Locus 6973

Sequence ID 3L_DroMel_CAF1
Location 18,819,998 – 18,820,121
Length 123
Max. P 0.978499
window11307 window11308 window11309

overview

Window 7

Location 18,819,998 – 18,820,092
Length 94
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 82.44
Mean single sequence MFE -28.65
Consensus MFE -22.86
Energy contribution -22.80
Covariance contribution -0.06
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.80
SVM decision value 1.82
SVM RNA-class probability 0.978499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18819998 94 + 23771897
GCGAGUGC-----AUUUGGAAAGACCUUGUGCUGGUCAGUAAAGAAUGUAGAACCGGCCAAUGGCCAAUGGCCACUGGCCAAUGGGUAUGGCAACAAAA
((...(((-----((((..(..((((.......))))..)...)))))))..((((((((.(((((...))))).)))))....)))...))....... ( -32.50)
>DroSec_CAF1 27521 87 + 1
GCGAGUGG-----AUUUGGAAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA-------UGGCCACUGGCCAAGGGGUAUGGGAACAAAA
((.(((((-----.(((....)))(((((.((((((((((....))))....)))))))))-------.))))))).)).........((....))... ( -27.10)
>DroSim_CAF1 28151 87 + 1
GCGAGUGC-----AUUUGGAAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA-------UGGCCACUGGCCAACGGGUAUGGGAACAAAA
.((...((-----((..((.....))..))))((((((((...((........))((((..-------.)))))))))))).))....((....))... ( -27.60)
>DroAna_CAF1 19819 87 + 1
GCAAGAGGGCUAAAAAUGGAAAGACCUUGUGCUGGUCAGUAAAGGU----AAACUGGCCAA-------UGGCCAUCGGCCG-UGGGUAUGGGAACAAAA
(((.((((.(((....))).....)))).)))((((((((......----..))))))))(-------(((((...)))))-).....((....))... ( -27.40)
>consensus
GCGAGUGC_____AUUUGGAAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA_______UGGCCACUGGCCAAUGGGUAUGGGAACAAAA
.......................((((.....((((((((...((........))(((((........)))))))))))))..)))).((....))... (-22.86 = -22.80 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,819,998 – 18,820,092
Length 94
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 82.44
Mean single sequence MFE -22.50
Consensus MFE -14.96
Energy contribution -15.28
Covariance contribution 0.31
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 0.59
SVM RNA-class probability 0.793499
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18819998 94 - 23771897
UUUUGUUGCCAUACCCAUUGGCCAGUGGCCAUUGGCCAUUGGCCGGUUCUACAUUCUUUACUGACCAGCACAAGGUCUUUCCAAAU-----GCACUCGC
......(((.......((((((((((((((...))))))))))))))...............((((.......)))).........-----)))..... ( -30.30)
>DroSec_CAF1 27521 87 - 1
UUUUGUUCCCAUACCCCUUGGCCAGUGGCCA-------UUGGCCGGUUCUACAGCCUUUACUGACCAGCACAAGGUCUUUCCAAAU-----CCACUCGC
...............(((((((((((((((.-------..))))(((......)))...))))....)).)))))...........-----........ ( -19.30)
>DroSim_CAF1 28151 87 - 1
UUUUGUUCCCAUACCCGUUGGCCAGUGGCCA-------UUGGCCGGUUCUACAGCCUUUACUGACCAGCACAAGGUCUUUCCAAAU-----GCACUCGC
................(((((.((((((((.-------..))))(((......)))...)))).)))))....((.....))....-----........ ( -21.90)
>DroAna_CAF1 19819 87 - 1
UUUUGUUCCCAUACCCA-CGGCCGAUGGCCA-------UUGGCCAGUUU----ACCUUUACUGACCAGCACAAGGUCUUUCCAUUUUUAGCCCUCUUGC
.................-.((((...)))).-------.(((.((((..----......)))).)))(((..(((.((..........)).)))..))) ( -18.50)
>consensus
UUUUGUUCCCAUACCCAUUGGCCAGUGGCCA_______UUGGCCGGUUCUACAGCCUUUACUGACCAGCACAAGGUCUUUCCAAAU_____CCACUCGC
.................((((....((((((........)))))).................((((.......))))...))))............... (-14.96 = -15.28 +   0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,820,012 – 18,820,121
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.18
Mean single sequence MFE -30.48
Consensus MFE -23.98
Energy contribution -24.60
Covariance contribution 0.62
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.79
SVM decision value 0.50
SVM RNA-class probability 0.759958
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18820012 109 + 23771897
AAAGACCUUGUGCUGGUCAGUAAAGAAUGUAGAACCGGCCAAUGGCCAAUGGCCACUGGCCAAUGGGUAUGGCAACAAAAUGGCAUAGUUGAAGGUAAA----ACGCGAG-------CUC
....(((((..((((((((..............((((((((.(((((...))))).)))))....))).((....))...)))).))))..)))))...----.......-------... ( -34.00)
>DroSec_CAF1 27535 102 + 1
AAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA-------UGGCCACUGGCCAAGGGGUAUGGGAACAAAAUGUUAUAGUUGAAGGUAAA----ACGAGAG-------CUC
....(((((....((((((((...((........))((((..-------.)))))))))))).))))).((....))....(((...(((........)----))...))-------).. ( -27.50)
>DroSim_CAF1 28165 102 + 1
AAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA-------UGGCCACUGGCCAACGGGUAUGGGAACAAAAUGGCAUAGUUGAAGGUAAA----ACGAGAG-------CUC
....(((((..((((((((((...(((((......)))))..-------(((((...))))))).....((....))...)))).))))..)))))...----.......-------... ( -28.50)
>DroAna_CAF1 19838 108 + 1
AAAGACCUUGUGCUGGUCAGUAAAGGU----AAACUGGCCAA-------UGGCCAUCGGCCG-UGGGUAUGGGAACAAAAUGGCAAAGUUGACCGUACACUUUACGUAAACAUUUUCCAC
......((..(((((((((((......----..))))))).(-------(((((...)))))-).))))..)).......(((.((((((...((((.....))))..))).))).))). ( -31.90)
>consensus
AAAGACCUUGUGCUGGUCAGUAAAGGCUGUAGAACCGGCCAA_______UGGCCACUGGCCAAUGGGUAUGGGAACAAAAUGGCAUAGUUGAAGGUAAA____ACGAGAG_______CUC
....(((((..((((((((((...((........))(((((........))))))))))))........((....)).........)))..)))))........................ (-23.98 = -24.60 +   0.62)

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 12:34:29 2006