Locus 1430

Sequence ID 3R_DroMel_CAF1
Location 4,137,423 – 4,137,623
Length 200
Max. P 0.963225
window2384 window2385 window2386 window2387

overview

Window 4

Location 4,137,423 – 4,137,543
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -48.54
Consensus MFE -33.51
Energy contribution -34.10
Covariance contribution 0.59
Combinations/Pair 1.30
Mean z-score -1.46
Structure conservation index 0.69
SVM decision value 0.08
SVM RNA-class probability 0.573845
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137423 120 + 27905053
GCUCGACAAUCUGUUGCUUGCCGGCCAGAGCAGCUUCUGCCGCCUUGGCUGCGGCCAGCGCUUUGUCGGCCAGUUGCUGCUUCACCUGGCGGGCAGCUGCCUCGCCAGCCUCUAUCUGGG
...(((......((((((((((((...(((((((..((((((.(..(((.((.....)))))..).))).)))..)))))))...))))))))))))....)))((((.......)))). ( -52.20)
>DroPse_CAF1 7526 120 + 1
GUUCGACGAUUUGCUGUUUUCCUGCAAGAGCAGCCUCUGCGGCGUUGGCUGCAGCCAGGGCCCUAUCGGCCAAUUGUUGUUUCACAUGUCGUGCAGCAGCCUCAGCGGCCGAAAUCUGCG
............((((((((......))))))))....(((((.(((((....))))).)))...((((((....((((((.(((.....))).))))))......)))))).....)). ( -44.00)
>DroSec_CAF1 4191 120 + 1
GCUCGACAAUCUGUUGCUUGCCGGCCAGCGCAGCUUCUGCCGCCUUGGCGGCGGCCAGCGCCUUGUCGGCCAGUUGCUGCUUCACCUGGCGGGCAGCUGCCUCGCCAGCUUCUAUCUGGG
...(((......((((((((((((..(((((((((...(((((....)))))((((.((.....)).)))))))))).)))....))))))))))))....)))((((.......)))). ( -55.00)
>DroEre_CAF1 4685 120 + 1
GCUCUACAAUUUGUUGCUUGCCGGCCAGAGCAGCUUCUGCCGCCUUGGCGGCUGCCUGCGCCUUGUCGGCCAGUUGCUGCUUCACCUGGCGGGCUGCUGCCUCACCAGCCUCCAACUGAG
.(((...........(((((((((...(((((((....(((((....)))))...(((.(((.....))))))..)))))))...))))))))).((((......))))........))) ( -50.20)
>DroYak_CAF1 8039 120 + 1
GCUCCACAAUUUGCUGCUUGCCGGCCAGUGCAGCCUCUGCCGCCUUGGCUGCGGCCUCCGCCUUGUCGGCCAGCUGCUGCUUUACCUGGCGGGCUGCGGCCUCUGCAGCUUCCAACUGGG
...(((......(((((.....((((...(((((((..((((....(((.(((((....(((.....)))..))))).))).....)))))))))))))))...))))).......))). ( -51.22)
>DroAna_CAF1 4019 120 + 1
GCUCCACAAUCUGUUGCUUUCCCGCCAAUGCUGCCUCCGCCGCCUUAGCAGCGGCCUGAGCCUUCUCCGCCAACUGCUGCUUCACCUGGCGGGCAGCAGCCUCUCCUGCCUCCACCUGUG
....((((....(..((......((...(((((((..(((((....((((((((..((.((.......)))).)))))))).....)))))))))))))).......))..)....)))) ( -38.62)
>consensus
GCUCGACAAUCUGUUGCUUGCCGGCCAGAGCAGCCUCUGCCGCCUUGGCUGCGGCCAGCGCCUUGUCGGCCAGUUGCUGCUUCACCUGGCGGGCAGCUGCCUCACCAGCCUCCAUCUGGG
(((.........((((((((((.(((((.((.((....)).)).))))).(((((....(((.....))).....))))).......)))))))))).........)))........... (-33.51 = -34.10 +   0.59)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,137,423 – 4,137,543
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.78
Mean single sequence MFE -52.60
Consensus MFE -31.33
Energy contribution -33.50
Covariance contribution 2.17
Combinations/Pair 1.28
Mean z-score -2.19
Structure conservation index 0.60
SVM decision value 0.29
SVM RNA-class probability 0.671698
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137423 120 - 27905053
CCCAGAUAGAGGCUGGCGAGGCAGCUGCCCGCCAGGUGAAGCAGCAACUGGCCGACAAAGCGCUGGCCGCAGCCAAGGCGGCAGAAGCUGCUCUGGCCGGCAAGCAACAGAUUGUCGAGC
.((((.......((((((.(((....)))))))))((......))..)))).((((((...(((.((((..((((..(((((....)))))..)))))))).)))......))))))... ( -55.30)
>DroPse_CAF1 7526 120 - 1
CGCAGAUUUCGGCCGCUGAGGCUGCUGCACGACAUGUGAAACAACAAUUGGCCGAUAGGGCCCUGGCUGCAGCCAACGCCGCAGAGGCUGCUCUUGCAGGAAAACAGCAAAUCGUCGAAC
.......((((((.((((.((((((.((......(((......)))...((((.....))))...)).))))))....((((((((....))).))).))....)))).....)))))). ( -41.80)
>DroSec_CAF1 4191 120 - 1
CCCAGAUAGAAGCUGGCGAGGCAGCUGCCCGCCAGGUGAAGCAGCAACUGGCCGACAAGGCGCUGGCCGCCGCCAAGGCGGCAGAAGCUGCGCUGGCCGGCAAGCAACAGAUUGUCGAGC
.((((.......((((((.(((....))))))))).....(((((..(((((((.(.....).)))))(((((....)))))))..))))).)))).((((((........))))))... ( -58.50)
>DroEre_CAF1 4685 120 - 1
CUCAGUUGGAGGCUGGUGAGGCAGCAGCCCGCCAGGUGAAGCAGCAACUGGCCGACAAGGCGCAGGCAGCCGCCAAGGCGGCAGAAGCUGCUCUGGCCGGCAAGCAACAAAUUGUAGAGC
....((((...((((((.(((((((.(((.(((((.((......)).)))(((.....))))).))).(((((....)))))....))))).)).))))))...))))............ ( -56.70)
>DroYak_CAF1 8039 120 - 1
CCCAGUUGGAAGCUGCAGAGGCCGCAGCCCGCCAGGUAAAGCAGCAGCUGGCCGACAAGGCGGAGGCCGCAGCCAAGGCGGCAGAGGCUGCACUGGCCGGCAAGCAGCAAAUUGUGGAGC
(((((((....(((((...((((.....(((((.(((..(((....))).))).....))))).))))((.((((..(((((....)))))..))))..))..))))).))))).))... ( -54.60)
>DroAna_CAF1 4019 120 - 1
CACAGGUGGAGGCAGGAGAGGCUGCUGCCCGCCAGGUGAAGCAGCAGUUGGCGGAGAAGGCUCAGGCCGCUGCUAAGGCGGCGGAGGCAGCAUUGGCGGGAAAGCAACAGAUUGUGGAGC
(((((.((..(((((......))))).((((((((((......)).((((.(.(((....)))...(((((((....))))))).).)))).)))))))).......))..))))).... ( -48.70)
>consensus
CCCAGAUGGAGGCUGGAGAGGCAGCUGCCCGCCAGGUGAAGCAGCAACUGGCCGACAAGGCGCAGGCCGCAGCCAAGGCGGCAGAAGCUGCUCUGGCCGGCAAGCAACAAAUUGUCGAGC
...........((((((.((((((((..(((((..((......))...((((.(....(((....))).).)))).)))))....)))))).)).))))))................... (-31.33 = -33.50 +   2.17)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,137,503 – 4,137,623
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.50
Mean single sequence MFE -42.40
Consensus MFE -20.79
Energy contribution -22.23
Covariance contribution 1.45
Combinations/Pair 1.29
Mean z-score -2.49
Structure conservation index 0.49
SVM decision value 1.55
SVM RNA-class probability 0.963225
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137503 120 + 27905053
UUCACCUGGCGGGCAGCUGCCUCGCCAGCCUCUAUCUGGGCAUCGGAUGCCUCCAUGGCUUCCUUGGCCGCCUUCUGCGCAAUGCAUGAGGCCUUUACCCUGGUCUUUCCAUUCAUCUUG
.....(((((((((....))).))))))..........(((...(((.(((.....))).)))...)))(((((.(((.....))).)))))........(((.....)))......... ( -43.60)
>DroPse_CAF1 7606 120 + 1
UUCACAUGUCGUGCAGCAGCCUCAGCGGCCGAAAUCUGCGAAUCAGAGGCAUCUUUAGCCUCCUGUGCGGCUUUCUGUGCUAUGUUGGAGGUUUUCUGCUUGCCAACACCAGACAUAUUG
.....((((((..(((.((((.((((((.......))))....(((((((.......)))).))))).))))..)))..)..((((((((((.....)))).))))))...))))).... ( -41.20)
>DroSec_CAF1 4271 120 + 1
UUCACCUGGCGGGCAGCUGCCUCGCCAGCUUCUAUCUGGGCAUCGGAGGCCUCCUUGGCUUCCUUGGCCGCCUUCUGGGCAAUGUUGGAGGCCUUUCCCCUACUCUUUCCACUCACCUUG
.....(((((((((....))).)))))).........(((....((((((((((..((((.....))))(((.....)))......)))))))))).))).................... ( -49.10)
>DroEre_CAF1 4765 120 + 1
UUCACCUGGCGGGCUGCUGCCUCACCAGCCUCCAACUGAGCAUCGGAGGCCUCCUUGGCUUCCUUGGCCGCCUUCUGGGCAAUACAGGAGGCCUUCAUCCUAGACUUUCCAUCCAUCUUA
((((..(((.((((((.((...)).)))))))))..))))....(((((((((((.((((.....))))(((.....))).....)))))))))))........................ ( -46.90)
>DroYak_CAF1 8119 120 + 1
UUUACCUGGCGGGCUGCGGCCUCUGCAGCUUCCAACUGGGCAUCGGAUGCGUCCUUGGCUUCCUUGGCCGCCUUCUGGGCAAUGCUGGAGGCCUUCAUCCUAGACUUCCCAUCCAUUUUG
......(((.(((((((((...))))))))))))..((((..(((((((.......(((((((..(((.(((.....)))...))))))))))..)))))..))...))))......... ( -42.60)
>DroAna_CAF1 4099 120 + 1
UUCACCUGGCGGGCAGCAGCCUCUCCUGCCUCCACCUGUGCAUCAGAAGCAUCCUUUGCCUCCUUAGCCGCUUUCUGGGCAAUACACGACGCCUUCAUCUUGCACGAGGCAUCCAUUCUG
......(((.((((((.((...)).)))))))))((((((((...(((((.((..((((((....((...))....)))))).....)).).))))....))))).)))........... ( -31.00)
>consensus
UUCACCUGGCGGGCAGCUGCCUCACCAGCCUCCAUCUGGGCAUCGGAGGCCUCCUUGGCUUCCUUGGCCGCCUUCUGGGCAAUGCAGGAGGCCUUCAUCCUACACUUUCCAUCCAUCUUG
......(((.((((....))).).)))(((((......(((...(((.(((.....))).)))...)))(((.....))).......)))))............................ (-20.79 = -22.23 +   1.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,137,503 – 4,137,623
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.50
Mean single sequence MFE -44.92
Consensus MFE -19.91
Energy contribution -20.88
Covariance contribution 0.98
Combinations/Pair 1.29
Mean z-score -2.16
Structure conservation index 0.44
SVM decision value 0.49
SVM RNA-class probability 0.758046
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137503 120 - 27905053
CAAGAUGAAUGGAAAGACCAGGGUAAAGGCCUCAUGCAUUGCGCAGAAGGCGGCCAAGGAAGCCAUGGAGGCAUCCGAUGCCCAGAUAGAGGCUGGCGAGGCAGCUGCCCGCCAGGUGAA
.........(((.....)))(((((..((((.(.(((.....)))....).))))..(((.(((.....))).)))..))))).........((((((.(((....)))))))))..... ( -47.30)
>DroPse_CAF1 7606 120 - 1
CAAUAUGUCUGGUGUUGGCAAGCAGAAAACCUCCAACAUAGCACAGAAAGCCGCACAGGAGGCUAAAGAUGCCUCUGAUUCGCAGAUUUCGGCCGCUGAGGCUGCUGCACGACAUGUGAA
..((((((((((((((((..((........)))))))))(((...((((.(.((...((((((.......)))))).....)).).))))((((.....))))))).)).)))))))... ( -37.90)
>DroSec_CAF1 4271 120 - 1
CAAGGUGAGUGGAAAGAGUAGGGGAAAGGCCUCCAACAUUGCCCAGAAGGCGGCCAAGGAAGCCAAGGAGGCCUCCGAUGCCCAGAUAGAAGCUGGCGAGGCAGCUGCCCGCCAGGUGAA
.........(((.....(((..(((..(((((((......(((.....)))(((.......)))..))))))))))..))))))........((((((.(((....)))))))))..... ( -47.20)
>DroEre_CAF1 4765 120 - 1
UAAGAUGGAUGGAAAGUCUAGGAUGAAGGCCUCCUGUAUUGCCCAGAAGGCGGCCAAGGAAGCCAAGGAGGCCUCCGAUGCUCAGUUGGAGGCUGGUGAGGCAGCAGCCCGCCAGGUGAA
.....(((((.....))))).......((((((((.....(((.....)))(((.......))).))))))))((((((.....))))))..((((((.(((....)))))))))..... ( -47.90)
>DroYak_CAF1 8119 120 - 1
CAAAAUGGAUGGGAAGUCUAGGAUGAAGGCCUCCAGCAUUGCCCAGAAGGCGGCCAAGGAAGCCAAGGACGCAUCCGAUGCCCAGUUGGAAGCUGCAGAGGCCGCAGCCCGCCAGGUAAA
.....(((.((((...((......)).((((((((((...(((.....)))(((...(((.((.......)).)))...))).........))))..))))))....)))))))...... ( -41.10)
>DroAna_CAF1 4099 120 - 1
CAGAAUGGAUGCCUCGUGCAAGAUGAAGGCGUCGUGUAUUGCCCAGAAAGCGGCUAAGGAGGCAAAGGAUGCUUCUGAUGCACAGGUGGAGGCAGGAGAGGCUGCUGCCCGCCAGGUGAA
.......((((((((((.....))).)))))))(((((((((((.....).)))...(((((((.....)))))))))))))).(((((.(((((......)))))..)))))....... ( -48.10)
>consensus
CAAGAUGGAUGGAAAGUCCAGGAUGAAGGCCUCCAGCAUUGCCCAGAAGGCGGCCAAGGAAGCCAAGGAGGCCUCCGAUGCCCAGAUGGAGGCUGGAGAGGCAGCUGCCCGCCAGGUGAA
........................................((.......))(((...(((.(((.....))).)))...)))........(.((((((.(((....))))))))).)... (-19.91 = -20.88 +   0.98)

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 10:10:26 2006