Locus 971

Sequence ID 2R_DroMel_CAF1
Location 4,116,789 – 4,117,038
Length 249
Max. P 0.956719
window1728 window1729 window1730

overview

Window 8

Location 4,116,789 – 4,116,897
Length 108
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 90.62
Mean single sequence MFE -33.98
Consensus MFE -29.26
Energy contribution -29.52
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.86
SVM decision value 0.65
SVM RNA-class probability 0.810169
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4116789 108 - 20766785
CGCUUCUGGCUGCGAGCAGCUGCGUCAUCGGGCUGCUCAAUUGAAAGCUAUUGUUUAUUGCAUUUGUCACCAGGAAGAUGAAAGAUAUACACAUGCGGGCAGCGCCAA
........(((((((((((((.((....))))))))))........((...(((.((((.(((((..(....)..)))))...)))).)))...))..)))))..... ( -34.90)
>DroSim_CAF1 29863 108 - 1
CGCUUCUGGCUGCGAGCAGCUGCGUCAUCGGGCUGCUCAAUUGAAAGCUAUUGUUUAUUGCAUUUGUCACCAGGAAGAUGAGAGAUAUACAUAUGCGGGCAGCGCCAA
........(((((((((((((.((....))))))))))........((...(((.((((.(((((..(....)..)))))...)))).)))...))..)))))..... ( -35.60)
>DroEre_CAF1 7341 100 - 1
--AUUCUGGCUGCGAGCAGCUGCGUCAUCGGGCUGCUCAAUUAAAAGCUAUUGUUUAUUGCAUUUGUCACCAGGAAAAUGAGAGAUA------UGCGGGCUGCGCCAA
--....((((.((((((((((.((....)))))))))).......((((...((.((((.(((((..(....)..)))))...))))------.)).)))))))))). ( -33.80)
>DroYak_CAF1 13901 100 - 1
--AUUCUGGCUGCGAGCAGCUGCGUCAUCGGGCAGCUCAAUUAAAAGCUAUUGUUUAUUGCAUUUGUCACCAGGAAAAUGGGAGAUA------UGCGGGCAGCACCAA
--......(((((((((.(((.((....))))).))))......((((....)))).((((((.(.((.(((......))))).).)------))))))))))..... ( -31.60)
>consensus
__AUUCUGGCUGCGAGCAGCUGCGUCAUCGGGCUGCUCAAUUAAAAGCUAUUGUUUAUUGCAUUUGUCACCAGGAAAAUGAGAGAUA______UGCGGGCAGCGCCAA
........(((((((((((((.((....))))))))))........((.......((((.(((((..(....)..)))))...)))).......))..)))))..... (-29.26 = -29.52 +   0.25)

alignment

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secondary structure

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Window 9

Location 4,116,897 – 4,117,009
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.30
Mean single sequence MFE -33.17
Consensus MFE -22.03
Energy contribution -23.03
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.38
Structure conservation index 0.66
SVM decision value 0.43
SVM RNA-class probability 0.734648
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4116897 112 + 20766785
AUUCUGGUCUAGACUGGCAUUGCUUGACCCACGGAUUCCCGACUUUGAUAUGGACCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCGGCGGUAUGU--------GCAUAUGUGGCGAAUU
...(..((....))..)..(((((.....((((.((..(((((((((((.(((.((((((.....))))))))))))...))))))))..)).)))--------).......)))))... ( -34.70)
>DroSim_CAF1 29971 120 + 1
ACUCUGGUCUAGACUGGCAUUGCUUGACCCACGGAUUCCCGACUUUGAUAUGGGCCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCGACAGUAUGUAUGUAUAUCCAUAUGUGGCGAAUU
...(..((....))..)..(((((((((...(((....))).(((((((...((((((((.....)))))))).)))))))..)))))...((((((((......))))))))))))... ( -37.80)
>DroYak_CAF1 14001 85 + 1
----UGGUCUAGACUGGCAUUGCUUGACCAACGGAUUCUGCACUUUGAUAUGGGCCGCACUGCAAAUGUGGCUACUCGAAGAAUC-------------------------------CAUU
----(((((.((.(.......))).)))))..(((((((.....((((....(((((((.......)))))))..))))))))))-------------------------------)... ( -27.00)
>consensus
A_UCUGGUCUAGACUGGCAUUGCUUGACCCACGGAUUCCCGACUUUGAUAUGGGCCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCG_C_GUAUGU_________CAUAUGUGGCGAAUU
.....((((.((.(.......))).)))).............(((((((...((((((((.....)))))))).)))))))....................................... (-22.03 = -23.03 +   1.00)

alignment

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secondary structure

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Window 0

Location 4,116,937 – 4,117,038
Length 101
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.73
Mean single sequence MFE -30.47
Consensus MFE -23.02
Energy contribution -23.36
Covariance contribution 0.34
Combinations/Pair 1.12
Mean z-score -1.67
Structure conservation index 0.76
SVM decision value 1.47
SVM RNA-class probability 0.956719
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4116937 101 + 20766785
GACUUUGAUAUGGACCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCGGCGGUAUGU--------GCAUAUGUGGCGAAUUAUGCAAUCGACAUCAGAAUUUGAACGAAU-----------
..(((((((.(((.((((((.....))))))))))))))))..(((((..((((((--------((.......)))...)))))..)))))..................----------- ( -29.50)
>DroSim_CAF1 30011 110 + 1
GACUUUGAUAUGGGCCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCGACAGUAUGUAUGUAUAUCCAUAUGUGGCGAAUUAUGCAAUCGACAUCAGAAGAUGAACGAAUC----------
..(((((((...((((((((.....)))))))).)))))))..(((((...((((((((......))))))))(((.....)))..))))).(((.....))).......---------- ( -33.30)
>DroEre_CAF1 7454 104 + 1
GACUUUGAUAUGAACCGCACUGCAAGUGUGGCUAAUCGAAGAAGUUGGCAGCAUG--------------UGUGGCGUAUUAUGCAGCC--CAUCAAAAGAUGACCUAAUCCGCAUGGCAG
..(((((((.....((((((.....))))))...)))))))......((..((((--------------((.(((((.....)).)))--((((....))))........)))))))).. ( -28.60)
>consensus
GACUUUGAUAUGGACCGCACUGCAAGUGUGGCUAAUCGAAGAAGUCGGCAGUAUGU_________CAUAUGUGGCGAAUUAUGCAAUCGACAUCAGAAGAUGAACGAAUC__________
..(((((((.(((.((((((.....))))))))))))))))..(((((..(((((........................)))))..)))))............................. (-23.02 = -23.36 +   0.34)

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 09:53:05 2006