Locus 1518

Sequence ID 3R_DroMel_CAF1
Location 4,328,792 – 4,328,933
Length 141
Max. P 0.877115
window2524 window2525

overview

Window 4

Location 4,328,792 – 4,328,893
Length 101
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.49
Mean single sequence MFE -27.64
Consensus MFE -20.19
Energy contribution -20.92
Covariance contribution 0.72
Combinations/Pair 1.05
Mean z-score -1.53
Structure conservation index 0.73
SVM decision value 0.66
SVM RNA-class probability 0.815651
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4328792 101 + 27905053
--ACCG-C----------CAUUCGCCACCGCCAUUUUCCCACCCAUUCCA---UUUUC--CCAGCUUUUCCCGCCGCUGCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGA
--....-.----------................................---...((--((((((...((.(((((....)).(((((((.....))))))).))).)).)))))))) ( -30.20)
>DroSec_CAF1 16130 101 + 1
--ACCG-C----------CUUUCGCCACCGCCAUUUUCCCACCCAUUCCA---UUUUC--CCAGCUUUUCCCGCCGCUGCUGCUGCAUUGCCUGAAGCCAUGCUGGCUGGCAGUUGGGA
--....-.----------................................---...((--((((((...((.(((((....)).((((.((.....)).)))).))).)).)))))))) ( -26.10)
>DroSim_CAF1 5172 101 + 1
--ACCG-C----------CUUUCGCCACCGCCAUUUUCCCACCCAUUCCG---UUUUC--CCAGCUUUUCCCGCCGCUGCUGCUGCAUUGCCUGAAGCCAUGCUGGCUGGCAGUUGGGA
--....-.----------................................---...((--((((((...((.(((((....)).((((.((.....)).)))).))).)).)))))))) ( -26.10)
>DroEre_CAF1 16194 100 + 1
--ACCG-C----------CUCUCACCAUC-CCAUUUUCCCACCCAUUCCA---UUUUC--CCCGCUCUUCCCGCCGCUGCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGA
--....-.----------.........((-(((.................---.....--...((.......)).((((((((((((((((.....))))))).))).))))))))))) ( -27.80)
>DroYak_CAF1 7740 110 + 1
--ACCG-CCUUCCACUGCCUUUCACCCUC-CCAUUUUGCCACCCAUUUCA---UUUUC--CCAGCUUUUCCCGCCGCUGCUGCUGCAUUGCCCGAAGCAAUGCUGGCUGGCAGUUGGGA
--....-....................((-(((..((((((.(((.....---.....--.((((.............))))..(((((((.....)))))))))).)))))).))))) ( -32.52)
>DroAna_CAF1 3631 101 + 1
CGACCAUC----------CCGUCCAUACCGCCGUCC-ACCAUCCAUUCCCCGAAUCCCUCAACGCUUUUCC-------GCUGCUGCAGCGCCUCGGGCAUUGCCGUCUGGCAGUUGGGA
......((----------(((...........((((-..............((.....))..........(-------((((...)))))....))))((((((....))))))))))) ( -23.10)
>consensus
__ACCG_C__________CUUUCGCCACCGCCAUUUUCCCACCCAUUCCA___UUUUC__CCAGCUUUUCCCGCCGCUGCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGA
....................................................................(((((..(((((((((((((.((.....)).)))).))).))))))))))) (-20.19 = -20.92 +   0.72)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,328,819 – 4,328,933
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.48
Mean single sequence MFE -34.02
Consensus MFE -21.93
Energy contribution -23.10
Covariance contribution 1.17
Combinations/Pair 1.05
Mean z-score -1.64
Structure conservation index 0.64
SVM decision value 0.90
SVM RNA-class probability 0.877115
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4328819 114 + 27905053
ACCCAUUCCA---UUUUC--CCAGCUUUUCCCGCCGCU-GCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
..........---.((((--((((((...((.(((((.-...)).(((((((.....))))))).))).)).)))))))))).....((....))(((((.........)))))...... ( -39.10)
>DroPse_CAF1 8223 89 + 1
--------------------------CUCCUCUCCGCUCUCUGCUGCAUUGCCUGGGGCAUCG-----UGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
--------------------------.((..((((((((((.(((((..((((...))))...-----..))))).)))).....((((....)))))))).))..))............ ( -26.60)
>DroEre_CAF1 16220 114 + 1
ACCCAUUCCA---UUUUC--CCCGCUCUUCCCGCCGCU-GCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
..........---.....--.((((..((((((..(((-(((((((((((((.....))))))).))).))))))))))))....((((....))))))))..((.....))........ ( -39.10)
>DroYak_CAF1 7776 114 + 1
ACCCAUUUCA---UUUUC--CCAGCUUUUCCCGCCGCU-GCUGCUGCAUUGCCCGAAGCAAUGCUGGCUGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
..........---.((((--((((((...((.(((((.-...)).(((((((.....))))))).))).)).)))))))))).....((....))(((((.........)))))...... ( -39.10)
>DroAna_CAF1 3660 112 + 1
AUCCAUUCCCCGAAUCCCUCAACGCUUUUCC--------GCUGCUGCAGCGCCUCGGGCAUUGCCGUCUGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
.......................((..(((.--------((((((((((((((...)))((((((....))))))..................)).))))))))).))).))........ ( -33.60)
>DroPer_CAF1 4776 89 + 1
--------------------------CUCCUCUCCGCUCUCUGCUGCAUUGCCUGGGGCAUCG-----UGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
--------------------------.((..((((((((((.(((((..((((...))))...-----..))))).)))).....((((....)))))))).))..))............ ( -26.60)
>consensus
ACCCAUUCCA___UUUUC__CC_GCUCUUCCCGCCGCU_GCUGCUGCAUUGCCUGAAGCAAUGCUGGCUGGCAGUUGGGAAAUUUAUGCAAACGCAUGCGGCAGCCGAACGCAUAAUUCA
.......................................((((((((((((((...(((...)))....))))))..........((((....))))))))))))............... (-21.93 = -23.10 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:40 2006