Locus 5638

Sequence ID 2R_DroMel_CAF1
Location 17,939,993 – 17,940,289
Length 296
Max. P 0.924854
window9033 window9034 window9035 window9036 window9037

overview

Window 3

Location 17,939,993 – 17,940,091
Length 98
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.04
Mean single sequence MFE -33.80
Consensus MFE -21.01
Energy contribution -21.02
Covariance contribution 0.01
Combinations/Pair 1.13
Mean z-score -1.95
Structure conservation index 0.62
SVM decision value 1.16
SVM RNA-class probability 0.924854
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17939993 98 - 20766785
UGCCAUUAUGGCAGCGGCAGAAGCUAGAUGCUAUU------------------GCUGCAGGGUUCCAUUAGCCGAAAUAUUAUAACAGACUUGCACGUUGCGGGGGCAAAUA----UGGC
(((((((.((((.(((((((.(((.....))).))------------------))))).((...))....)))).)))...........(((((.....)))))))))....----.... ( -32.40)
>DroEre_CAF1 1914 85 - 1
UGCCAUUAUGGCUGCAGCAGGAGC-------------------------------UGCAGGGUUCCAUUAGCCGAAAUAUUAUAACAGACUUGCACGUUGCGGGGGCAAAUA----UGGC
((((.(((((((((((((....))-------------------------------)))))((((.....))))......))))))....(((((.....)))))))))....----.... ( -27.50)
>DroYak_CAF1 1555 120 - 1
UGCCAUUACGGCUGCAGCAGGAGCUAGUUGCUAUUGCUAUUGCUUUUGCUUUUGCUGCAGGGUUCCAUUAGCCGAAAUAUUAUAACAGACUUGCACGUUGCGGGGGCGAAUAUGUAUGGC
.(((....((((((((((((((((.(((.((....))....)))...))))))))))).((...))...)))))...............(((((.....))))))))............. ( -41.50)
>consensus
UGCCAUUAUGGCUGCAGCAGGAGCUAG_UGCUAUU__________________GCUGCAGGGUUCCAUUAGCCGAAAUAUUAUAACAGACUUGCACGUUGCGGGGGCAAAUA____UGGC
(((((((.((((.(((((...................................))))).((...))....)))).)))...........(((((.....)))))))))............ (-21.01 = -21.02 +   0.01)

alignment

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secondary structure

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Window 4

Location 17,940,029 – 17,940,129
Length 100
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 76.83
Mean single sequence MFE -32.40
Consensus MFE -16.40
Energy contribution -17.18
Covariance contribution 0.78
Combinations/Pair 1.05
Mean z-score -2.57
Structure conservation index 0.51
SVM decision value 0.42
SVM RNA-class probability 0.730490
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17940029 100 - 20766785
AAAUAUGAGCAGUGUGAUAUGGGAUACA--CAUAGGUGAUUGCCAUUAUGGCAGCGGCAGAAGCUAGAUGCUAUU------------------GCUGCAGGGUUCCAUUAGCCGAAAUAU
...........(.((...(((((((.((--(....)))..((((.....))))(((((((.(((.....))).))------------------)))))...)))))))..)))....... ( -30.60)
>DroEre_CAF1 1950 88 - 1
AAAUAUGAGCAGUGUGAUAUGGGAUACAC-CAUAGGUGAUUGCCAUUAUGGCUGCAGCAGGAGC-------------------------------UGCAGGGUUCCAUUAGCCGAAAUAU
...........(.((...(((((((...(-(((((((....)))..)))))(((((((....))-------------------------------))))).)))))))..)))....... ( -27.60)
>DroYak_CAF1 1595 120 - 1
AAAUAUGAGCACUGUGAUAUGGGAUAUACACAUAGGUGAUUGCCAUUACGGCUGCAGCAGGAGCUAGUUGCUAUUGCUAUUGCUUUUGCUUUUGCUGCAGGGUUCCAUUAGCCGAAAUAU
......((((.(((((((((((......).))))(((....))).))))))(((((((((((((.(((.((....))....)))...))))))))))))).))))............... ( -39.00)
>consensus
AAAUAUGAGCAGUGUGAUAUGGGAUACAC_CAUAGGUGAUUGCCAUUAUGGCUGCAGCAGGAGCUAG_UGCUAUU__________________GCUGCAGGGUUCCAUUAGCCGAAAUAU
.............((...(((((((.........(((....))).......(((((((...................................))))))).)))))))..))........ (-16.40 = -17.18 +   0.78)

alignment

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secondary structure

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Window 5

Location 17,940,129 – 17,940,249
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -41.00
Consensus MFE -39.04
Energy contribution -39.37
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.57
Structure conservation index 0.95
SVM decision value 0.07
SVM RNA-class probability 0.569112
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17940129 120 - 20766785
CUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAUAUUUGCAACGAGUUUUCAGCUCCGCCGCCGGCAGAACCUC
....((..((((.((.(((....))).))......(((((((....))))))).(((.((((((((..(((((.(((((....))))).....)))))))))))))))).))))..)).. ( -42.30)
>DroEre_CAF1 2038 120 - 1
CUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAUAUUUGCAACGAGUUUUCAGCUCCGCCGCCGGCAGACCGUC
....((((((((.((.(((....))).))......(((((((....))))))).(((.((((((((..(((((.(((((....))))).....)))))))))))))))).))))..)))) ( -41.30)
>DroYak_CAF1 1715 120 - 1
CUGUGGCGCUGCAUGUGUAAAAUUACCGAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAUAUUUGCAACGAGUUUUCACCUCCGCCGCCGGCAGACCGUC
((((((((..((...........(((((((............))))))).....((.(((((..(.(((.(...(((((....)))))).))))..))))))))))))).))))...... ( -39.40)
>consensus
CUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAUAUUUGCAACGAGUUUUCAGCUCCGCCGCCGGCAGACCGUC
((((.((((((...(((((..................)))))..))))))....(((.((((((((..(((((.(((((....))))).....)))))))))))))))).))))...... (-39.04 = -39.37 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,940,169 – 17,940,289
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -32.37
Consensus MFE -30.33
Energy contribution -31.33
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.94
SVM decision value -0.01
SVM RNA-class probability 0.529290
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17940169 120 + 20766785
AUGCAAAUUCCAGUGCCCCACCUGCCUAAUGCACCGAAAUGCAUUUGGAAUUGGGUAAUUUUACACAUGCAGCGCCACAGGCGACAUUCUGGGCUUAAAAAUGCAUUUUGGCUUUUGCAU
(((((((..(((((((((......((.((((((......)))))).))....))))).........(((((..(((.((((......))))))).......))))).))))..))))))) ( -36.40)
>DroEre_CAF1 2078 120 + 1
AUGCAAAUUCCAGUGCCCCACCUGCCUAAUGCACCGAAAUGCAUUUGGAAUUGGGUAAUUUUACACAUGCAGCGCCACAGGCGACAUUCUGGGCUUAAAAAUGCAUUUUGGCUUUUGGAU
........(((((.(((..((((.((.((((((......)))))).))....))))..........(((((..(((.((((......))))))).......)))))...)))..))))). ( -32.10)
>DroYak_CAF1 1755 120 + 1
AUGCAAAUUCCAGUGCCCCACCUGCCUAAUGCACCGAAAUGCAUUUGGAAUUCGGUAAUUUUACACAUGCAGCGCCACAGGCGACAUUCUGGGCUUAAAAAUGCAUUUUGGCUUUUCCAU
.((((.....(((........))).....))))(((((((((((((........(((....))).........(((.((((......)))))))....)))))))))))))......... ( -28.60)
>consensus
AUGCAAAUUCCAGUGCCCCACCUGCCUAAUGCACCGAAAUGCAUUUGGAAUUGGGUAAUUUUACACAUGCAGCGCCACAGGCGACAUUCUGGGCUUAAAAAUGCAUUUUGGCUUUUGCAU
(((((((..(((((((((......((.((((((......)))))).))....))))).........(((((..(((.((((......))))))).......))))).))))..))))))) (-30.33 = -31.33 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,940,169 – 17,940,289
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -36.74
Consensus MFE -34.53
Energy contribution -35.20
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.94
SVM decision value 0.63
SVM RNA-class probability 0.806447
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17940169 120 - 20766785
AUGCAAAAGCCAAAAUGCAUUUUUAAGCCCAGAAUGUCGCCUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAU
(((((((..(((..(((((.......((((((........))).)))..)))))((((.......((((...((.(((((((....))))))).))....)))))))))))..))))))) ( -39.01)
>DroEre_CAF1 2078 120 - 1
AUCCAAAAGCCAAAAUGCAUUUUUAAGCCCAGAAUGUCGCCUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAU
.((((...(((....(((((......((((((........))).))).......))))).......(((...((.(((((((....))))))).))....))))))..))))........ ( -33.82)
>DroYak_CAF1 1755 120 - 1
AUGGAAAAGCCAAAAUGCAUUUUUAAGCCCAGAAUGUCGCCUGUGGCGCUGCAUGUGUAAAAUUACCGAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAU
.(((.....)))..(((((..(((..((((((........))).)))(((.(((.(((..((((((((((............))))))).)))..))).))).)))....)))..))))) ( -37.40)
>consensus
AUGCAAAAGCCAAAAUGCAUUUUUAAGCCCAGAAUGUCGCCUGUGGCGCUGCAUGUGUAAAAUUACCCAAUUCCAAAUGCAUUUCGGUGCAUUAGGCAGGUGGGGCACUGGAAUUUGCAU
(((((((..(((..(((((.......((((((........))).)))..)))))((((....(((((.....((.(((((((....))))))).))..))))).)))))))..))))))) (-34.53 = -35.20 +   0.67)

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 11:50:41 2006