Locus 1647

Sequence ID 3R_DroMel_CAF1
Location 4,781,371 – 4,781,565
Length 194
Max. P 0.756349
window2716 window2717 window2718

overview

Window 6

Location 4,781,371 – 4,781,485
Length 114
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 85.90
Mean single sequence MFE -22.49
Consensus MFE -15.60
Energy contribution -15.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.69
SVM decision value 0.49
SVM RNA-class probability 0.756349
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4781371 114 + 27905053
CAUACUUCCGCGAUCGGCAAAGCCCGAACG-UUUUUGCCGAAGCCCGGCUUCGCUGUUUCCCCCUCUCUU-CACUAAGCGUCUCU--CUUUUUCUCUUGAAACUCCCUCUCUCGCUCU
.........((((((((((((((......)-.))))))))).....((...((((...............-.....)))).....--...((((....))))...))....))))... ( -20.55)
>DroSec_CAF1 16763 116 + 1
CAUACUUCCGCGAUCGGCAAAGCCCGAACG-CUUUUGACGAAGCCCGGCUUCGCUGUUUCCCCCACUCUC-CACUGAGCCUCUCUCUCUUCUUCUCUUGGAACUCCCUCUCUCGCUCU
.........((((.((((.(((((.(...(-((((....)))))).))))).))))............((-((..(((...............))).))))..........))))... ( -24.26)
>DroSim_CAF1 12263 116 + 1
CAUACUUCCGCGAUCGGCAAAGCCCGAACG-CUUUUGCCGAAGCCCGGCUUCGCUGUUUCCCCCACUCUC-CACUAAGCCUCUCUUUCUACUUCUCUUGGAACUCCCUCUCUCGCUCU
.....((((((..((((((((((......)-).)))))))).))..(((((.(.((..............-))).)))))..................))))................ ( -23.84)
>DroEre_CAF1 17023 105 + 1
CAUACUUCCGCGAUCGGCAAAACCCGAACGGCAUUUGCCGAAGCCCGGCUUCGCUGUUUCCCCU-CUCUCACU------------CUCUCCCUCUCCUGCAACUCCCUCUCUCGCUCU
.........((((((((......))))(((((....((((.....))))...))))).......-........------------..........................))))... ( -21.30)
>consensus
CAUACUUCCGCGAUCGGCAAAGCCCGAACG_CUUUUGCCGAAGCCCGGCUUCGCUGUUUCCCCCACUCUC_CACUAAGCCUCUCUCUCUUCUUCUCUUGGAACUCCCUCUCUCGCUCU
.........((((((((......)))).........(.((((((...))))))).........................................................))))... (-15.60 = -15.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,781,371 – 4,781,485
Length 114
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 85.90
Mean single sequence MFE -30.75
Consensus MFE -23.24
Energy contribution -23.05
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -1.37
Structure conservation index 0.76
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4781371 114 - 27905053
AGAGCGAGAGAGGGAGUUUCAAGAGAAAAAG--AGAGACGCUUAGUG-AAGAGAGGGGGAAACAGCGAAGCCGGGCUUCGGCAAAAA-CGUUCGGGCUUUGCCGAUCGCGGAAGUAUG
...((((..(.(((.(((((...........--.))))).)))....-.........(....).((((((((..((....)).....-(....))))))))))..))))......... ( -29.10)
>DroSec_CAF1 16763 116 - 1
AGAGCGAGAGAGGGAGUUCCAAGAGAAGAAGAGAGAGAGGCUCAGUG-GAGAGUGGGGGAAACAGCGAAGCCGGGCUUCGUCAAAAG-CGUUCGGGCUUUGCCGAUCGCGGAAGUAUG
..............(.((((............((..(((((((.((.-....((...(....).))...)).))))))).))....(-((.((((......)))).))))))).)... ( -32.00)
>DroSim_CAF1 12263 116 - 1
AGAGCGAGAGAGGGAGUUCCAAGAGAAGUAGAAAGAGAGGCUUAGUG-GAGAGUGGGGGAAACAGCGAAGCCGGGCUUCGGCAAAAG-CGUUCGGGCUUUGCCGAUCGCGGAAGUAUG
...((((.....((....))................((((((..((.-....((...(....).))...))..))))))((((((.(-(......))))))))..))))......... ( -32.90)
>DroEre_CAF1 17023 105 - 1
AGAGCGAGAGAGGGAGUUGCAGGAGAGGGAGAG------------AGUGAGAG-AGGGGAAACAGCGAAGCCGGGCUUCGGCAAAUGCCGUUCGGGUUUUGCCGAUCGCGGAAGUAUG
...((((.....((..((((.............------------..(....)-...(....).))))..)).....((((((((.(((.....)))))))))))))))......... ( -29.00)
>consensus
AGAGCGAGAGAGGGAGUUCCAAGAGAAGAAGAGAGAGAGGCUUAGUG_GAGAGUGGGGGAAACAGCGAAGCCGGGCUUCGGCAAAAG_CGUUCGGGCUUUGCCGAUCGCGGAAGUAUG
...((((..(...............................................(....).((((((((.((...((........)).)).)))))))))..))))......... (-23.24 = -23.05 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,781,449 – 4,781,565
Length 116
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 92.51
Mean single sequence MFE -25.98
Consensus MFE -22.34
Energy contribution -23.28
Covariance contribution 0.94
Combinations/Pair 1.06
Mean z-score -1.61
Structure conservation index 0.86
SVM decision value 0.37
SVM RNA-class probability 0.709349
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4781449 116 + 27905053
UCUCU--CUUUUUCUCUUGAAACUCCCUCUCUCGCUCUGGCAUUGUAAUAAUUGUGGAGUUUUUGGAUGCUCACGCUCAUUCUCAUUACCAACUUUUUGUUGGCACAGUUUCGGGGGA
.....--.....(((((((((((..........((....))...........(((((((......((.((....))))...)))....(((((.....)))))))))))))))))))) ( -28.10)
>DroSec_CAF1 16841 118 + 1
UCUCUCUCUUCUUCUCUUGGAACUCCCUCUCUCGCUCUGCCAUUGUAAUAAUUGUGGAGUUUUUGGAUGCUCACGCUCAUUCUCAUUACCAACUUUUUGUUGGCACAGUUUCGGGGGA
............((((((((((((.........((((..(.((((...)))).)..))))....(((((........)))))......(((((.....)))))...)))))))))))) ( -27.50)
>DroSim_CAF1 12341 117 + 1
UCUCUUUCUACUUCUCUUGGAACUCCCUCUCUCGCUCUGCCAUUGUAAUAAUUGUGGAGUUUUUGGAUGCUCACGCUCAUUCUCAUUACAAACUUUUUGUUGGCACAGUUUCGG-GGA
.....(((((.......))))).(((((.....(((.(((((((((((((((.(((((((........)))).)))..)))...)))))))((.....))))))).)))...))-))) ( -24.90)
>DroEre_CAF1 17095 113 + 1
-----CUCUCCCUCUCCUGCAACUCCCUCUCUCGCUCUGCCAUUGUAAUAAUUGUGGAGUUUUUGGAUGCUCACGCUCAUUCUCAUUACCAACUUUUUGUUGGCACAGUUUCGGUGGA
-----..................................((((((....((((((((((......((.((....))))...)))....(((((.....)))))))))))).)))))). ( -23.40)
>consensus
UCUCUCUCUUCUUCUCUUGGAACUCCCUCUCUCGCUCUGCCAUUGUAAUAAUUGUGGAGUUUUUGGAUGCUCACGCUCAUUCUCAUUACCAACUUUUUGUUGGCACAGUUUCGGGGGA
............((((((((((((.........(((((((.((((...)))).)))))))....(((((........)))))......(((((.....)))))...)))))))))))) (-22.34 = -23.28 +   0.94)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:49 2006