Locus 7534

Sequence ID 2L_DroMel_CAF1
Location 20,917,239 – 20,917,398
Length 159
Max. P 0.983600
window12107 window12108 window12109

overview

Window 7

Location 20,917,239 – 20,917,358
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.93
Mean single sequence MFE -35.34
Consensus MFE -25.62
Energy contribution -27.38
Covariance contribution 1.76
Combinations/Pair 1.03
Mean z-score -1.58
Structure conservation index 0.72
SVM decision value -0.05
SVM RNA-class probability 0.509543
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917239 119 + 22407834
AAUAAAUAUU-CAUCUACUGACCUCAAGUGCCAGCUUCAGAAGGUGCUCGAAACUCGACCGACCCGUCUGGAGCACCAUCCCGUAAAAGACUUUGCUCCACGAUUGGGUCAGUAGUUCGA
..........-...((((((((((...(((...((((((((.((((.(((.....))).).)))..))))))))........(((((....)))))..)))....))))))))))..... ( -38.70)
>DroSec_CAF1 2597 119 + 1
AAUAAGAGUA-CAUCUACUGACCUCAUGUGCCGUCUUCAGAAGGUGCUCGAAACUCGAACGACCCGUUUGGAGCACCAACCCGUAAAAGACUUUGCUCCACGAUUGGGUCAGUAGUUCGA
..........-...((((((((((.(((((............(((((((.((((((....))...)))).))))))).....(((((....)))))..))).)).))))))))))..... ( -37.80)
>DroSim_CAF1 1857 119 + 1
AAUAAAAGUA-CAUCUACUGACCUCAUGUGCCGUCUUCAGAAGGUGCUCGAAACUCGACCGACCCGUCUGGAGCACCAUCCCGUAAAAGACUUUGCUCCACGAUUGGGUCAGUAGUUCGA
..........-...((((((((((...(..((.((....)).))..)(((......(((......)))(((((((...((........))...))))))))))..))))))))))..... ( -36.00)
>DroEre_CAF1 1650 117 + 1
--UAU-UUUACUGUACACUGACCUGGUGGGCCAUCUUCAGAAGGUGCUCGAAACUUGAUCGACCCGUCUGGAACACCAUCCCGUAAAAGACUUUGCUCGCCGAUUGCGUCAGUAGUUCGA
--...-.....((.((((((((.((((.(((....((((((.((.(.((((.......))))))).))))))..........(((((....)))))..))).)))).)))))).)).)). ( -30.10)
>DroYak_CAF1 1653 118 + 1
AAUAA-UCCG-CGUAUACUGACCUGAUGUGCCAUCUUCAGAAGGUGCUCGAAACUGGACCGACCCGUCUGGAGCACCAUCCCGUAAAAGACUUGGCUCCCCGAUUGCGUCAGUAGUUCGA
.....-....-((..(((((((.(((((.((((((((..((.(((((((.(.((.((.....)).)).).))))))).))......))))..)))).)....)))).)))))))...)). ( -34.10)
>consensus
AAUAA_UGUA_CAUCUACUGACCUCAUGUGCCAUCUUCAGAAGGUGCUCGAAACUCGACCGACCCGUCUGGAGCACCAUCCCGUAAAAGACUUUGCUCCACGAUUGGGUCAGUAGUUCGA
..............((((((((((..((((............(((((((.(.((...........)).).))))))).....(((((....)))))..))))...))))))))))..... (-25.62 = -27.38 +   1.76)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,917,239 – 20,917,358
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.93
Mean single sequence MFE -43.48
Consensus MFE -33.70
Energy contribution -34.42
Covariance contribution 0.72
Combinations/Pair 1.14
Mean z-score -2.66
Structure conservation index 0.78
SVM decision value 1.95
SVM RNA-class probability 0.983600
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917239 119 - 22407834
UCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUUCUGAAGCUGGCACUUGAGGUCAGUAGAUG-AAUAUUUAUU
.....(((((((((...((.(((((((..((((......))))..)))))))))(((((..(((.(((((((((....))).)))))))))))))).)))))))))...-.......... ( -44.20)
>DroSec_CAF1 2597 119 - 1
UCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGUUGGUGCUCCAAACGGGUCGUUCGAGUUUCGAGCACCUUCUGAAGACGGCACAUGAGGUCAGUAGAUG-UACUCUUAUU
.....(((((((((...(((((..((...(((((...((((..(((((((.((((.((....))..)))).))))))).))))))))).)).))))))))))))))...-.......... ( -46.50)
>DroSim_CAF1 1857 119 - 1
UCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUUCUGAAGACGGCACAUGAGGUCAGUAGAUG-UACUUUUAUU
.....(((((((((...(((((..((...(((((...(((((.(((((((.((((..(.....)..)))).))))))))))))))))).)).))))))))))))))...-.......... ( -47.90)
>DroEre_CAF1 1650 117 - 1
UCGAACUACUGACGCAAUCGGCGAGCAAAGUCUUUUACGGGAUGGUGUUCCAGACGGGUCGAUCAAGUUUCGAGCACCUUCUGAAGAUGGCCCACCAGGUCAGUGUACAGUAAA-AUA--
......(((((((((.(((((.(.((...(((((...(((((.(((((((.((((..(.....)..)))).))))))))))))))))).)).).)).)))..)))).)))))..-...-- ( -37.40)
>DroYak_CAF1 1653 118 - 1
UCGAACUACUGACGCAAUCGGGGAGCCAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCCAGUUUCGAGCACCUUCUGAAGAUGGCACAUCAGGUCAGUAUACG-CGGA-UUAUU
(((...(((((((......((....))..(((((((.(((((.(((((((.((((.((.....)).)))).)))))))))))))))).))).......)))))))....-))).-..... ( -41.40)
>consensus
UCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUUCUGAAGAUGGCACAUGAGGUCAGUAGAUG_UACA_UUAUU
.....(((((((((...(((....((...(((((...(((((.(((((((.((((..(.....)..)))).))))))))))))))))).))...)))))))))))).............. (-33.70 = -34.42 +   0.72)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,917,278 – 20,917,398
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -45.54
Consensus MFE -37.92
Energy contribution -39.00
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -1.70
Structure conservation index 0.83
SVM decision value 1.01
SVM RNA-class probability 0.900240
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20917278 120 - 22407834
GUUCUGGACGCUGGUACUCUAGUGGAGUUCGGAUCACCAUUCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUU
((((..((((((((....)))))..(((((((((....)))))))))((((((((..((.(((((((..((((......))))..))))))))).))))))))...)))..))))..... ( -50.70)
>DroSec_CAF1 2636 120 - 1
GUUCUGGACGCUGGCACUCUAGUGGAGUUUGGGUCACCAUUCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGUUGGUGCUCCAAACGGGUCGUUCGAGUUUCGAGCACCUU
((((..(((.(..(.((((.....)))))..))))...((((((((....(((((.....(((((((.(..((.....))..)..)))))))...)))))))))))))...))))..... ( -42.90)
>DroSim_CAF1 1896 120 - 1
GUUCUGGACGCUGGCACUCUAGUGGAGUUCGGGUCACCAUUCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUU
((((..((((((((....)))))..(((((((((....)))))))))((((((((..((.(((((((..((((......))))..))))))))).))))))))...)))..))))..... ( -49.20)
>DroEre_CAF1 1687 120 - 1
GUUCUGGACGCUGGCACUCUGGUGGAGUUCGGGUCUCCAUUCGAACUACUGACGCAAUCGGCGAGCAAAGUCUUUUACGGGAUGGUGUUCCAGACGGGUCGAUCAAGUUUCGAGCACCUU
((...(((((((.((......(((.(((((((((....))))))))).....))).....)).)))...))))...)).....(((((((.((((..(.....)..)))).))))))).. ( -37.60)
>DroYak_CAF1 1691 120 - 1
GUUCUGGACGCUGGCACUCUGGUAGAGUUCGGGUCUCCAUUCGAACUACUGACGCAAUCGGGGAGCCAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCCAGUUUCGAGCACCUU
((...((((..((((.((((((((((((((((((....))))))))).))......))))))).)))).))))...)).....(((((((.((((.((.....)).)))).))))))).. ( -47.30)
>consensus
GUUCUGGACGCUGGCACUCUAGUGGAGUUCGGGUCACCAUUCGAACUACUGACCCAAUCGUGGAGCAAAGUCUUUUACGGGAUGGUGCUCCAGACGGGUCGGUCGAGUUUCGAGCACCUU
((((..((((((((....)))))..(((((((((....)))))))))((((((((.....(((((((..((((......))))..)))))))...))))))))...)))..))))..... (-37.92 = -39.00 +   1.08)

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 12:39:10 2006