Locus 184

Sequence ID 3L_DroMel_CAF1
Location 539,708 – 539,848
Length 140
Max. P 0.994419
window265 window266 window267

overview

Window 5

Location 539,708 – 539,811
Length 103
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 81.72
Mean single sequence MFE -39.95
Consensus MFE -23.81
Energy contribution -27.00
Covariance contribution 3.19
Combinations/Pair 1.07
Mean z-score -2.15
Structure conservation index 0.60
SVM decision value 0.52
SVM RNA-class probability 0.766764
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 539708 103 + 23771897
GAAAUGUGGAC---------CCCCGCCCUCUCCUCCACCAACCUAUCUGCAAUUUGUGCUGGCGGAAAAGCGGGGAAAAGCGGGAAAAGCCGACGGA-AAGGGCAAACAUUCC
..(((((((..---------..))(((((.((((((.((.........(((.....)))..((......)))))))...((((......))).))))-.)))))..))))).. ( -30.80)
>DroSec_CAF1 13738 112 + 1
GAAAUGUGCCCCCUCCUUCCCCCUGCCCUCCGCUCCACCAGCCCAUCUGCAAUUUGUGCAGGCGGGAAAAUGGGGAAAAGCGGGGAAAGCCGACGGA-AAGGGCAAACAUUCC
(((...(((((..(((.((...((..((.(((((((.(((.(((..(((((.....)))))..)))....))))))...))))))..))..)).)))-..)))))....))). ( -46.00)
>DroSim_CAF1 14647 112 + 1
GAAAUGUGCCCCCUCCUUCCCCCUGCCCUCCGCUCCACCAGCCCAUCUGCAAUUUGUGCAGGCGGGAAAAUGGGGAAAAGCGGGGAAAGCCGACGGA-AAGGGCAAACAUUCC
(((...(((((..(((.((...((..((.(((((((.(((.(((..(((((.....)))))..)))....))))))...))))))..))..)).)))-..)))))....))). ( -46.00)
>DroEre_CAF1 14151 98 + 1
GAAAUGUGGCCCUCCCUC--------------CUCCACCAGCCCUUCUGCAAUUUGUGCAGGCGGAAAAGCGGGG-AAAGCGGGGAAAGCCGGGGGAAAAGGGCAAACAUUCC
..(((((.(((((...((--------------((((.((..((((.(((((.....)))))((......))))))-.....))((....))))))))..)))))..))))).. ( -37.00)
>consensus
GAAAUGUGCCCCCUCCUU__CCCUGCCCUCCGCUCCACCAGCCCAUCUGCAAUUUGUGCAGGCGGAAAAACGGGGAAAAGCGGGGAAAGCCGACGGA_AAGGGCAAACAUUCC
..(((((.............((((((......((((((...(((..(((((.....)))))..)))...))))))....))))))...(((..........)))..))))).. (-23.81 = -27.00 +   3.19)

alignment

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secondary structure

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Window 6

Location 539,708 – 539,811
Length 103
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 81.72
Mean single sequence MFE -49.67
Consensus MFE -29.81
Energy contribution -35.12
Covariance contribution 5.31
Combinations/Pair 1.11
Mean z-score -3.54
Structure conservation index 0.60
SVM decision value 2.48
SVM RNA-class probability 0.994419
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 539708 103 - 23771897
GGAAUGUUUGCCCUU-UCCGUCGGCUUUUCCCGCUUUUCCCCGCUUUUCCGCCAGCACAAAUUGCAGAUAGGUUGGUGGAGGAGAGGGCGGGG---------GUCCACAUUUC
(((((((..((((..-.(((.(((......)))......(((.(((((((((((((...............))))))))))))).))))))))---------))..))))))) ( -40.36)
>DroSec_CAF1 13738 112 - 1
GGAAUGUUUGCCCUU-UCCGUCGGCUUUCCCCGCUUUUCCCCAUUUUCCCGCCUGCACAAAUUGCAGAUGGGCUGGUGGAGCGGAGGGCAGGGGGAAGGAGGGGGCACAUUUC
(((((((..((((((-((((....)((((((((((((((((((((..((((.(((((.....))))).))))..))))).).))))))).))))))))))))))))))))))) ( -58.50)
>DroSim_CAF1 14647 112 - 1
GGAAUGUUUGCCCUU-UCCGUCGGCUUUCCCCGCUUUUCCCCAUUUUCCCGCCUGCACAAAUUGCAGAUGGGCUGGUGGAGCGGAGGGCAGGGGGAAGGAGGGGGCACAUUUC
(((((((..((((((-((((....)((((((((((((((((((((..((((.(((((.....))))).))))..))))).).))))))).))))))))))))))))))))))) ( -58.50)
>DroEre_CAF1 14151 98 - 1
GGAAUGUUUGCCCUUUUCCCCCGGCUUUCCCCGCUUU-CCCCGCUUUUCCGCCUGCACAAAUUGCAGAAGGGCUGGUGGAG--------------GAGGGAGGGCCACAUUUC
(((((((..((((...((((.(((......)))...(-(((((((..(((..(((((.....)))))..)))..))))).)--------------)))))))))).))))))) ( -41.30)
>consensus
GGAAUGUUUGCCCUU_UCCGUCGGCUUUCCCCGCUUUUCCCCACUUUCCCGCCUGCACAAAUUGCAGAUGGGCUGGUGGAGCGGAGGGCAGGG__AAGGAGGGGCCACAUUUC
(((((((..((((((..((...))(((((((((((((((((((((..((((.(((((.....))))).))))..))))).).))))))).))))))))..))))))))))))) (-29.81 = -35.12 +   5.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 539,733 – 539,848
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -32.52
Consensus MFE -28.80
Energy contribution -28.36
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.89
SVM decision value 2.36
SVM RNA-class probability 0.992838
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 539733 115 + 23771897
CCACCAACCUAUCUGCAAUUUGUGCUGGCGGAAA-AGCGGGGAAAAGCGGGAAAAGCCGACGGA-AAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
.......(.((((((((.((((((...((.....-.))(((.....(((((((..(((......-...))).....)))))))......)))...)))))).)))))))).)..... ( -33.90)
>DroSec_CAF1 13772 115 + 1
CCACCAGCCCAUCUGCAAUUUGUGCAGGCGGGAA-AAUGGGGAAAAGCGGGGAAAGCCGACGGA-AAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
..........(((((((.((((((..((((((..-.(((((((...((((......))).)...-..(......).)))))))......)))))))))))).)))))))........ ( -32.30)
>DroSim_CAF1 14681 115 + 1
CCACCAGCCCAUCUGCAAUUUGUGCAGGCGGGAA-AAUGGGGAAAAGCGGGGAAAGCCGACGGA-AAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
..........(((((((.((((((..((((((..-.(((((((...((((......))).)...-..(......).)))))))......)))))))))))).)))))))........ ( -32.30)
>DroEre_CAF1 14171 115 + 1
CCACCAGCCCUUCUGCAAUUUGUGCAGGCGGAAA-AGCGGGG-AAAGCGGGGAAAGCCGGGGGAAAAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
...........((((((.((((((...((.....-.))(((.-...(((((((..(((..........))).....)))))))......)))...)))))).))))))......... ( -30.30)
>DroYak_CAF1 14395 109 + 1
--------CCCUUUGCAAUUUGUGCAGGCGGAAUGGGCGGGGAAAAGCGGGGAAAGCCGGGGGAAAAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
--------((.((((((.....)))))).)).(((((((((.....(((((((..(((..........))).....)))))))......)))))))))................... ( -33.80)
>consensus
CCACCAGCCCAUCUGCAAUUUGUGCAGGCGGAAA_AGCGGGGAAAAGCGGGGAAAGCCGACGGA_AAGGGCAAACAUUCCCGUGUAAAACUCGUCCAUAAAAUGCAGAUAAGAAAAG
...........((((((.((((((..(((((.....(((((((....(((......)))........(......).))))))).......))))))))))).))))))......... (-28.80 = -28.36 +  -0.44)

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 09:35:13 2006