF1 75861 102 + 1
-----GAAAAUUGCGAUAGUCGCAAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCUCAUGCCAACAGGCAGCUGUGAGAAAAAUU
-----.....(((((.....)))))(((....)))(((((((((((((............)))))))))))))..(((((((((....))))....)))))...... ( -28.60)
>DroGri_CAF1 74617 78 + 1
---U-GAGCAAUGCGG-AAU-----AUGAUC---------UCAUGUAACUCAA------UUCACAUGAUUCAUGC--GCUUGCCAGC-GGUAGCUGUGAGAAAAA-U
---.-..((((.(((.-..(-----((((..---------((((((.......------...)))))).))))))--))))))((((-....)))).........-. ( -20.00)
>DroEre_CAF1 62091 103 + 1
---UUGAAAAUUGCGG-AUUCCCGAAUGAUGUCAUGUUGAUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCGCAUGCCAACGGGUAGCUGUGAGAAAAAUA
---.(((..(((.(((-....))))))....))).(((((((((((((............))))))))))))).((((((((((....))))..))))))....... ( -29.00)
>DroAna_CAF1 62820 105 + 1
UGGA-GAAAAUUGCAA-AUUCCCGAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCGCAUGCCAACGGGUAGCUGUGAGAAAAAUU
.((.-(((........-.)))))..(((....)))(((((((((((((............))))))))))))).((((((((((....))))..))))))....... ( -25.50)
>DroPer_CAF1 75968 102 + 1
-----GAAAAUUGCGAUAGUCGCAAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCUCAUGCCAACAGGCAGCUGUGAGAAAAAUU
-----.....(((((.....)))))(((....)))(((((((((((((............)))))))))))))..(((((((((....))))....)))))...... ( -28.60)
>consensus
___U_GAAAAUUGCGA_AUUCCCGAAUGAUGUCAUGUUGGUCAUGUAACUCAAUUUCAAUUUACAUGAUCGAUGCUCGCAUGCCAACGGGUAGCUGUGAGAAAAAUU
...................................(((((((((((((............))))))))))))).((((((((((....))))..))))))....... (-18.66 = -20.10 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:21 2006