Locus 5772

Sequence ID 2R_DroMel_CAF1
Location 18,298,666 – 18,298,808
Length 142
Max. P 0.998772
window9247 window9248 window9249

overview

Window 7

Location 18,298,666 – 18,298,785
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 91.94
Mean single sequence MFE -28.52
Consensus MFE -25.85
Energy contribution -25.85
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.91
SVM decision value 3.22
SVM RNA-class probability 0.998772
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18298666 119 + 20766785
AUGUCGUAGAAUCGUCGCCGUCGCAUUGCACAUAAAACACUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
.((((((((((((...((....))...(((.(((((.....)))))))).......))).)))))).))).....((((((((((((((((..((....))..)))))))))))))))) ( -29.90)
>DroVir_CAF1 151928 105 + 1
-----G--------CU-GCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCUGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGAGCGGUUUUUAUUGUGAU
-----(--------((-((.(((((((((((((((((((........((.(((..(....)..))).))))))))))...(((....)))))))).)))))))))))............ ( -27.20)
>DroPse_CAF1 96969 111 + 1
AUGUCG--------UUGCCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
((((((--------.(((....))).)).))))...........(((((.(((..(....)..))).)))))...((((((((((((((((..((....))..)))))))))))))))) ( -29.30)
>DroGri_CAF1 155834 105 + 1
-----G--------CU-GCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCUGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
-----.--------..-(((.(((((.(((.(((((.....))))))))((.....)).....))))).)))...((((((((((((((((..((....))..)))))))))))))))) ( -27.70)
>DroMoj_CAF1 167835 105 + 1
-----G--------CU-GCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCUGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
-----.--------..-(((.(((((.(((.(((((.....))))))))((.....)).....))))).)))...((((((((((((((((..((....))..)))))))))))))))) ( -27.70)
>DroPer_CAF1 97189 111 + 1
AUGUCG--------UUGCCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
((((((--------.(((....))).)).))))...........(((((.(((..(....)..))).)))))...((((((((((((((((..((....))..)))))))))))))))) ( -29.30)
>consensus
_____G________CU_CCGUCGCAUUGCACAUAAAACAUUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAU
...................(.(((((.(((.(((((.....))))))))((.....)).....))))))......((((((((((((((((..((....))..)))))))))))))))) (-25.85 = -25.85 +  -0.00)

alignment

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secondary structure

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Window 8

Location 18,298,666 – 18,298,785
Length 119
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 91.94
Mean single sequence MFE -18.71
Consensus MFE -15.05
Energy contribution -15.22
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.06
Structure conservation index 0.80
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18298666 119 - 20766785
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACUGCGCAUAAAUAUCUAAAUGAGCAAUAAAAGUGUUUUAUGUGCAAUGCGACGGCGACGAUUCUACGACAU
.((...........((((.((....))......................((((((((((...((..............))...)))))))))).)))).((....)).......))... ( -19.24)
>DroVir_CAF1 151928 105 - 1
AUCACAAUAAAAACCGCUCGCAUACGCACAAUUUUCAUUAUAAUAAAACAGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGC-AG--------C-----
...............((((((((..(((((.............(((((((...........((.....))..........)))))))))))).)))))).))-..--------.----- ( -19.81)
>DroPse_CAF1 96969 111 - 1
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACUGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGGCAA--------CGACAU
..............((((.((....))......................((((((((((..((.....))(((.......))))))))))))).)))).((....--------)).... ( -19.70)
>DroGri_CAF1 155834 105 - 1
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACAGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGC-AG--------C-----
...............((.(((((..(((((.............(((((((...........((.....))..........)))))))))))).)))))..))-..--------.----- ( -16.91)
>DroMoj_CAF1 167835 105 - 1
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACAGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGC-AG--------C-----
...............((.(((((..(((((.............(((((((...........((.....))..........)))))))))))).)))))..))-..--------.----- ( -16.91)
>DroPer_CAF1 97189 111 - 1
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACUGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGGCAA--------CGACAU
..............((((.((....))......................((((((((((..((.....))(((.......))))))))))))).)))).((....--------)).... ( -19.70)
>consensus
AUCACAAUAAAAACCGCACGCAUACGCACAAUUUUCAUUAUAAUAAAACAGCGCAUAAAUAUCUAAAUGAGCAAUAAAAAUGUUUUAUGUGCAAUGCGACGC_AA________C_____
..............((((.((....)).......................(((((((((..((.....))(((.......))))))))))))..))))..................... (-15.05 = -15.22 +   0.17)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,298,705 – 18,298,808
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.88
Mean single sequence MFE -30.58
Consensus MFE -23.57
Energy contribution -23.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.03
Structure conservation index 0.77
SVM decision value 1.30
SVM RNA-class probability 0.939427
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18298705 103 + 20766785
CUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCAUCGAGGC-CA-ACGAAAGA---------------GU
(((((..(((.(((..(....)..))).)))((...((((((((((((((((..((....))..)))))))))))))))).))........-..-..))))).---------------.. ( -27.50)
>DroVir_CAF1 151953 101 + 1
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCUGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGAGCGGUUUUUAUUGUGAUUGCAGUGGACU-CCAAGAUCAA------------------
.................(((.....(.((((((...(((((((((((((((((.((....)).))))))))))))))))).)))))).)..-.....)))..------------------ ( -26.80)
>DroPse_CAF1 97000 115 + 1
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCAUUGAGGC-CA-AG---AGCGCAGAGAGAAGGAGAGA
.........(((.(((.....(((.(((((.((...((((((((((((((((..((....))..)))))))))))))))).)).(((....-))-).---.))))).))).))))))... ( -32.40)
>DroMoj_CAF1 167860 104 + 1
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCUGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCACUGGACCACCAACAACAA----------------CA
........((.(((..(....)..))).))(((...((((((((((((((((..((....))..)))))))))))))))).))).(((....))).......----------------.. ( -25.50)
>DroAna_CAF1 101098 119 + 1
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCAUUGAGGC-CAAACGAAAGGCCAGAGAAAGUGUGCGU
........................(((((((.((((((((((((((((((((..((....))..))))))))))))))))........(((-(........))))...)))).))))))) ( -38.90)
>DroPer_CAF1 97220 115 + 1
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCAUUGAGGC-CA-AG---AGCGCAGAGAGAAGGAGAGA
.........(((.(((.....(((.(((((.((...((((((((((((((((..((....))..)))))))))))))))).)).(((....-))-).---.))))).))).))))))... ( -32.40)
>consensus
UUUUUAUUGCUCAUUUAGAUAUUUAUGCGCAGUUUUAUUAUAAUGAAAAUUGUGCGUAUGCGUGCGGUUUUUAUUGUGAUUGCAUUGAGGC_CA_AC_A_AG________________GA
........((.(((..(....)..))).)).((...((((((((((((((((..((....))..)))))))))))))))).))..................................... (-23.57 = -23.57 +  -0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:04 2006