Locus 2721

Sequence ID 3R_DroMel_CAF1
Location 7,317,808 – 7,318,035
Length 227
Max. P 0.991739
window4413 window4414 window4415 window4416

overview

Window 3

Location 7,317,808 – 7,317,919
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.36
Mean single sequence MFE -44.82
Consensus MFE -43.74
Energy contribution -43.58
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.98
SVM decision value 2.17
SVM RNA-class probability 0.989466
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7317808 111 + 27905053
---------CGGAUACGGGUGCGGAUGUCGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
---------((.((....)).))..(((((((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))))))).. ( -44.00)
>DroSec_CAF1 10682 111 + 1
---------CGGAUACGGGUGCGGAUGUCGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
---------((.((....)).))..(((((((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))))))).. ( -44.00)
>DroSim_CAF1 7713 111 + 1
---------CGGAUACGGGUGCGGAUGUCGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
---------((.((....)).))..(((((((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))))))).. ( -44.00)
>DroEre_CAF1 10770 117 + 1
---CGGAUACGGAUACGGGUGCGGAUGUUGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
---((.(..((....))..).))..(((..((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))..))).. ( -44.90)
>DroYak_CAF1 5259 120 + 1
AUGGGGAUGCGGAUACGGGUGCGGAUGUCGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
....(.((.((....)).)).)...(((((((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))))))).. ( -47.20)
>consensus
_________CGGAUACGGGUGCGGAUGUCGGGGCGGAGCCAUGACUACGCCAAAUGGCAAAACAAACUCGAACUGCGGCUCCGUUUCCGCAUUUCGAGGUUGAGUUGCGGCCCUGACGAA
.........((.((....)).))..(((((((((.(.(((((...........)))))....(((.((((((.(((((........))))).)))))).))).....).))))))))).. (-43.74 = -43.58 +  -0.16)

alignment

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secondary structure

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Window 4

Location 7,317,808 – 7,317,919
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.36
Mean single sequence MFE -38.94
Consensus MFE -38.30
Energy contribution -38.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.19
Structure conservation index 0.98
SVM decision value 0.79
SVM RNA-class probability 0.851063
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7317808 111 - 27905053
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCGACAUCCGCACCCGUAUCCG---------
...(((.((...((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).))))))))).................--------- ( -39.00)
>DroSec_CAF1 10682 111 - 1
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCGACAUCCGCACCCGUAUCCG---------
...(((.((...((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).))))))))).................--------- ( -39.00)
>DroSim_CAF1 7713 111 - 1
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCGACAUCCGCACCCGUAUCCG---------
...(((.((...((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).))))))))).................--------- ( -39.00)
>DroEre_CAF1 10770 117 - 1
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCAACAUCCGCACCCGUAUCCGUAUCCG---
.......(((..((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).))))............))).............--- ( -38.30)
>DroYak_CAF1 5259 120 - 1
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCGACAUCCGCACCCGUAUCCGCAUCCCCAU
...(((.((...((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).)))))))))....((..........))........ ( -39.40)
>consensus
UUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAUGGCUCCGCCCCGACAUCCGCACCCGUAUCCG_________
.......(((..((((..(((.((((((.(((((........))))).)))))).)))..)))).....((((.(((....))).))))............)))................ (-38.30 = -38.30 +   0.00)

alignment

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secondary structure

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Window 5

Location 7,317,839 – 7,317,958
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.49
Mean single sequence MFE -44.56
Consensus MFE -44.20
Energy contribution -44.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.99
SVM decision value 2.29
SVM RNA-class probability 0.991739
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7317839 119 - 27905053
ACUUUCC-CCGUCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
.......-...........((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. ( -44.20)
>DroSec_CAF1 10713 120 - 1
GCUUUCCACCGGCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
(((.......)))......((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. ( -45.10)
>DroSim_CAF1 7744 120 - 1
GCUUUCCACCGGCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
(((.......)))......((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. ( -45.10)
>DroEre_CAF1 10807 119 - 1
GCUUCUC-CCGUCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
.......-...........((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. ( -44.20)
>DroYak_CAF1 5299 119 - 1
GUUUUUC-CCGUCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
.......-...........((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. ( -44.20)
>consensus
GCUUUCC_CCGUCUUUUCCGACUGCAGGCAGGCGGUGCAAUUCGUCAGGGCCGCAACUCAACCUCGAAAUGCGGAAACGGAGCCGCAGUUCGAGUUUGUUUUGCCAUUUGGCGUAGUCAU
...................((((((.(((.(((((......)))))...)))((((..(((.((((((.(((((........))))).)))))).)))..))))........)))))).. (-44.20 = -44.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,317,919 – 7,318,035
Length 116
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 82.85
Mean single sequence MFE -40.56
Consensus MFE -28.12
Energy contribution -28.25
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.67
Structure conservation index 0.69
SVM decision value 0.23
SVM RNA-class probability 0.642235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7317919 116 + 27905053
UUGCACCGCCUGCCUGCAGUCGGAAAAGACGG-GGAAAGUCCGGGA--AAUGCCUGGGAAAGGUCGGGGAAAAACCGGAAAGAGGGGUCGCGGCGGUACACGCGCGUUAAGUGGUGCAG
.((((((((..((((...(((......)))..-......(((((..--..(.(((((......))))).)....))))).....))))((((.((.....))))))....)))))))). ( -42.80)
>DroSec_CAF1 10793 106 + 1
UUGCACCGCCUGCCUGCAGUCGGAAAAGCCGGUGGAAAGCCCGGGA-------------AAGGCCGGGGAAAAACCGGAAAGAGGGGUCGCGGCGGUACACGCGCGUUAAGUGGUGCAG
.(((((((((((((.((..((.......(((((......(((((..-------------....))))).....))))).......))..)))))))...((....))...)))))))). ( -42.04)
>DroSim_CAF1 7824 105 + 1
UUGCACCGCCUGCCUGCAGUCGGAAAAGCCGGUGGAAAGCCCGGGA-------------AA-ACCGAGGAAAAACCGGAAAGUGGGGUCGCGGCGGUACACGCGCGUUAAGUGGUGCAG
.((((((((...((..(..((((.....))(((......(((((..-------------..-.))).))....))).))..)..))..((((.((.....))))))....)))))))). ( -41.30)
>DroYak_CAF1 5379 111 + 1
UUGCACCGCCUGCCUGCAGUCGGAAAAGACGG-GAAAAAC-AG---GAAGAGAC-GGGAAAGGCCG-GGAAAAUGUGGAA-AAGGGGACGCGGCGGUACACGCGCGUUAAGUGGUGCAG
.((((((((((..(..(((((......)))..-.......-..---.......(-((......)))-......))..)..-.))..((((((.((.....))))))))..)))))))). ( -36.10)
>consensus
UUGCACCGCCUGCCUGCAGUCGGAAAAGACGG_GGAAAGCCCGGGA_____________AAGGCCGGGGAAAAACCGGAAAGAGGGGUCGCGGCGGUACACGCGCGUUAAGUGGUGCAG
.((((((((...(((....(((.......)))...............................((((.......)))).....)))..((((.((.....))))))....)))))))). (-28.12 = -28.25 +   0.12)

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 10:43:06 2006