Locus 5395

Sequence ID 3R_DroMel_CAF1
Location 14,180,904 – 14,181,143
Length 239
Max. P 0.999018
window8785 window8786

overview

Window 5

Location 14,180,904 – 14,181,023
Length 119
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -48.74
Consensus MFE -46.56
Energy contribution -46.92
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -2.03
Structure conservation index 0.96
SVM decision value 3.33
SVM RNA-class probability 0.999018
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14180904 119 + 27905053
GGAGAGGAGCUUAGUUGGUAUAAUCGGCGCCUGACAGGCCAGCGUUUGGUAAUCGAUGGCCGUCGGCUCCACCGGCCGCGCCACUAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((....((((...))))...))))((((((((((..((.((((((..(....)..))))))))....))))))))))..)))))))))..)))......... ( -50.10)
>DroVir_CAF1 61893 119 + 1
GGAGAGGAGCUUAGUUGGUAUAAUGGGCGCAUGACUGGCCAGCGUAUGAUAAUCGAUGGCCGUCGGCUCCACCGGCCGUGCCACAAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((....(((((((..(((.(((((.((.((....)))).))))))))((((.....))))))))).)).....)).)).)))))))))..)))......... ( -50.30)
>DroGri_CAF1 49151 119 + 1
GGAGAGGAGCUUAGUUGGUAUAAUGGGCGCAUUGCUGGCAAGCGUAUUAUAAUCGAUGGCCGUUGGCUCCACGGGCCGCGCCACAAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((....(((((((......(((...((.........))...)))...((((.....))))))))).)).....)).)).)))))))))..)))......... ( -45.80)
>DroWil_CAF1 51519 119 + 1
GGAGAGGAGCUUAGUUGGUAUAAUAGGCGCAUGACUGGCCAGCGUUUGGUAAUCGAUGGCCGUCGGCUCCACGGGCCGUGCCACAAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((......(((((..(((.(((((.((.........)).))))))))((((.....)))))))))........)).)).)))))))))..)))......... ( -49.64)
>DroMoj_CAF1 65411 119 + 1
GGAGAGGAGCUUAGUUGGUAUAAUGGGCGCAUGACUGGCCAGCGUAUUGUAGUCGAUGGCCGUCGGCUCCACGGGCCGAGCCACAAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((....(((((.(..(((.(((((.((.........)).))))))))((((.....))))).))).)).....)).)).)))))))))..)))......... ( -47.70)
>DroPer_CAF1 62310 119 + 1
GGAGAGGAGCUUAGUUGGUAUAAUCGGCGCAUGACUGGCCAGCGUUUGGUAAUCGAUGGCAGUCGGCUCUACCGGCCGCGCCACUAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((...........(((.((....))))).((((((((((...(.((((.(.(((((.....)))))))))))))))))))))..)))))))))..)))......... ( -48.90)
>consensus
GGAGAGGAGCUUAGUUGGUAUAAUGGGCGCAUGACUGGCCAGCGUAUGGUAAUCGAUGGCCGUCGGCUCCACCGGCCGCGCCACAAUCAGACGCACCUGAGCUCCGGUCUGACGAAGAA
(((..(((((((((.((((......(((((..(((.(((((.((.........)).))))))))((((.....)))))))))........)).)).)))))))))..)))......... (-46.56 = -46.92 +   0.36)

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 14,181,023 – 14,181,143
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.83
Mean single sequence MFE -50.12
Consensus MFE -36.51
Energy contribution -35.98
Covariance contribution -0.52
Combinations/Pair 1.37
Mean z-score -2.19
Structure conservation index 0.73
SVM decision value 0.31
SVM RNA-class probability 0.681831
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14181023 120 + 27905053
CUGUUGCCACCUGCUCCGAGCUGAAGCCCCGCAGAUUGACCUCGCCGAUCUGCAGCAGAUGAUCGCCCAGCUGCAGUCGGCCAUCCCGCUCGGCCACGCCCCCGGGCGUUAGGGCCUUGA
.....(((.......((((((.((.(((..((((((((.......)))))))).((((.((......)).))))....)))..))..))))))..(((((....)))))...)))..... ( -45.70)
>DroVir_CAF1 62012 120 + 1
CUGUGGCCACCUGCUCCGAGCUGAAGCCACGUAGAUUUACAUCGCCAAUCUGCAGCAGAUGAUCGCCCACCUGCAAACGCUGAUCACGCUCAGCGACGCCGCCCGGUGUCAGCGCCUUAA
....((((....(((..((((((((((...(((((((.........))))))).((((.((......)).))))....)))..))).)))))))((((((....)))))).).))).... ( -40.00)
>DroGri_CAF1 49270 120 + 1
CUGUGGCCACUUGCUCCGAGCUGAAACCACGCAGAUUCACCUCGCCAAUCUGCAGCAGAUGAUCGCCCAACUGCAGGCGCUGAUCCCGCUCAGCGACGCCGCCCGGCGUCAGCGCCUUAA
..((((......((.....)).....))))(((((((.........))))))).((((.((......)).))))((((((((((.(((....(((....))).))).))))))))))... ( -46.20)
>DroWil_CAF1 51638 120 + 1
CUGUGGCCACUUGCUCCGAGCUAAAGCCACGCAGAUUUACCUCGCCAAUCUGCAGCAGAUGGUCGCCCAUCUGUAGGCGGCCAUCGCGCUCCCCAACACCCCCAGGUGUUAGGGCUUUGA
..(((((.....((.....))....)))))(((((((.........)))))))(((.((((((((((........))))))))))..)))(((.((((((....)))))).)))...... ( -52.00)
>DroAna_CAF1 49506 120 + 1
CUGUGGCCACCUGCUCCGAGCUGAAGCCCCGCAGAUUGACCUCCCCGAUCUGCAGUAGGUGGUCGCCCAGCUGCAGCCUCCCAUCUCGCUCGGCAACGCCGCCCGGCGUUAGGGCCUUGA
....(((((((((((....((....))...((((((((.......)))))))))))))))))))((((.((((.(((..........)))))))((((((....)))))).))))..... ( -56.30)
>DroPer_CAF1 62429 120 + 1
CUGUGGCCACCUGCUCCGAGCUGAAGCCGCGCAGGUUGACCUCUCCGAUCUGCAGGAGGUGGUCGCCUAGCUGGAGGCGUCCGUCCCGCUCGGCGACGCCACCCGGCGUCAAGGCCUUGA
....((((((((((..((.((....)))).)))))).(((((((((........))))).))))(((.(((.((.(((....)))))))).)))((((((....))))))..)))).... ( -60.50)
>consensus
CUGUGGCCACCUGCUCCGAGCUGAAGCCACGCAGAUUGACCUCGCCAAUCUGCAGCAGAUGAUCGCCCAGCUGCAGGCGCCCAUCCCGCUCGGCGACGCCGCCCGGCGUCAGGGCCUUGA
....((((....(((..((((.........(((((((.........))))))).((((.((......)).)))).............)))))))((((((....))))))..)))).... (-36.51 = -35.98 +  -0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:40 2006