Locus 5640

Sequence ID 3L_DroMel_CAF1
Location 15,491,476 – 15,491,676
Length 200
Max. P 0.906749
window8911 window8912 window8913 window8914

overview

Window 1

Location 15,491,476 – 15,491,596
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -38.68
Consensus MFE -34.00
Energy contribution -35.12
Covariance contribution 1.12
Combinations/Pair 1.03
Mean z-score -2.25
Structure conservation index 0.88
SVM decision value 1.05
SVM RNA-class probability 0.906749
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15491476 120 + 23771897
UCGCAUUUUCCGGUGAGUGAAUUAAAGUGCAAACUGGUGGCACAACUCAUGGGAAGUGCCACACCGCGAUAGCAAAUGUAAUAAUCUGAACAGGAGUUCUGAUUUGGCAGCAAUGCGAUA
(((((((.((((((...........(((....))).(((((((..((....))..))))))))))).))..((...(((...((((.((((....)))).))))..)))))))))))).. ( -38.70)
>DroSec_CAF1 32696 120 + 1
UCGCAUUUUCCGGUGCGUGAAUUAAAAUGCAAACUGGUGGCACAGCUCAUGGGAAGUGCCACUCCGCGAUAGCAAAUGUAAUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUA
(((((((.((((((((((........)))))....((((((((..((....))..))))))))))).))..((....((((..(((.((((....)))).)))))))..))))))))).. ( -38.70)
>DroSim_CAF1 34722 120 + 1
UCGCAUUUUCCGGUGCGUGAAUUAAAAUGCAAACUGGUGGCACAGCUCAUGGGAAGUGCCACUCCGCGAUAGCAAAUGUAAUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUA
(((((((.((((((((((........)))))....((((((((..((....))..))))))))))).))..((....((((..(((.((((....)))).)))))))..))))))))).. ( -38.70)
>DroYak_CAF1 115096 120 + 1
UCGCAUUUUCCGGUGCGGGAAUUAAAGUGCAAACUGGUGGCACAACUCAUGGGGAGUGCCUCGCCGCGAUAGCAGAUGUAAUAAUCUGAACAGGAGUUCUGAUUUGGCAGCAAUGCGAUA
((((((((((((...))))))......(((......(.(((((..((....))..))))).)(((((....)).........((((.((((....)))).)))).))).))))))))).. ( -38.60)
>consensus
UCGCAUUUUCCGGUGCGUGAAUUAAAAUGCAAACUGGUGGCACAACUCAUGGGAAGUGCCACUCCGCGAUAGCAAAUGUAAUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUA
(((((((.((((((((((........))))).....(((((((..((....))..))))))).))).))..((...(((...((((.((((....)))).))))..)))))))))))).. (-34.00 = -35.12 +   1.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,491,476 – 15,491,596
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -33.78
Consensus MFE -29.15
Energy contribution -29.90
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.86
SVM decision value 0.60
SVM RNA-class probability 0.795527
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15491476 120 - 23771897
UAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAUUACAUUUGCUAUCGCGGUGUGGCACUUCCCAUGAGUUGUGCCACCAGUUUGCACUUUAAUUCACUCACCGGAAAAUGCGA
..(((((((..((((.((((.((((....)))).))))...(((((.((....))))))))))).((((..(((((.((((.........))))........)))))..))))))))))) ( -33.60)
>DroSec_CAF1 32696 120 - 1
UAUCGCAUUGCUGGCAAAUCAGAACUCCUGUUCAGAUUAUUACAUUUGCUAUCGCGGAGUGGCACUUCCCAUGAGCUGUGCCACCAGUUUGCAUUUUAAUUCACGCACCGGAAAAUGCGA
..(((((((.((((..((((.((((....)))).))))...............((((((((((((............)))))))..(....)........)).))).))))..))))))) ( -34.10)
>DroSim_CAF1 34722 120 - 1
UAUCGCAUUGCUGGCAAAUCAGAACUCCUGUUCAGAUUAUUACAUUUGCUAUCGCGGAGUGGCACUUCCCAUGAGCUGUGCCACCAGUUUGCAUUUUAAUUCACGCACCGGAAAAUGCGA
..(((((((.((((..((((.((((....)))).))))...............((((((((((((............)))))))..(....)........)).))).))))..))))))) ( -34.10)
>DroYak_CAF1 115096 120 - 1
UAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAUUACAUCUGCUAUCGCGGCGAGGCACUCCCCAUGAGUUGUGCCACCAGUUUGCACUUUAAUUCCCGCACCGGAAAAUGCGA
..(((((((((((((.((((.((((....)))).)))).........((....)))))).(((((..(......)..)))))........)).......((((......))))))))))) ( -33.30)
>consensus
UAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAUUACAUUUGCUAUCGCGGAGUGGCACUUCCCAUGAGCUGUGCCACCAGUUUGCACUUUAAUUCACGCACCGGAAAAUGCGA
..(((((((.((((..((((.((((....)))).))))........(((....((.(.(((((((............)))))))).))..)))..............))))..))))))) (-29.15 = -29.90 +   0.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,491,556 – 15,491,676
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.39
Mean single sequence MFE -38.88
Consensus MFE -33.71
Energy contribution -34.77
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -2.29
Structure conservation index 0.87
SVM decision value 0.78
SVM RNA-class probability 0.849730
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15491556 120 + 23771897
AUAAUCUGAACAGGAGUUCUGAUUUGGCAGCAAUGCGAUACGACUCUGAUUAUCCAGUUGUGGGCACACAUUGGUCACAAUAAUCUCUAUAGCAGGCGAUACGGAAGUCGUACUGCUGGC
..((((.((((....)))).)))).....((...(((.(((((((((((((..((.((((((((.....((((....))))....)))))))).)).))).))).))))))).)))..)) ( -33.00)
>DroSec_CAF1 32776 120 + 1
AUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUACGACUCUGAUUAUCCAGUUGUGGGCACACAUUGGUCACAAUAAUCUCUAUAGCAGGCGAUACGGAAGUCGCAUUGCUGGC
..((((.((((....)))).)))).((((((((((((((.....(((((((..((.((((((((.....((((....))))....)))))))).)).))).)))).)))))))))))))) ( -42.70)
>DroSim_CAF1 34802 120 + 1
AUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUACGACUCUGAUUAUCCAGUUGUGGGCACACAUUGGUCACAAUAAUGUCUAUAGCAGGCGAUACGGAAGUCGCAUUGCUGGC
..((((.((((....)))).)))).((((((((((((((.....(((((((..((.((((((((((...((((....))))..)))))))))).)).))).)))).)))))))))))))) ( -47.90)
>DroYak_CAF1 115176 120 + 1
AUAAUCUGAACAGGAGUUCUGAUUUGGCAGCAAUGCGAUACGACUCUGAUUAUCCAGUUGCGGGCACACAUUGGUCACAAUAAUCUCUAUGCCAGGCGAUACGGAAGUCGUAUUGGUGGC
..((((.((((....)))).))))..(((....)))(((((((((.......(((.(((((.((((...((((....))))........))))..)))))..))))))))))))...... ( -31.91)
>consensus
AUAAUCUGAACAGGAGUUCUGAUUUGCCAGCAAUGCGAUACGACUCUGAUUAUCCAGUUGUGGGCACACAUUGGUCACAAUAAUCUCUAUAGCAGGCGAUACGGAAGUCGCAUUGCUGGC
..((((.((((....)))).)))).((((((((((((((.....(((((((..((.((((((((.....((((....))))....)))))))).)).))).)))).)))))))))))))) (-33.71 = -34.77 +   1.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,491,556 – 15,491,676
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.39
Mean single sequence MFE -34.30
Consensus MFE -30.16
Energy contribution -30.85
Covariance contribution 0.69
Combinations/Pair 1.07
Mean z-score -1.87
Structure conservation index 0.88
SVM decision value 0.38
SVM RNA-class probability 0.713304
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15491556 120 - 23771897
GCCAGCAGUACGACUUCCGUAUCGCCUGCUAUAGAGAUUAUUGUGACCAAUGUGUGCCCACAACUGGAUAAUCAGAGUCGUAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAU
(.((((((((((((((..(((.....)))......((((((.....(((.((((....))))..))))))))).))))))))).....))))).).((((.((((....)))).)))).. ( -29.70)
>DroSec_CAF1 32776 120 - 1
GCCAGCAAUGCGACUUCCGUAUCGCCUGCUAUAGAGAUUAUUGUGACCAAUGUGUGCCCACAACUGGAUAAUCAGAGUCGUAUCGCAUUGCUGGCAAAUCAGAACUCCUGUUCAGAUUAU
(((((((((((((((...(((.....)))...)).((((((.....(((.((((....))))..))))))))).........))))))))))))).((((.((((....)))).)))).. ( -39.40)
>DroSim_CAF1 34802 120 - 1
GCCAGCAAUGCGACUUCCGUAUCGCCUGCUAUAGACAUUAUUGUGACCAAUGUGUGCCCACAACUGGAUAAUCAGAGUCGUAUCGCAUUGCUGGCAAAUCAGAACUCCUGUUCAGAUUAU
(((((((((((((.....(((.....)))....(((....(((((..((.....))..)))))(((......))).)))...))))))))))))).((((.((((....)))).)))).. ( -40.40)
>DroYak_CAF1 115176 120 - 1
GCCACCAAUACGACUUCCGUAUCGCCUGGCAUAGAGAUUAUUGUGACCAAUGUGUGCCCGCAACUGGAUAAUCAGAGUCGUAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAU
.......(((((((((...((((...((((((((......))))).))).((((....))))....))))....))))))))).(((....)))..((((.((((....)))).)))).. ( -27.70)
>consensus
GCCAGCAAUACGACUUCCGUAUCGCCUGCUAUAGAGAUUAUUGUGACCAAUGUGUGCCCACAACUGGAUAAUCAGAGUCGUAUCGCAUUGCUGCCAAAUCAGAACUCCUGUUCAGAUUAU
(((((((((((((......(((.(((((.(((((......))))).(((.((((....))))..))).....))).)).)))))))))))))))).((((.((((....)))).)))).. (-30.16 = -30.85 +   0.69)

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 11:55:21 2006