Locus 1260

Sequence ID 3R_DroMel_CAF1
Location 3,776,446 – 3,776,715
Length 269
Max. P 0.961561
window2053 window2054 window2055 window2056 window2057

overview

Window 3

Location 3,776,446 – 3,776,566
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -29.85
Consensus MFE -24.35
Energy contribution -25.60
Covariance contribution 1.25
Combinations/Pair 1.03
Mean z-score -2.11
Structure conservation index 0.82
SVM decision value 0.75
SVM RNA-class probability 0.842106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3776446 120 + 27905053
GCAUUUUCUUGCAGUGCACGGCUUAGUCGUAAGUCGUAAAGAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUUAGCGCUGCAACUCA
........(((((((((((((((((....)))))))).((((.((((.(((.....)))))))....((((......((......))......)))).....)))).))))))))).... ( -34.30)
>DroSec_CAF1 5978 120 + 1
GCAUUUUCUUGCAGUGCAUGGCUUAGUCGUUAGUCGUUAAGAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCCCAGCUCUGCAACUCA
........((((((.((.((((((((.((.....)))))))..((((.(((.....)))))))....((((......((......))...(((....)))))))))))).)))))).... ( -27.70)
>DroSim_CAF1 9615 120 + 1
UCAUUUUCUUGCAGUGCAUGGCUUAGUCGUUAGUCGUUAAGAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUCAGCUCUGCAACUCA
........((((((.((((((((........))))))...((.((((.(((.....)))))))....((((......((......))...(((....))))))))).)).)))))).... ( -26.90)
>DroYak_CAF1 7716 113 + 1
ACAUUUUCUCGCAGUGCACGGCUUAGUCGUAAGUCGUUAAGAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUUAAAGAAACUCAGCUCUGAG-------CGCUGCAACUCA
..........(((((((((((((((....))))))))......((((.(((.....)))))))....((((......((......))......))))...)-------))))))...... ( -30.50)
>consensus
GCAUUUUCUUGCAGUGCACGGCUUAGUCGUAAGUCGUUAAGAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUCAGCGCUGCAACUCA
........(((((((((((((((((....))))))))......((((.(((.....)))))))....((((......((......))......))))..........))))))))).... (-24.35 = -25.60 +   1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,776,486 – 3,776,606
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -32.45
Consensus MFE -29.38
Energy contribution -30.62
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.91
SVM decision value 1.53
SVM RNA-class probability 0.961561
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3776486 120 + 27905053
GAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUUAGCGCUGCAACUCAGCGGCGCGCAGCUCAUUAAAUGCGUCUGCGCAACGUAAUU
...((((.(((.....)))))))....((((......((......))......))))((((((....(((((((......)))))))..)))))).....((((....))))........ ( -36.30)
>DroSec_CAF1 6018 120 + 1
GAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCCCAGCUCUGCAACUCAGCGGCGCGCAGCUCAUUAAAUGCGUCUGCGCAACGUAAUU
...((((.(((.....)))))))...((((.......((......))......((...((((.....)))).))..))))(((..(((((((.(((...))).).))))))..))).... ( -30.90)
>DroSim_CAF1 9655 120 + 1
GAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUCAGCUCUGCAACUCAGCGGCGCGCAGCUCAUUAAAUGCGUCUGCGCAACGUAAUU
...((((.(((.....)))))))...((((.......((......))......((...((((.....)))).))..))))(((..(((((((.(((...))).).))))))..))).... ( -30.90)
>DroYak_CAF1 7756 113 + 1
GAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUUAAAGAAACUCAGCUCUGAG-------CGCUGCAACUCAGCGGCGCGCAGCUCAUUAAAUGCGUCUGCGCAACGUAAUU
...((((.(((.....)))))))...(((((......((......))..........((.(-------((((((......))))))).))))))).....((((....))))........ ( -31.70)
>consensus
GAACCUAACAAAAAUAUUGUAGGAAUUGAGCAAAACAUCGUAAAAGAAACUCAGCUCUGAGCUCUCAGCGCUGCAACUCAGCGGCGCGCAGCUCAUUAAAUGCGUCUGCGCAACGUAAUU
...((((.(((.....)))))))....((((......((......))......))))((((((....(((((((......)))))))..)))))).....((((....))))........ (-29.38 = -30.62 +   1.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,776,486 – 3,776,606
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -34.58
Consensus MFE -30.45
Energy contribution -31.45
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.53
Structure conservation index 0.88
SVM decision value -0.04
SVM RNA-class probability 0.513643
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3776486 120 - 27905053
AAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGCGCUAAGAGCUCAGAGCUGAGUUUCUUUUACGAUGUUUUGCUCAAUUCCUACAAUAUUUUUGUUAGGUUC
.....((.(((((((...(((...)))..))))))).)).(((((.(((.((..(((((((((....)))).)))))...)).)))...)))))...(((((((.....))).))))... ( -35.50)
>DroSec_CAF1 6018 120 - 1
AAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGGGAGCUCAGAGCUGAGUUUCUUUUACGAUGUUUUGCUCAAUUCCUACAAUAUUUUUGUUAGGUUC
.....((.(((((((...(((...)))..))))))).)).(((((.(((..(..(((((((((....)))))))))....)..)))...)))))...(((((((.....))).))))... ( -37.00)
>DroSim_CAF1 9655 120 - 1
AAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGAGAGCUCAGAGCUGAGUUUCUUUUACGAUGUUUUGCUCAAUUCCUACAAUAUUUUUGUUAGGUUC
.....((.(((((((...(((...)))..))))))).)).(((((.(((..(..(((((((((....)))).)))))...)..)))...)))))...(((((((.....))).))))... ( -34.80)
>DroYak_CAF1 7756 113 - 1
AAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGCG-------CUCAGAGCUGAGUUUCUUUAACGAUGUUUUGCUCAAUUCCUACAAUAUUUUUGUUAGGUUC
.........((((((...(((...)))..))))))((.((((.....)))))-------)...((((.(((..((......))..))).))))....(((((((.....))).))))... ( -31.00)
>consensus
AAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGAGAGCUCAGAGCUGAGUUUCUUUUACGAUGUUUUGCUCAAUUCCUACAAUAUUUUUGUUAGGUUC
.....((.(((((((...(((...)))..))))))).)).(((((.(((.....(((((((((....)))).)))))......)))...)))))...(((((((.....))).))))... (-30.45 = -31.45 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,776,526 – 3,776,646
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -40.98
Consensus MFE -37.91
Energy contribution -38.48
Covariance contribution 0.56
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.93
SVM decision value 0.22
SVM RNA-class probability 0.641520
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3776526 120 - 27905053
GCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCAAAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGCGCUAAGAGCUCAGAGCUGAGUUUCUUUUA
..(((((((((.(((((....).((((((((.....))).(((...)))))))))))).......((((((..((((.((......)).))))....))))))....))))))))).... ( -40.40)
>DroSec_CAF1 6058 120 - 1
GCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCAAAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGGGAGCUCAGAGCUGAGUUUCUUUUA
..(((((((((((((.....))))(((((.((((..(((.(((...)))((((((...(((...)))..)))))))))..)))).))).((((.....))))...))))))))))).... ( -42.00)
>DroSim_CAF1 9695 120 - 1
GCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCAAAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGAGAGCUCAGAGCUGAGUUUCUUUUA
..(((((((((((((.....))))(((((.((((..(((.(((...)))((((((...(((...)))..)))))))))..)))).))).((((.....))))...))))))))))).... ( -42.00)
>DroYak_CAF1 7796 113 - 1
GCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCAAAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGCG-------CUCAGAGCUGAGUUUCUUUAA
..(((((((((.(...(....)(((((((.((((..(((.(((...)))((((((...(((...)))..)))))))))..)))).))).)))-------).....).))))))))).... ( -39.50)
>consensus
GCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCAAAUUACGUUGCGCAGACGCAUUUAAUGAGCUGCGCGCCGCUGAGUUGCAGAGCUGAGAGCUCAGAGCUGAGUUUCUUUUA
..(((((((((((((.....))))(((((.((((..(((.(((...)))((((((...(((...)))..)))))))))..)))).))).((((.....))))...))))))))))).... (-37.91 = -38.48 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,776,606 – 3,776,715
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.06
Mean single sequence MFE -35.65
Consensus MFE -30.46
Energy contribution -30.52
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.06
Structure conservation index 0.85
SVM decision value 1.00
SVM RNA-class probability 0.898162
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3776606 109 - 27905053
G-----------GAGUAGAUGGGGAGUAUAUGGGCAGUAUAUGGGGUGUAACGAUAUGGGAAAUACGCCGGGAAACCUGCGCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCA
.-----------..(((((((..((((...((.(((........((((((.............))))))((....))))).))...))))..))))(....).)))..(((.....))). ( -32.02)
>DroSec_CAF1 6138 120 - 1
GGAGCAGUUGGGGAGUAGAUGGGGAGUAUAUGGGCAGUAUAUGGGGUGUAACGAUAUGGGAAAUACGCCGGGAAACCUGCGCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCA
...((..((((((.(((((((..((((...((.(((........((((((.............))))))((....))))).))...))))..))))(....).)))...))))))..)). ( -40.22)
>DroSim_CAF1 9775 120 - 1
GGAGCAGUUGGGGAGUAGAUGGGGAGUAUAUGGGCAGUAUAUGGGGUGUAACGAUAUGGGAAAUACGCCGGGAAACCUGCGCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCA
...((..((((((.(((((((..((((...((.(((........((((((.............))))))((....))))).))...))))..))))(....).)))...))))))..)). ( -40.22)
>DroYak_CAF1 7869 120 - 1
GGAGUAUAUGGAUAGUAAAUGGGCAGUAUAUGGGCAGUAUAUGGGGUGUAACGAUAUGGGAAAUACGCCGGGAAACCUGCGCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCA
...(((((((...(((...((.(((((((((.....))))))..((((((.............))))))((....))))).))...)))...))).(....)))))..(((.....))). ( -30.12)
>consensus
GGAGCAGUUGGGGAGUAGAUGGGGAGUAUAUGGGCAGUAUAUGGGGUGUAACGAUAUGGGAAAUACGCCGGGAAACCUGCGCAGGAACUUAACGUUGGAAACGUGCGCGCCUCAAAGGCA
..............(((((((..((((...((.(((........((((((.............))))))((....))))).))...))))..))))(....).)))..(((.....))). (-30.46 = -30.52 +   0.06)

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 10:04:57 2006