Locus 977

Sequence ID 3R_DroMel_CAF1
Location 3,161,314 – 3,161,501
Length 187
Max. P 0.981716
window1573 window1574

overview

Window 3

Location 3,161,314 – 3,161,421
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.67
Mean single sequence MFE -33.04
Consensus MFE -23.15
Energy contribution -22.83
Covariance contribution -0.32
Combinations/Pair 1.05
Mean z-score -2.16
Structure conservation index 0.70
SVM decision value 0.76
SVM RNA-class probability 0.843938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3161314 107 - 27905053
CCUGCAUUUAGGCGCUUCAGAAGUGAUUGCUACUAAACGAAGAAACCAGAAGACC-------GAAGACAGCCAACUUGCAACUGCAAA------GCUGCAAGCUGCAGGCGCCGAGAUGA
....(((((.((((((((((.((((.....)))).....................-------............((((((.((....)------).))))))))).))))))).))))). ( -29.00)
>DroSec_CAF1 9189 106 - 1
CCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGAAGA-ACCAGAAGACU-------GAAGACAGCCAACUCGCAACUGCAAA------GUUGCAAACUGCAGGCGCCGAGAUGA
....(((((.((((((...(((((...................-.......(.((-------(....))).).....((((((....)------)))))..))))).)))))).))))). ( -33.00)
>DroSim_CAF1 11359 107 - 1
CCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGAAGAAACCAGAAGACU-------GAAGACAGCCAACUCGCAACUGCAAA------GCUGCAAACUGCAGGCGCCGAGAUGA
....(((((.((((((...(((((....(((....................(.((-------(....))).).....((....))..)------)).....))))).)))))).))))). ( -29.80)
>DroEre_CAF1 976 92 - 1
CCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAAGCAAAGAAACCAGAAG--------------ACUGCCAACUCGCAACUGCA--------------AACUGCAGGCGCCGAGAUGA
....(((((.(((((...((((((..(((((....))))).(....).....--------------)))))).........((((.--------------....))))))))).))))). ( -32.90)
>DroYak_CAF1 10764 120 - 1
CCUGCAUUUAGGCGCUUUGGCAGUGAUUGCUACCAACCAAAGCAACCAGAAGACUGAAAACUGAAGACUGCCAACUCGCAACUGCAAACUGCAAACUGCAAACUGCAGGCGCCGAGAUGA
....(((((.(((((.((((((((..(((((.........))))).(((....)))..........)))))))).......(((((...(((.....)))...)))))))))).))))). ( -40.50)
>consensus
CCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGAAGAAACCAGAAGACU_______GAAGACAGCCAACUCGCAACUGCAAA______GCUGCAAACUGCAGGCGCCGAGAUGA
....(((((.(((((...((.(((....))).))...................................((......))..(((((.................)))))))))).))))). (-23.15 = -22.83 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,161,381 – 3,161,501
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.75
Mean single sequence MFE -44.28
Consensus MFE -39.10
Energy contribution -39.62
Covariance contribution 0.52
Combinations/Pair 1.12
Mean z-score -1.79
Structure conservation index 0.88
SVM decision value 1.89
SVM RNA-class probability 0.981716
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3161381 120 - 27905053
GAGGUGCUGGCUAGUAAUUAAGGCGACAAACAGUCAGAACGGGGCGUGGCCGGCCAUCUGACAUGUGCGAUGAUGUAUGGCCUGCAUUUAGGCGCUUCAGAAGUGAUUGCUACUAAACGA
(((((((((((((...((((...((....(((((((((...((.((....)).)).)))))).))).)).))))...)))))........))))))))((.(((....))).))...... ( -37.20)
>DroSec_CAF1 9255 120 - 1
GAGGUGCUGGCUAGUAAUUAAGGCGACAAACAGUCAGAACGGGGCGUGGCCAGCCAUCUGGCAUGUGCGAUGAUGUAUGUCCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGA
..(((..(((.(((((((((..(((((.....)))....((((((((.(((((....)))))..(((((..(((....))).)))))....))))))))))..))))))))))))))).. ( -45.90)
>DroSim_CAF1 11426 120 - 1
GAGGUGCUGGCUAGUAAUUAAGGCGACAAACAGUCAGAACGGGGCGUGGCCAGCCAUCUGGCAUGUGCGAUGAUGUAUGGCCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGA
..(((..(((.(((((((((..(((((.....)))....((((((..(((((..(((((.((....)).).))))..))))).((......))))))))))..))))))))))))))).. ( -49.10)
>DroEre_CAF1 1028 120 - 1
GAGGCGCUGGCUAGUAAUUAAGGCGACAAAGAGUCAGAACGGGGCGUGGUCGGCCAUCUGGCAUGUGCGAUGAUGUAUGGCCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAAGCAA
.....(((((.(((((((((..(((((.....)))....((((((..(((((..(((((.((....)).).))))..))))).((......))))))))))..))))))))))).))).. ( -45.80)
>DroYak_CAF1 10844 120 - 1
GAGGUGCUGGCUGGUAAUUAAGGCGACAAAGAGUCAGAACGGGGCGUGGUCGGCCAUCUGGCAUGUGCGAUGAUGUAUGGCCUGCAUUUAGGCGCUUUGGCAGUGAUUGCUACCAACCAA
..(((..(((.(((((((((..(((((.....)))....((((((..(((((..(((((.((....)).).))))..))))).((......))))))))))..))))))))))))))).. ( -43.40)
>consensus
GAGGUGCUGGCUAGUAAUUAAGGCGACAAACAGUCAGAACGGGGCGUGGCCGGCCAUCUGGCAUGUGCGAUGAUGUAUGGCCUGCAUUUAGGCGCUUCGGCAGUGAUUGCUACCAACCGA
..(((..(((.(((((((((..(((((.....)))....((((((..(((((..(((((.((....)).).))))..))))).((......))))))))))..))))))))))))))).. (-39.10 = -39.62 +   0.52)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:16 2006