Locus 666

Sequence ID 2R_DroMel_CAF1
Location 3,304,321 – 3,304,512
Length 191
Max. P 0.991073
window1177 window1178 window1179

overview

Window 7

Location 3,304,321 – 3,304,436
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 99.42
Mean single sequence MFE -45.78
Consensus MFE -45.09
Energy contribution -45.42
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 0.98
SVM decision value 0.22
SVM RNA-class probability 0.641470
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3304321 115 - 20766785
GAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAACUGUGGCGCGAUGGACGUGGCGCCGCCCAGAACAUCAUC
(((((((((.(((((..((......(((........))).......))..))))).)))))))))..(((((......(((((((.((....)).))))))))))))........ ( -46.92)
>DroEre_CAF1 388 115 - 1
GAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAACUGUGGCGCGAUGGACGUGGCGCCGCCCAAAACAUCAUC
(((.((((..((((....))))..)).((.((((((((((((((((((((.(((((....)))))..)))))......)))))).).)))...)))))..)).....)))))... ( -43.50)
>DroYak_CAF1 388 115 - 1
GAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAACUGUGGCGCGAUGGACGUGGCGCCGCCCAGAACAUCAUC
(((((((((.(((((..((......(((........))).......))..))))).)))))))))..(((((......(((((((.((....)).))))))))))))........ ( -46.92)
>consensus
GAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAACUGUGGCGCGAUGGACGUGGCGCCGCCCAGAACAUCAUC
(((((((((.(((((..((......(((........))).......))..))))).)))))))))..(((((......(((((((.((....)).))))))))))))........ (-45.09 = -45.42 +   0.33) 

alignment

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secondary structure

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dotplot

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Window 8

Location 3,304,359 – 3,304,474
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 99.42
Mean single sequence MFE -45.33
Consensus MFE -45.33
Energy contribution -45.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.28
Structure conservation index 1.00
SVM decision value 2.25
SVM RNA-class probability 0.991073
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3304359 115 - 20766785
CUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAAC
.((((.....((((...((((((((..(((..((((((.....)))))))))))))))))...(....))))).....)))).(((((.(((((....)))))..)))))..... ( -45.20)
>DroEre_CAF1 426 115 - 1
CUGGCUCCCCUGGCUAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAAC
.((((.....((((...((((((((..(((..((((((.....)))))))))))))))))...(....))))).....)))).(((((.(((((....)))))..)))))..... ( -45.60)
>DroYak_CAF1 426 115 - 1
CUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAAC
.((((.....((((...((((((((..(((..((((((.....)))))))))))))))))...(....))))).....)))).(((((.(((((....)))))..)))))..... ( -45.20)
>consensus
CUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCACUGCCACCCAGAAGACCGUCGACGGUCCCUCUGGCAAAC
.((((.....((((...((((((((..(((..((((((.....)))))))))))))))))...(....))))).....)))).(((((.(((((....)))))..)))))..... (-45.33 = -45.33 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,304,398 – 3,304,512
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 98.83
Mean single sequence MFE -43.45
Consensus MFE -43.10
Energy contribution -43.43
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.94
Structure conservation index 0.99
SVM decision value 2.08
SVM RNA-class probability 0.987501
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3304398 114 - 20766785
UGAAGGUGGUCUCCAACGCCUCGUGCACCACCAACUGCCUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCA
....(((((............(((((((...........(((((.....))))).((((((((..(((..((((((.....)))))))))))))))))...)))))))))))). ( -44.80)
>DroEre_CAF1 465 114 - 1
UGAAGGUGGUCUCCAACGCCUCUUGCACCACCAACUGCCUGGCUCCCCUGGCUAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCA
....((((((.............(((((........(((.((....)).)))...((((((((..(((..((((((.....)))))))))))))))))...))))).)))))). ( -40.74)
>DroYak_CAF1 465 114 - 1
UGAAGGUGGUCUCCAACGCCUCGUGCACCACCAACUGCCUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCA
....(((((............(((((((...........(((((.....))))).((((((((..(((..((((((.....)))))))))))))))))...)))))))))))). ( -44.80)
>consensus
UGAAGGUGGUCUCCAACGCCUCGUGCACCACCAACUGCCUGGCUCCCCUGGCCAAGGUCAUCAAUGACAACUUCGAGAUCGUCGAGGGUCUGAUGACCACCGUGCACGCCACCA
....((((((............((((((........(((.((....)).)))...((((((((..(((..((((((.....)))))))))))))))))...)))))))))))). (-43.10 = -43.43 +   0.33) 

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 09:44:07 2006