Locus 1033

Sequence ID X_DroMel_CAF1
Location 3,018,855 – 3,019,038
Length 183
Max. P 0.984303
window1673 window1674 window1675 window1676

overview

Window 3

Location 3,018,855 – 3,018,964
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -32.16
Consensus MFE -28.80
Energy contribution -29.08
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -1.40
Structure conservation index 0.90
SVM decision value 0.83
SVM RNA-class probability 0.862584
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3018855 109 + 22224390
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCAAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUA
..(((((((((((...(((((..((((...(((..((((((..(((.((((....))))))).)))))).))).))))..))))).)))))))).)))........... ( -34.00)
>DroSec_CAF1 6531 109 + 1
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUA
..(((((((((((...(((((..((((...(((..((((((..(((.((((....))))))).)))))).))).))))..))))).)))))))).)))........... ( -33.70)
>DroSim_CAF1 6713 109 + 1
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUA
..(((((((((((...(((((..((((...(((..((((((..(((.((((....))))))).)))))).))).))))..))))).)))))))).)))........... ( -33.70)
>DroEre_CAF1 6858 109 + 1
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUACGAAAAGUAGCCAAAGCCAGGCAAAGAAAAAUGUA
..(((((((((((...(((((..(((((..(((..((((((..(((.((((....))))))).)))))).))))))))..))))).)))).)))))))........... ( -33.80)
>DroYak_CAF1 6784 109 + 1
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCGGCAAAAGAUUCGAAAAGUAGCCAAUGCAAGGCAAAGAAAAAUAUA
..((((((((......(((((..((((((((((.....((.......))(((((...))))).)))))).....))))..)))))....)).))))))........... ( -25.60)
>consensus
CCUUGUCUGUUUUCACGUUACACUUUGUUUGCCCAUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUA
..(((((((((((...(((((..((((...(((..((((((..(((.((((....))))))).)))))).))).))))..))))).)))))))).)))........... (-28.80 = -29.08 +   0.28) 

alignment

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secondary structure

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Window 4

Location 3,018,855 – 3,018,964
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 95.14
Mean single sequence MFE -33.94
Consensus MFE -33.06
Energy contribution -32.30
Covariance contribution -0.76
Combinations/Pair 1.14
Mean z-score -1.49
Structure conservation index 0.97
SVM decision value 1.92
SVM RNA-class probability 0.982481
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3018855 109 - 22224390
UACAUUUUUCUUUGCUCCGCUUCGGCUACUUUUUGAACCUUUCGCUGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..(((((.((((....))...........(.(((((((((((((...))))).)).)))))).)...))))))).))))))))..((....))........ ( -34.00)
>DroSec_CAF1 6531 109 - 1
UACAUUUUUCUUUGCUCCGCUUCGGCUACUUUUCGAACCUUUCGCUGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..(((((.((((....)).....((((....(((((((((((((...))))).)).)))))))))).))))))).))))))))..((....))........ ( -35.40)
>DroSim_CAF1 6713 109 - 1
UACAUUUUUCUUUGCUCCGCUUCGGCUACUUUUCGAACCUUUCGCUGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..(((((.((((....)).....((((....(((((((((((((...))))).)).)))))))))).))))))).))))))))..((....))........ ( -35.40)
>DroEre_CAF1 6858 109 - 1
UACAUUUUUCUUUGCCUGGCUUUGGCUACUUUUCGUACCUUUCGCUGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..((((((((((....)))....(((((....((((((((((((...))))).)).)))))))))).))))))).))))))))..((....))........ ( -36.10)
>DroYak_CAF1 6784 109 - 1
UAUAUUUUUCUUUGCCUUGCAUUGGCUACUUUUCGAAUCUUUUGCCGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..(((((((.((....)).....((((..(((..((((((((....))))).)))...))).)))).))))))).))))))))..((....))........ ( -28.80)
>consensus
UACAUUUUUCUUUGCUCCGCUUCGGCUACUUUUCGAACCUUUCGCUGGCAGCACUGCUGCGCAUGCGGAGCGAAUGGGCAAACAAAGUGUAACGUGAAAACAGACAAGG
((((((((..(((((((.((....)).....((((....(((((((((((((...))))).)).)))))))))).))))))).))))))))..((....))........ (-33.06 = -32.30 +  -0.76) 

alignment

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secondary structure

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dotplot

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Window 5

Location 3,018,889 – 3,019,003
Length 114
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 89.25
Mean single sequence MFE -40.72
Consensus MFE -32.22
Energy contribution -32.58
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -2.52
Structure conservation index 0.79
SVM decision value 1.97
SVM RNA-class probability 0.984303
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3018889 114 + 22224390
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCAAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-UUAGGGCUCAUAAUUGUGGCCGCAGUUGGCGG
....(((((((.((((((((...)))))..)))...(((((.....).))))...))))))).............((..(((-...((.(.((....)).).))..)))..)).. ( -41.50)
>DroSec_CAF1 6565 113 + 1
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-UUAGGGCUCAUAAUCG-GGCUGGAGUUGGCGG
....(((((((.((((((((...)))))..)))...(((((.....).))))...))))))).............((..(((-((..(((((......)-)))))))))..)).. ( -44.00)
>DroSim_CAF1 6747 114 + 1
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-CUAGGGCUCAUAAUUGCGGCUGGAGUUGGCGG
....(((((((.((((((((...)))))..)))...(((((.....).))))...))))))).............((..(((-((((.((........))..)))))))..)).. ( -46.00)
>DroEre_CAF1 6892 112 + 1
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUACGAAAAGUAGCCAAAGCCAGGCAAAGAAAAAUGUAGCUGGCUUUUAGGGCUC---AUUGUAGCUAAAGUUGGCGG
....(((.((....)).)))....((((((((...((.(((((...(.(((((((((((((((........)))..))))))))...)))))---.))))).))...)))))))) ( -40.00)
>DroYak_CAF1 6818 114 + 1
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCGGCAAAAGAUUCGAAAAGUAGCCAAUGCAAGGCAAAGAAAAAUAUAGCUAACU-UUAGGGCUCAACAUUGUGGCUAGCGUUGGCGG
....((.(.(((.((((....))))))).))).................((((((((.((.((...........((((....-....))))........)).)).)))))))).. ( -32.11)
>consensus
AUUCGCUCCGCAUGCGCAGCAGUGCUGCCAGCGAAAGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU_UUAGGGCUCAUAAUUGUGGCUGGAGUUGGCGG
....(((((((.((((((((...)))))..)))...(((((.....).))))...))))))).............(((((((.....(((((......).))))..))))))).. (-32.22 = -32.58 +   0.36) 

alignment

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secondary structure

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dotplot

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Window 6

Location 3,018,924 – 3,019,038
Length 114
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 83.48
Mean single sequence MFE -33.19
Consensus MFE -20.54
Energy contribution -20.30
Covariance contribution -0.24
Combinations/Pair 1.28
Mean z-score -1.96
Structure conservation index 0.62
SVM decision value 0.17
SVM RNA-class probability 0.615495
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3018924 114 + 22224390
AGGUUCAAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-UUAGGGCUCAUAAUUGUGGCCGCAGUUGGCGGGAAAUAAGCCAAAAGGAGCAGCGCUGAUGCGCUGC
.((((.........(((((.((((.((((......(((.((((....-....)))))))..))))..))))..)))))........)))).......(((((((....))))))) ( -37.33)
>DroSec_CAF1 6600 112 + 1
AGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-UUAGGGCUCAUAAUCG-GGCUGGAGUUGGCGGGAAAAGAGCCAA-AGAGGCAGCGCCAGCGCGCAGU
.(((((.....((..(((...))).)).............((..(((-((..(((((......)-)))))))))..)).......)))))..-.......((((....))))... ( -32.70)
>DroSim_CAF1 6782 113 + 1
AGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU-CUAGGGCUCAUAAUUGCGGCUGGAGUUGGCGGGAAAAAAGCCAA-AGAGGCAGCGCCAGCGCGCAGC
.(((((.....).))))...(((..((.............((..(((-((((.((........))..)))))))..)).((......(((..-...)))....)).)).)))... ( -34.60)
>DroEre_CAF1 6927 111 + 1
AGGUACGAAAAGUAGCCAAAGCCAGGCAAAGAAAAAUGUAGCUGGCUUUUAGGGCUC---AUUGUAGCUAAAGUUGGCGGGAAAGAAGCCAA-AGGGGCAACGCUGCGGCGCAGA
.(((((.....)).)))(((((((((((........)))..))))))))..(.((((---(.(((.(((....(((((.........)))))-...))).))).)).))).)... ( -33.20)
>DroYak_CAF1 6853 113 + 1
AGAUUCGAAAAGUAGCCAAUGCAAGGCAAAGAAAAAUAUAGCUAACU-UUAGGGCUCAACAUUGUGGCUAGCGUUGGCGGGAAAAAAACCAA-AGGGGCAACGCUGGUGCGCAGC
..............(((.......)))............((((....-....)))).....(((((((((((((((.(((........))..-...).)))))))))).))))). ( -28.10)
>consensus
AGGUUCGAAAAGUAGCCGAAGCGGAGCAAAGAAAAAUGUAGCUGACU_UUAGGGCUCAUAAUUGUGGCUGGAGUUGGCGGGAAAAAAGCCAA_AGGGGCAGCGCUGGCGCGCAGC
.(((((.....).))))...(((..((.............(((((((.....(((((......).))))..))))))).........(((......)))...))...)))..... (-20.54 = -20.30 +  -0.24) 

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 09:59:54 2006