Locus 1240

Sequence ID 2L_DroMel_CAF1
Location 3,288,413 – 3,288,529
Length 116
Max. P 0.980998
window2030 window2031

overview

Window 0

Location 3,288,413 – 3,288,529
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.14
Mean single sequence MFE -39.22
Consensus MFE -27.74
Energy contribution -29.94
Covariance contribution 2.20
Combinations/Pair 1.11
Mean z-score -2.64
Structure conservation index 0.71
SVM decision value 1.88
SVM RNA-class probability 0.980998
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3288413 116 + 22407834
AAGCCGCAGACAAUCGAACUGAAAAGCAGAUCGACCAUUCAUAACCGGAAACGCACUGCUU----GUGUGCGGUUGUCCAACGGCAGCGGAUGCGAAUGAAAGGAUAGUUCACUUCCGGA
..((((..((((((((.((....((((((...((....)).....((....))..))))))----..)).))))))))...))))..((((.(.((((.........)))).).)))).. ( -38.30)
>DroSec_CAF1 12433 116 + 1
AAGCCGCAGACAAUCGAACUGAAAAGCAGAUCGACCAUUCAUAACCGGAAACGCACUGCUU----GUGUGCGGUUGUCCCACGGCAGCGGAAGCGAAUGAAAGGAUAGUUCACUUCCGGA
..((((..((((((((.((....((((((...((....)).....((....))..))))))----..)).))))))))...))))..((((((.((((.........)))).)))))).. ( -42.40)
>DroSim_CAF1 12798 116 + 1
AAGCCGCAGACAAUCGAACUGAAAAGCAGAUCGACCAUUCAUAACCGGAAACGCACUGCUU----GUGUGCGGUUGUCCAACGGCAGCGGAAGCGAAUGAAAGGAUAGUUCACUUCCGGA
..((((..((((((((.((....((((((...((....)).....((....))..))))))----..)).))))))))...))))..((((((.((((.........)))).)))))).. ( -42.40)
>DroYak_CAF1 12501 116 + 1
AAGCCACAGACAAUCGAACUGAAAAGCAUAUCGCCCAUUCAUAACCGGAAACGCACUGCUU----GUAUGCGGUUGUCCAACGGCAACGGAAGCGAAUGAAAGGAUAGUUCUCUUCCGGA
..(((...((((((((.......(((((....((...(((......)))...))..)))))----.....))))))))....)))..((((((.((((.........)))).)))))).. ( -33.00)
>DroAna_CAF1 26425 107 + 1
AAGCCACAAGCAAUCCGACUGAAUAGCGAGCCAAACAUCCAUAUCCGGAAGUGCGAUGUUUGGCUGUGUGCGGUUGGGCCGGAGCACCGGAAG-------------AGCUCACUUCCCUA
........(((..((((((((....(((((((((((((((((........))).))))))))))).))).))))))))((((....))))...-------------.))).......... ( -40.00)
>consensus
AAGCCGCAGACAAUCGAACUGAAAAGCAGAUCGACCAUUCAUAACCGGAAACGCACUGCUU____GUGUGCGGUUGUCCAACGGCAGCGGAAGCGAAUGAAAGGAUAGUUCACUUCCGGA
..((((..((((((((.((....((((((..((....(((......)))..))..))))))....))...))))))))...))))..((((((.((((.........)))).)))))).. (-27.74 = -29.94 +   2.20)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,288,413 – 3,288,529
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.14
Mean single sequence MFE -37.42
Consensus MFE -25.34
Energy contribution -27.82
Covariance contribution 2.48
Combinations/Pair 1.14
Mean z-score -1.59
Structure conservation index 0.68
SVM decision value -0.03
SVM RNA-class probability 0.519606
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3288413 116 - 22407834
UCCGGAAGUGAACUAUCCUUUCAUUCGCAUCCGCUGCCGUUGGACAACCGCACAC----AAGCAGUGCGUUUCCGGUUAUGAAUGGUCGAUCUGCUUUUCAGUUCGAUUGUCUGCGGCUU
..((((.(((((...........))))).))))..(((((.((((((.((.((..----((((((..((...(((........))).))..))))))....)).)).))))))))))).. ( -36.30)
>DroSec_CAF1 12433 116 - 1
UCCGGAAGUGAACUAUCCUUUCAUUCGCUUCCGCUGCCGUGGGACAACCGCACAC----AAGCAGUGCGUUUCCGGUUAUGAAUGGUCGAUCUGCUUUUCAGUUCGAUUGUCUGCGGCUU
..((((((((((...........))))))))))..((((..(.((((.((.((..----((((((..((...(((........))).))..))))))....)).)).)))))..)))).. ( -40.50)
>DroSim_CAF1 12798 116 - 1
UCCGGAAGUGAACUAUCCUUUCAUUCGCUUCCGCUGCCGUUGGACAACCGCACAC----AAGCAGUGCGUUUCCGGUUAUGAAUGGUCGAUCUGCUUUUCAGUUCGAUUGUCUGCGGCUU
..((((((((((...........))))))))))..(((((.((((((.((.((..----((((((..((...(((........))).))..))))))....)).)).))))))))))).. ( -40.40)
>DroYak_CAF1 12501 116 - 1
UCCGGAAGAGAACUAUCCUUUCAUUCGCUUCCGUUGCCGUUGGACAACCGCAUAC----AAGCAGUGCGUUUCCGGUUAUGAAUGGGCGAUAUGCUUUUCAGUUCGAUUGUCUGUGGCUU
..((((((.(((...........))).))))))..(((...((((((.(((((..----.....)))))....(((...((((.((((.....))))))))..))).))))))..))).. ( -31.10)
>DroAna_CAF1 26425 107 - 1
UAGGGAAGUGAGCU-------------CUUCCGGUGCUCCGGCCCAACCGCACACAGCCAAACAUCGCACUUCCGGAUAUGGAUGUUUGGCUCGCUAUUCAGUCGGAUUGCUUGUGGCUU
..(((..(.((((.-------------(.....).)))))..)))....((.((((((((((((((.((..(....)..))))))))))))..((.((((....)))).)).)))))).. ( -38.80)
>consensus
UCCGGAAGUGAACUAUCCUUUCAUUCGCUUCCGCUGCCGUUGGACAACCGCACAC____AAGCAGUGCGUUUCCGGUUAUGAAUGGUCGAUCUGCUUUUCAGUUCGAUUGUCUGCGGCUU
..((((((((((...........))))))))))..(((((.((((((.((.((......((((((..((...(((........))).))..))))))....)).)).))))))))))).. (-25.34 = -27.82 +   2.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:30 2006