Locus 800

Sequence ID 2R_DroMel_CAF1
Location 3,801,632 – 3,801,761
Length 129
Max. P 0.999866
window1402 window1403 window1404

overview

Window 2

Location 3,801,632 – 3,801,727
Length 95
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 95.93
Mean single sequence MFE -18.12
Consensus MFE -16.07
Energy contribution -16.10
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.86
Structure conservation index 0.89
SVM decision value 1.49
SVM RNA-class probability 0.958136
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3801632 95 + 20766785
UUUGACCCAAAACCUAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCACCGGCCACAUCCU
................(((........((....)).....((.(((((((.....))))))).))...................)))........ ( -17.50)
>DroSec_CAF1 58037 95 + 1
UUUGACCCAAAACCUAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCGCCGGCCACAUCCU
................(((...((((.((....)).....((.(((((((.....))))))).))..))))((........)).)))........ ( -18.10)
>DroSim_CAF1 71596 95 + 1
UUUGACCCAAAACCUAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCGCCGGCCACAUCCU
................(((...((((.((....)).....((.(((((((.....))))))).))..))))((........)).)))........ ( -18.10)
>DroEre_CAF1 59401 95 + 1
UUUGACCCAAAACCCAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCGCCGGCCACAUCCU
................(((...((((.((....)).....((.(((((((.....))))))).))..))))((........)).)))........ ( -18.10)
>DroYak_CAF1 54988 95 + 1
UUUGACCCAAAACCCAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCGCCGGCCACAUCCU
................(((...((((.((....)).....((.(((((((.....))))))).))..))))((........)).)))........ ( -18.10)
>DroAna_CAF1 55143 95 + 1
UUUGACCCAAAACCUUGCCAAUAAAGACAUUUUUGACAUCAUCCUGCCACAUACACUGGCAGAGCUCCUUCGCCCCACUUUGUCGGCCACAUCCU
................(((.((((((.................((((((.......)))))).((......))....)))))).)))........ ( -18.80)
>consensus
UUUGACCCAAAACCUAGCCAAUAAAGACAUUUUUGACAUCGCCCUGCCACAUCCAGUGGCAGAGUUCCUUUGCCCCACUUCGCCGGCCACAUCCU
................(((........................(((((((.....))))))).((......))...........)))........ (-16.07 = -16.10 +   0.03)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,801,632 – 3,801,727
Length 95
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 95.93
Mean single sequence MFE -32.42
Consensus MFE -30.44
Energy contribution -30.17
Covariance contribution -0.28
Combinations/Pair 1.17
Mean z-score -2.75
Structure conservation index 0.94
SVM decision value 4.30
SVM RNA-class probability 0.999866
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3801632 95 - 20766785
AGGAUGUGGCCGGUGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUAGGUUUUGGGUCAAA
(((((.((((((((((((...((((..(...(((((((((.....))))))))))..))))........)))))))))))).)))))........ ( -36.60)
>DroSec_CAF1 58037 95 - 1
AGGAUGUGGCCGGCGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUAGGUUUUGGGUCAAA
(((((.(((((((..(((...((((..(...(((((((((.....))))))))))..))))........)))..))))))).)))))........ ( -33.20)
>DroSim_CAF1 71596 95 - 1
AGGAUGUGGCCGGCGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUAGGUUUUGGGUCAAA
(((((.(((((((..(((...((((..(...(((((((((.....))))))))))..))))........)))..))))))).)))))........ ( -33.20)
>DroEre_CAF1 59401 95 - 1
AGGAUGUGGCCGGCGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUGGGUUUUGGGUCAAA
..(((.((.(((((.((..((((((...((.(((((((((.....))))))))).....)).....))))))..)).))))).)...).)))... ( -32.10)
>DroYak_CAF1 54988 95 - 1
AGGAUGUGGCCGGCGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUGGGUUUUGGGUCAAA
..(((.((.(((((.((..((((((...((.(((((((((.....))))))))).....)).....))))))..)).))))).)...).)))... ( -32.10)
>DroAna_CAF1 55143 95 - 1
AGGAUGUGGCCGACAAAGUGGGGCGAAGGAGCUCUGCCAGUGUAUGUGGCAGGAUGAUGUCAAAAAUGUCUUUAUUGGCAAGGUUUUGGGUCAAA
......(((((.(((..(..((((......))))..)...)))......((((((..((((((.((.....)).))))))..))))))))))).. ( -27.30)
>consensus
AGGAUGUGGCCGGCGAAGUGGGGCAAAGGAACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUUUAUUGGCUAGGUUUUGGGUCAAA
(((((.(((((((.((((...((((..(...(((((((((.....))))))))))..))))........)))).))))))).)))))........ (-30.44 = -30.17 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,801,655 – 3,801,761
Length 106
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 82.05
Mean single sequence MFE -33.60
Consensus MFE -19.88
Energy contribution -21.52
Covariance contribution 1.64
Combinations/Pair 1.14
Mean z-score -1.97
Structure conservation index 0.59
SVM decision value 0.00
SVM RNA-class probability 0.534988
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3801655 106 - 20766785
GCAAGACGACGCGCAGACAAAAUGUUUGCUAGACAGGAUGUGGCCGGUGAAGUGGGG-CAAAGG---AACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUU
((........))((((((.....)))))).(((((.(((((.(((........((..-(....)---..))(((((((.....)))))))))).))))).....))))). ( -36.70)
>DroPse_CAF1 53945 105 - 1
ACAAGACGACGCGCAGACGAAAUAUUUGUUAGACAGGAAACGG-----GAAGUGGAGUCGAAGGGCGGACACUGCCAUCGAACCGGCUGGAAAGAUGUCAAAAAUGUCUC
...(((((.......(((((.....))))).(((((....)..-----..(((.(..((((..(((((...))))).))))..).))).......)))).....))))). ( -26.50)
>DroEre_CAF1 59424 106 - 1
GCAAGACGACGCGCAGACAAAAUGUUUGCUAGACAGGAUGUGGCCGGCGAAGUGGGG-CAAAGG---AACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUU
..((((((....((((((.....))))))..((((.....((.((.((...)).)).-))....---..(((((((((.....)))))))))...)))).....)))))) ( -38.60)
>DroYak_CAF1 55011 106 - 1
GCAAGACGACGCGCAGACAAAAUGUUUGCUAGACAGGAUGUGGCCGGCGAAGUGGGG-CAAAGG---AACUCUGCCACUGGAUGUGGCAGGGCGAUGUCAAAAAUGUCUU
..((((((....((((((.....))))))..((((.....((.((.((...)).)).-))....---..(((((((((.....)))))))))...)))).....)))))) ( -38.60)
>DroAna_CAF1 55166 106 - 1
GCAAGACGACGCGCAGACAAAAUGUUUGCUAGACAGGAUGUGGCCGACAAAGUGGGG-CGAAGG---AGCUCUGCCAGUGUAUGUGGCAGGAUGAUGUCAAAAAUGUCUU
..((((((....((((((.....))))))..((((..((.(.(((((((..(..(((-(.....---.))))..)...)))...)))).).))..)))).....)))))) ( -34.70)
>DroPer_CAF1 53097 105 - 1
ACAAGACGACGCGCAGACGAAAUAUUUGUUAGACAGGAAACGG-----GAAGUGGAGUCGAAGGGCGGACACUGCCAUCGAACCGGCUGGAAAGAUGUCAAAAAUGUCUC
...(((((.......(((((.....))))).(((((....)..-----..(((.(..((((..(((((...))))).))))..).))).......)))).....))))). ( -26.50)
>consensus
GCAAGACGACGCGCAGACAAAAUGUUUGCUAGACAGGAUGUGGCCGGCGAAGUGGGG_CAAAGG___AACUCUGCCACUGGAUGUGGCAGGACGAUGUCAAAAAUGUCUU
..((((((....((((((.....))))))..((((.......((((....(((((...((.((......)).))))))).....)))).......)))).....)))))) (-19.88 = -21.52 +   1.64)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:44 2006