Locus 2549

Sequence ID 2R_DroMel_CAF1
Location 9,068,283 – 9,068,423
Length 140
Max. P 0.996798
window4193 window4194

overview

Window 3

Location 9,068,283 – 9,068,402
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.74
Mean single sequence MFE -27.76
Consensus MFE -20.90
Energy contribution -20.82
Covariance contribution -0.08
Combinations/Pair 1.18
Mean z-score -1.49
Structure conservation index 0.75
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9068283 119 + 20766785
GUACACCGCACUGAUUGUUAACGAAUUCUUUCGAUGCAAAAA-AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCCAUC
................(((((.(((.....(((((((.....-.....((((((((....))))))))............(((((((....))))))).))))))).))))))))..... ( -29.10)
>DroSec_CAF1 33487 120 + 1
GUAUACCGCACUGAUUUUUAACGAAUUCUUUCGAUGCAAAAAAAAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAGGCCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCUAUC
(.((((((((.(((................))).)))...........((((((((....)))))))))).)))).(((((((((......(((((((...)))))))..))))))))). ( -30.09)
>DroSim_CAF1 35193 119 + 1
GUAUACCGCACUGAUUUUUAACGAAUUCUUUCGAUGCAAAAA-AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAGGCCGAUUAAAUAAUCGAUAGCAUCGAUUUCAUUGUCUAUC
............(((...(((.(((.....(((((((.....-.....((((((((....))))))))((((.......))))((((....))))....))))))).))).)))...))) ( -27.70)
>DroEre_CAF1 39019 116 + 1
GCUCACAGCACUGAUUUUUAUAGAAUUCUUUCGAUGCAAA----AAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUAAAAUAAUCGAUACUAUCGAUGUUUUGGGCUAUC
(((((.((((.((((..((((.(((....)))(((((...----....((((((((....)))))))).)).))).))))((((((......))))))...)))).)))).))))).... ( -28.50)
>DroYak_CAF1 35337 115 + 1
GUUCACCGAAAUGAUUUUUAACGAAUUCUUGCAAUGCAAA-----AAACUGGUCAAAGUUUUGACUAGGGCUGUCAAUAAGUCGAUGAAAUAAUCGAUAGUCUCGAUUUCUGGGCUUAUC
(((((..(((((((..............((((...)))).-----...((((((((....))))))))((((........((((((......)))))))))))).))))))))))..... ( -23.40)
>consensus
GUACACCGCACUGAUUUUUAACGAAUUCUUUCGAUGCAAAAA_AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCUAUC
..............................(((((((...........((((((((....))))))))((((.......))))(((......)))....))))))).............. (-20.90 = -20.82 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,068,323 – 9,068,423
Length 100
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 86.91
Mean single sequence MFE -29.84
Consensus MFE -23.94
Energy contribution -23.34
Covariance contribution -0.60
Combinations/Pair 1.17
Mean z-score -3.02
Structure conservation index 0.80
SVM decision value 2.75
SVM RNA-class probability 0.996798
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9068323 100 + 20766785
AA-AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCCAUCGCGAAAGUAAGCGCGAAAUUU
..-.((((((......))))))((((((((..(((.((..(((((((....)))))))...)).))).))))))))..(((((........)))))..... ( -28.00)
>DroSec_CAF1 33527 101 + 1
AAAAAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAGGCCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCUAUCGCGGCAGCAAGCGCGAAAUUU
........((((((((....)))))))).((((((.(((((((((......(((((((...)))))))..)))))))))...))))))............. ( -34.90)
>DroSim_CAF1 35233 100 + 1
AA-AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAGGCCGAUUAAAUAAUCGAUAGCAUCGAUUUCAUUGUCUAUCGCGAAAACAAGCGCGAAAUUU
..-.....((((((((....))))))))((((.......))))(((.....(((((((...))))))).....)))..(((((........)))))..... ( -27.90)
>DroEre_CAF1 39059 97 + 1
----AAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUAAAAUAAUCGAUACUAUCGAUGUUUUGGGCUAUCGCGAGAGGCAGCGCGGAAUUU
----....((((((((....)))))))).((((((....((((..(((((((.(((((...)))))))))))))))).((....))))))))......... ( -30.20)
>DroYak_CAF1 35377 96 + 1
-----AAACUGGUCAAAGUUUUGACUAGGGCUGUCAAUAAGUCGAUGAAAUAAUCGAUAGUCUCGAUUUCUGGGCUUAUCGCGUAAGCAAGCGCGAAAUUU
-----...((((((((....)))))))).........((((((.(.(((...(((((.....))))))))).))))))((((((......))))))..... ( -28.20)
>consensus
AA_AAAAACUGGUCAAAGUUUUGGCUAGGGCUGUCAAUAAGUCGAUUAAAUAAUCGAUAGCAUCGAUUUCUUGGCCUAUCGCGAAAGCAAGCGCGAAAUUU
........((((((((....))))))))((((.......))))........((((((.....))))))..........(((((........)))))..... (-23.94 = -23.34 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:43 2006