Locus 874

Sequence ID X_DroMel_CAF1
Location 2,456,622 – 2,456,755
Length 133
Max. P 0.932194
window1421 window1422

overview

Window 1

Location 2,456,622 – 2,456,718
Length 96
Sequences 4
Columns 108
Reading direction reverse
Mean pairwise identity 55.07
Mean single sequence MFE -25.71
Consensus MFE -13.30
Energy contribution -13.43
Covariance contribution 0.12
Combinations/Pair 1.18
Mean z-score -1.46
Structure conservation index 0.52
SVM decision value 1.22
SVM RNA-class probability 0.932194
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2456622 96 - 22224390
CUCGAAGAGCUGCUCAGCAGCCGAGAGGCACUGCAGCAGGAGCUGGACA------------AGCUUAGAGCCAAGAACAAGUCAAAAAGCAAGGCAGUUAAGUCCGAG
(((((..(((((((..((.(((....))).((...((..(((((.....------------)))))...))..)).............))..)))))))...).)))) ( -31.10)
>DroSim_CAF1 1520 96 - 1
CUCGAAGAGCUGCUCAGCAGCCGGGAGGCACUGCAGCAGGAGCUGGACA------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.((..((..((((((((..(((....))).))).)))))...)).))..------------............................................... ( -17.00)
>DroEre_CAF1 16177 96 - 1
CUCGAAGAACUGCUCAGCAGCCGAGAGGCACUGCAGCAUGAGCUGGACG------------AACUAAAAGCCAAGACCAAGUCAAAAGCCAAGCCAGUUCCGGCUACU
..........(((((((..(((....))).))).))))((.(((.(((.------------...................)))...)))))((((......))))... ( -25.25)
>DroAna_CAF1 15443 105 - 1
UUGGACGAGCUGAUUAGCAGCCGGGAGGCAUUGCAGCAGGAACUGGAAGCCCUGCGCUCGAAAAUGACCGCCAAGAAGAAGCCAAAGGA---GCCGGAAGUGAUUUUG
.....(((((......((((((....)))..))).(((((..........))))))))))(((((.((..((.....(....)...(..---..)))..)).))))). ( -29.50)
>consensus
CUCGAAGAGCUGCUCAGCAGCCGAGAGGCACUGCAGCAGGAGCUGGACA____________AACU_A_AGCCAAGAACAAGUCAAAAG____GCCAGUU__G_CU__G
.........((((((((..(((....))).))).)))))..................................................................... (-13.30 = -13.43 +   0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,456,658 – 2,456,755
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 66.24
Mean single sequence MFE -34.14
Consensus MFE -19.66
Energy contribution -19.92
Covariance contribution 0.26
Combinations/Pair 1.38
Mean z-score -1.36
Structure conservation index 0.58
SVM decision value 0.53
SVM RNA-class probability 0.771361
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2456658 97 - 22224390
ACGGUCCCCGGCGGAGGA---UCAGCAGCGCAAUCAGAUCCUCGAAGAGCUGCUCAGCAGCCGAGAGGCACUGCAGCAGGAGCUGGACA------------AGCUUAGA----GCC----
...((((..(((.(((((---((.............)))))))......((((((((..(((....))).))).)))))..))))))).------------.((.....----)).---- ( -36.92)
>DroSec_CAF1 728 97 - 1
UCAGUCACCGGCGGAGGA---UCAGCAGCGCAAUCAGAUCCUCGAAGAGCUGCUCAGCAGCCGGGAGGCACUGCAGCAGGAGCUGGACA------------AGCUUAGA----GCC----
.......(((((.(((((---((.............)))))))......((((((((..(((....))).))).)))))..)))))...------------.((.....----)).---- ( -36.42)
>DroSim_CAF1 1556 97 - 1
UCAGACACCGGCGGAGGA---UCAGCAGCGCAAUCAGAUCCUCGAAGAGCUGCUCAGCAGCCGGGAGGCACUGCAGCAGGAGCUGGACA------------NNNNNNNN----NNN----
.......(((((.(((((---((.............)))))))......((((((((..(((....))).))).)))))..)))))...------------........----...---- ( -35.92)
>DroEre_CAF1 16213 100 - 1
ACAGUCACCGGCGGAGGAGCUGAAGCAUCACAAUGAAAUCCUCGAAGAACUGCUCAGCAGCCGAGAGGCACUGCAGCAUGAGCUGGACG------------AACUAAAA----GCC----
.......(((((.(((((((....)).((.....))..))))).......(((((((..(((....))).))).))))...)))))...------------........----...---- ( -31.40)
>DroAna_CAF1 15476 109 - 1
GCAGGCACAGGAGCAGGA---ACAGCAGCGUCAACAGUUCUUGGACGAGCUGAUUAGCAGCCGGGAGGCAUUGCAGCAGGAACUGGAAGCCCUGCGCUCGAAAAUGACC----GCC----
...(((.(((((((.(..---((......))...).)))))))..(((((......((((((....)))..))).(((((..........)))))))))).........----)))---- ( -37.20)
>DroPer_CAF1 8284 92 - 1
---------GCAGGCGAA---UC----GCACCAAGAGAUUAUCGAGGAGCUGUUGAGCAGCCGCGAAGCCCUUCAGCAACAGGUCGAUC------------GUCUGAAGUCGAGCAAGGA
---------.(((((((.---((----(.(((..((.....))((((.(((.....((....))..))).)))).......))))))))------------))))).............. ( -27.00)
>consensus
ACAGUCACCGGCGGAGGA___UCAGCAGCGCAAUCAGAUCCUCGAAGAGCUGCUCAGCAGCCGGGAGGCACUGCAGCAGGAGCUGGACA____________AACUGAAA____GCC____
.......(((((.(((((....................)))))......((((((((..(((....))).))).)))))..))))).................................. (-19.66 = -19.92 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:01 2006