Locus 5327

Sequence ID 3L_DroMel_CAF1
Location 14,708,987 – 14,709,122
Length 135
Max. P 0.996607
window8420 window8421 window8422

overview

Window 0

Location 14,708,987 – 14,709,085
Length 98
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 69.15
Mean single sequence MFE -32.72
Consensus MFE -17.69
Energy contribution -19.87
Covariance contribution 2.17
Combinations/Pair 1.38
Mean z-score -2.16
Structure conservation index 0.54
SVM decision value 2.04
SVM RNA-class probability 0.986304
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14708987 98 + 23771897
AAGA-------------UUGUACCCAAAUUGGCCAAAGUGCGCAUUUCGU-UCAAGCCCUAUUUUCUGGGCUGGCCAAGUUGCGCU-UUUUGGUCAGCGCAGAAGAAAUGUGG
....-------------...........((((((((((.(((((.((.(.-.((.((((........))))))..).)).))))).-))))))))))((((.......)))). ( -33.80)
>DroPse_CAF1 44060 76 + 1
AAGA-------------UUGUAUCCAAAUUGGCCA-AGUGCGCGUUU-----------------------CCGACCAGCUUGCACCGUUUUGGUUAGCUGAGAAGUCGGCUGG
....-------------......(((((.(((.((-(((...((...-----------------------.))....)))))..))).))))).(((((((....))))))). ( -20.40)
>DroSim_CAF1 14584 98 + 1
AAGA-------------UUGUACCCAAAUUGGCCACAGUGCGCAUUUCGU-UCAAGCCUUAUUAUCUGGGCUGGCCAAGUUGCGCU-UUUUGGUCAGCGCAGAAGAAAUGUGC
...(-------------((((..((.....))..)))))(((((((((((-....)).......((((.((((((((((.......-.)))))))))).)))).))))))))) ( -38.00)
>DroEre_CAF1 14488 109 + 1
CUGAUUUGGUGGCUGAUUUGUACCCGAAUUGGCCGAAGUGCGCGUUUUGU-UCGAGCCUUGUUAUCUG-GCUGGCCAAGUUGCACU--UUUGGCCAGCGCAGAAGAAAUGUGG
.........((((..(((((....)))))..)))).....((((((((((-....)).......((((-((((((((((.......--)))))))))).)))).)))))))). ( -40.80)
>DroYak_CAF1 15190 99 + 1
AAGA-------------UUGUACCCAAAUUGGCCAGAGUGCGCAUUUCGUUUCGAGCCUUAUUAUCUGGGCUGGCCAAGUUGCAGU-UUUUGGUCAGCGCAGAAGAAAUGUGG
...(-------------((.(..((.....))..).))).((((((((((.....)).......((((.((((((((((.......-.)))))))))).)))).)))))))). ( -32.20)
>DroAna_CAF1 15307 84 + 1
AAGA-------------UAGUAUCCAAAUUAGCG-AAGUGCGCACUGGGU-UUGGGCCGUAUAAUUUGGCCUGGCCAAC----------UUGGUCAGCCCAGAAG----GCGC
....-------------.................-....((((.((((((-(.((((((.......))))))((((...----------..)))))))))))...----)))) ( -31.10)
>consensus
AAGA_____________UUGUACCCAAAUUGGCCAAAGUGCGCAUUUCGU_UCGAGCCUUAUUAUCUGGGCUGGCCAAGUUGCACU_UUUUGGUCAGCGCAGAAGAAAUGUGG
........................................((((((((((.....)).......((((.((((((((((.........)))))))))).)))).)))))))). (-17.69 = -19.87 +   2.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,708,987 – 14,709,085
Length 98
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 69.15
Mean single sequence MFE -26.47
Consensus MFE -8.90
Energy contribution -10.93
Covariance contribution 2.03
Combinations/Pair 1.25
Mean z-score -1.90
Structure conservation index 0.34
SVM decision value 0.23
SVM RNA-class probability 0.645441
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14708987 98 - 23771897
CCACAUUUCUUCUGCGCUGACCAAAA-AGCGCAACUUGGCCAGCCCAGAAAAUAGGGCUUGA-ACGAAAUGCGCACUUUGGCCAAUUUGGGUACAA-------------UCUU
(((.........((((((........-))))))..(((((((((((........))))....-.((.....)).....)))))))..)))......-------------.... ( -29.40)
>DroPse_CAF1 44060 76 - 1
CCAGCCGACUUCUCAGCUAACCAAAACGGUGCAAGCUGGUCGG-----------------------AAACGCGCACU-UGGCCAAUUUGGAUACAA-------------UCUU
((((((((.....(((((.(((.....)))...)))))((((.-----------------------...)).))..)-)))).....)))......-------------.... ( -20.50)
>DroSim_CAF1 14584 98 - 1
GCACAUUUCUUCUGCGCUGACCAAAA-AGCGCAACUUGGCCAGCCCAGAUAAUAAGGCUUGA-ACGAAAUGCGCACUGUGGCCAAUUUGGGUACAA-------------UCUU
((.(((((((((((((((........-))))))....((((..............)))).))-).)))))).))..((((.((.....)).)))).-------------.... ( -30.14)
>DroEre_CAF1 14488 109 - 1
CCACAUUUCUUCUGCGCUGGCCAAA--AGUGCAACUUGGCCAGC-CAGAUAACAAGGCUCGA-ACAAAACGCGCACUUCGGCCAAUUCGGGUACAAAUCAGCCACCAAAUCAG
..........((((.(((((((((.--........)))))))))-))))......(((.(((-(............)))))))......(((........))).......... ( -30.80)
>DroYak_CAF1 15190 99 - 1
CCACAUUUCUUCUGCGCUGACCAAAA-ACUGCAACUUGGCCAGCCCAGAUAAUAAGGCUCGAAACGAAAUGCGCACUCUGGCCAAUUUGGGUACAA-------------UCUU
(((.(((...((((.((((.((((..-........)))).)))).))))......((((.((..((.....))...)).))))))).)))......-------------.... ( -23.30)
>DroAna_CAF1 15307 84 - 1
GCGC----CUUCUGGGCUGACCAA----------GUUGGCCAGGCCAAAUUAUACGGCCCAA-ACCCAGUGCGCACUU-CGCUAAUUUGGAUACUA-------------UCUU
((((----((..(((((((.....----------.(((((...)))))......))))))).-....)).))))....-.................-------------.... ( -24.70)
>consensus
CCACAUUUCUUCUGCGCUGACCAAAA_AGUGCAACUUGGCCAGCCCAGAUAAUAAGGCUCGA_ACGAAAUGCGCACUUUGGCCAAUUUGGGUACAA_____________UCUU
..........((((.((((.((((...........)))).)))).)))).......((((((........((........))....))))))..................... ( -8.90 = -10.93 +   2.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,709,007 – 14,709,122
Length 115
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 72.79
Mean single sequence MFE -37.72
Consensus MFE -19.71
Energy contribution -21.60
Covariance contribution 1.89
Combinations/Pair 1.28
Mean z-score -2.72
Structure conservation index 0.52
SVM decision value 2.72
SVM RNA-class probability 0.996607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14709007 115 + 23771897
CAAAGUGCGCAUUUCGU-UCAAGCCCUAUUUUCUGGGCUGGCCAAGUUGCGCU-UUUUGGUCAGCGCAGAAGAAAUGUGGCUGAUUACAUAGAAAUGUGAAUGGAAAACGAGGAAU---G
.......((..((((((-((.(((((..(((((((.((((((((((.......-.)))))))))).)))))))...).))))....((((....))))))))))))..))......---. ( -41.00)
>DroSec_CAF1 14908 93 + 1
CACAGUGC--------------------------GGGCUGGCCAAGUUGCGCU-CUUUGGUCAGCGCAGAAGAAAUGUGCCUGAUUACAUAGAAAUGUGAAUGGAAAACGAGGAAUUGUG
((((((.(--------------------------(.((((((((((.......-.)))))))))).)........(((.((...((((((....))))))..))...)))..).)))))) ( -27.90)
>DroSim_CAF1 14604 118 + 1
CACAGUGCGCAUUUCGU-UCAAGCCUUAUUAUCUGGGCUGGCCAAGUUGCGCU-UUUUGGUCAGCGCAGAAGAAAUGUGCCUGAUUACAUAGAAAUGUGAAUGGAAAACGAGGAAUGGUG
..(((.(((((((((((-....)).......((((.((((((((((.......-.)))))))))).)))).))))))))))))....((((....))))..................... ( -42.40)
>DroEre_CAF1 14521 113 + 1
CGAAGUGCGCGUUUUGU-UCGAGCCUUGUUAUCUG-GCUGGCCAAGUUGCACU--UUUGGCCAGCGCAGAAGAAAUGUGGCCGAUUACAUAGAAAUGUGAAUGGAAAUCGCGGAAU---G
.......((((((((..-(((.(((...((.((((-((((((((((.......--)))))))))).)))).)).....))))))...((((....))))....)))).))))....---. ( -42.00)
>DroYak_CAF1 15210 116 + 1
CAGAGUGCGCAUUUCGUUUCGAGCCUUAUUAUCUGGGCUGGCCAAGUUGCAGU-UUUUGGUCAGCGCAGAAGAAAUGUGGCCGAUUACAUGGAAAUGUGAAUGGAAAACGGGGAAU---G
...........(..(((((((.(((.((((.((((.((((((((((.......-.)))))))))).))))...)))).))))))((((((....))))))......))))..)...---. ( -41.90)
>DroPer_CAF1 44191 91 + 1
CA-AGUGCGCGUUU-----------------------CCGACCAGCUUGCACCGUUUUGGUUAGCUGAGAAGUCGGCUGGCUUGUUA--UGGACGUCCCAAUGGGAAUGGAGGAAA---C
..-.......((((-----------------------((..(((.......((((...((((((((((....))))))))))....)--)))...((((...)))).))).)))))---) ( -31.10)
>consensus
CAAAGUGCGCAUUUCGU_UC_AGCCUUAUUAUCUGGGCUGGCCAAGUUGCACU_UUUUGGUCAGCGCAGAAGAAAUGUGGCUGAUUACAUAGAAAUGUGAAUGGAAAACGAGGAAU___G
...............................((((.((((((((((.........)))))))))).))))......((..(((.((((((....)))))).)))...))........... (-19.71 = -21.60 +   1.89)

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 11:47:25 2006