Locus 948

Sequence ID X_DroMel_CAF1
Location 2,663,764 – 2,663,925
Length 161
Max. P 0.822858
window1540 window1541 window1542 window1543

overview

Window 0

Location 2,663,764 – 2,663,863
Length 99
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 81.27
Mean single sequence MFE -18.80
Consensus MFE -16.73
Energy contribution -16.37
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 0.89
SVM decision value 0.22
SVM RNA-class probability 0.641973
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2663764 99 + 22224390
-C----ACGCCGCC--------CCCCG-CCCGCUAAGCCCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU-UUGUUUCUGUGCAACAAACAAGU
-.----..((.((.--------....)-)..))...................((((((((...((((.....))))...((((((((...-..)))))))).....)))))))) ( -17.20)
>DroGri_CAF1 103370 106 + 1
GUAGCUCUGCAUCU--------CGGCUUGAGCCUAAACCCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGU
...((((.((....--------..))..))))....................((((((((.((.(((...(((...((((((....)))))))))....)))))..)))))))) ( -24.10)
>DroSec_CAF1 70099 107 + 1
-C----CCACCACCCCAACCCGCCCCG-CCCGCUAAGCCCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU-UUGUUUCUGUGCAACAAACAAGU
-.----.....................-........................((((((((...((((.....))))...((((((((...-..)))))))).....)))))))) ( -16.10)
>DroEre_CAF1 80855 91 + 1
-U--------------------CCAUA-GCCGCUAAGCCCGAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU-UUGUUUCUGUGCAACAAACAAGU
-.--------------------.((((-(..((.((((..(....)..........((((((((..(((.....)))..)))))))))))-).))..)))))............ ( -17.50)
>DroYak_CAF1 76767 91 + 1
-U--------------------UCAUU-CCCGCUAAGCCCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU-UUGUUUCUGUGCAACAAACAAGU
-.--------------------.....-........................((((((((...((((.....))))...((((((((...-..)))))))).....)))))))) ( -16.10)
>DroMoj_CAF1 128355 101 + 1
-UA--GCUA--UCU--------CUGUUUAAGCCUAAGCUCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAACGCUUUUGUUUCUGUGCAACAAACAAGU
-.(--(((.--...--------((.....))....)))).............((((((((.((.(((...(((...((((((....)))))))))....)))))..)))))))) ( -21.80)
>consensus
_U____C_____C_________CCACU_CCCGCUAAGCCCAAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU_UUGUUUCUGUGCAACAAACAAGU
....................................................((((((((...((((.....))))...(((((((((....))))))))).....)))))))) (-16.73 = -16.37 +  -0.36)

alignment

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secondary structure

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Window 1

Location 2,663,790 – 2,663,892
Length 102
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 79.46
Mean single sequence MFE -22.22
Consensus MFE -16.39
Energy contribution -16.12
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -1.53
Structure conservation index 0.74
SVM decision value 0.69
SVM RNA-class probability 0.822858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2663790 102 + 22224390
AAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCAGAAGCGCU-UUGUUUCUGUGCAACAAACAAGUUUCCCUGCC-----------UCGCUGCCAACUGGCACCUC
............((((((((...((((.....))))...((((((((...-..)))))))).....)))))))).........-----------..(.((((....)))).).. ( -21.60)
>DroVir_CAF1 106084 110 + 1
AAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGUUUCUUUGGGCCCAGAGUCAGUCGCUGCCA-CUGCCAC---
....(((.....((((((((.((.(((...(((...((((((....)))))))))....)))))..)))))))).....)))...(((.(.(((...))).).-)))....--- ( -23.80)
>DroPse_CAF1 109213 83 + 1
AAAACCAUUAACACUUGUUUCUGUCAUUGUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGUUUCCUUUCG-------------------------------
............(((((((..(((...((((((.((((((((....))))....)))))))))))))))))))).........------------------------------- ( -19.60)
>DroGri_CAF1 103402 108 + 1
AAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGUUUUCUUGAGCCCA--GUUCGUCGACGACG-CCGCCCC---
.....((..((.((((((((.((.(((...(((...((((((....)))))))))....)))))..)))))))).))..)).((...--((.((....)))).-..))...--- ( -21.50)
>DroMoj_CAF1 128382 108 + 1
AAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAACGCUUUUGUUUCUGUGCAACAAACAAGUUUCUUUGCGCCCA--GUCAGUGGCUGCCA-CUGCCAC---
............((((((((.((.(((...(((...((((((....)))))))))....)))))..)))))))).............--(.((((((...)))-))).)..--- ( -27.20)
>DroPer_CAF1 126733 83 + 1
AAAACCAUUAACACUUGUUUCUGUCAUUGUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGUUUCCUUUCG-------------------------------
............(((((((..(((...((((((.((((((((....))))....)))))))))))))))))))).........------------------------------- ( -19.60)
>consensus
AAAACCAUUAACACUUGUUUCUGUCAUUUUACAUGAAAAGCGGAAGCGCUUUUGUUUCUGUGCAACAAACAAGUUUCCUUGCG___________UCGCUGCCA_CUGCCAC___
............((((((((...((((.....))))...(((((((((....))))))))).....))))))))........................................ (-16.39 = -16.12 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,663,828 – 2,663,925
Length 97
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 87.85
Mean single sequence MFE -28.72
Consensus MFE -22.30
Energy contribution -23.30
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.47
Structure conservation index 0.78
SVM decision value 0.09
SVM RNA-class probability 0.577864
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2663828 97 + 22224390
AGCAGAAGCGCUUUGUUUCUGUGCAACAAACAAGUUUCCCUGCCUCGCUGCCAACUGGCACCUCGCAACUGGCAACCGGCA-------ACCGGCAACUGGCAAC
.((((((((.....))))))))((........((((.((.((((..(.(((((....((.....))...))))).).))))-------...)).)))).))... ( -28.00)
>DroSec_CAF1 70171 97 + 1
AGCAGAAGCGCUUUGUUUCUGUGCAACAAACAAGUUUCCUUGCCACGCUGCCAACUGGCACCUCGCAACCGGCAACCGGCA-------ACCGGCAACUGGCAAC
.((((((((.....)))))))).................((((((.(.((((.....((.....))..((((...))))..-------...)))).))))))). ( -29.60)
>DroEre_CAF1 80911 104 + 1
AGCAGAAGCGCUUUGUUUCUGUGCAACAAACAAGUUUCCUUGCCUCGCCGCCAACUGGCACCUCGCAACUGGCAACCGGCAACUGGCAACUGGCAACUGGCAAC
.((((((((.....))))))))((........((((.(((((((..((((((....))).....((.....))....)))....)))))..)).)))).))... ( -32.00)
>DroYak_CAF1 76823 90 + 1
AGCAGAAGCGCUUUGUUUCUGUGCAACAAACAAGUUUCCUUGCCUCGCUGCCAACUGGCACCUCGCAACUG--------------GUAACUGGUAACUGGCAAC
.((((((((.....))))))))((.....((.((((.((((((...(.((((....)))).)..))))..)--------------).)))).)).....))... ( -25.30)
>consensus
AGCAGAAGCGCUUUGUUUCUGUGCAACAAACAAGUUUCCUUGCCUCGCUGCCAACUGGCACCUCGCAACUGGCAACCGGCA_______ACCGGCAACUGGCAAC
.((((((((.....))))))))...........(((.(((((((..((((((....))))....))..((((...))))............)))))..)).))) (-22.30 = -23.30 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,663,828 – 2,663,925
Length 97
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 87.85
Mean single sequence MFE -35.82
Consensus MFE -31.77
Energy contribution -33.90
Covariance contribution 2.13
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.89
SVM decision value 0.29
SVM RNA-class probability 0.669481
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2663828 97 - 22224390
GUUGCCAGUUGCCGGU-------UGCCGGUUGCCAGUUGCGAGGUGCCAGUUGGCAGCGAGGCAGGGAAACUUGUUUGUUGCACAGAAACAAAGCGCUUCUGCU
((.((..((.(((((.-------..))))).))..)).))(((((((..(((.((((((((.((((....)))))))))))).....)))...))))))).... ( -37.90)
>DroSec_CAF1 70171 97 - 1
GUUGCCAGUUGCCGGU-------UGCCGGUUGCCGGUUGCGAGGUGCCAGUUGGCAGCGUGGCAAGGAAACUUGUUUGUUGCACAGAAACAAAGCGCUUCUGCU
((.(((.((.(((((.-------..))))).)).))).))(((((((..(((.((((((.((((((....)))))))))))).....)))...))))))).... ( -41.30)
>DroEre_CAF1 80911 104 - 1
GUUGCCAGUUGCCAGUUGCCAGUUGCCGGUUGCCAGUUGCGAGGUGCCAGUUGGCGGCGAGGCAAGGAAACUUGUUUGUUGCACAGAAACAAAGCGCUUCUGCU
((.((..((.(((.((........)).))).))..)).))(((((((..(((.((((((((.((((....)))))))))))).....)))...))))))).... ( -34.70)
>DroYak_CAF1 76823 90 - 1
GUUGCCAGUUACCAGUUAC--------------CAGUUGCGAGGUGCCAGUUGGCAGCGAGGCAAGGAAACUUGUUUGUUGCACAGAAACAAAGCGCUUCUGCU
...................--------------.....(((((((((..(((.((((((((.((((....)))))))))))).....)))...))))))).)). ( -29.40)
>consensus
GUUGCCAGUUGCCAGU_______UGCCGGUUGCCAGUUGCGAGGUGCCAGUUGGCAGCGAGGCAAGGAAACUUGUUUGUUGCACAGAAACAAAGCGCUUCUGCU
((.((..((.((((((........)))))).))..)).))(((((((..(((.((((((((.((((....)))))))))))).....)))...))))))).... (-31.77 = -33.90 +   2.13)

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 09:57:54 2006