Locus 4932

Sequence ID 3R_DroMel_CAF1
Location 12,965,774 – 12,966,094
Length 320
Max. P 0.998551
window8068 window8069 window8070 window8071 window8072

overview

Window 8

Location 12,965,774 – 12,965,894
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -42.02
Consensus MFE -39.02
Energy contribution -38.90
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -2.00
Structure conservation index 0.93
SVM decision value 3.14
SVM RNA-class probability 0.998551
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12965774 120 + 27905053
AUGGAAAGGGCAGCAAGUGCAACAGUGCCAACCGCUGGAUGGAUAAGACAAUUCAAUUGGUGGUAAACCCAAAUGGACACGUUGGAUUCACCUAUGAGCACUCACCAGCCGAGGGCCAAC
.(((....(((.((....))...((((((((((((..(.(((((......))))).)..)))))....((((.((....)))))).........)).))))).....))).....))).. ( -33.30)
>DroSec_CAF1 5803 120 + 1
AUGGAAAGGGCAGCAAGUGCAACAGUGCCAACCGCUGGAUGGAUAAAACGAUUCAGUUGGUGGUGAACCCAAAUGGACACGUUGGAUUCACCUACGAGCACUCGCCAGCCGAGGGCCAAC
.(((....(((.((.(((((......((((...(((((((.(......).)))))))))))((((((.((((.((....)))))).)))))).....))))).))..))).....))).. ( -42.70)
>DroSim_CAF1 6007 120 + 1
AUGGAAAGGGCAGCAAGUGCAACAGUGCCAACCGCUGGAUGGAUAAAACGAUUCAGUUGGUGGUGAACCCAAAUGGACACGUUGGAUUCACCUACGAGCACUCGCCAGCCGAGGGCCAAC
.(((....(((.((.(((((......((((...(((((((.(......).)))))))))))((((((.((((.((....)))))).)))))).....))))).))..))).....))).. ( -42.70)
>DroEre_CAF1 5781 120 + 1
AUGGAAAGGGCAGCCAGUGCAACAGUGGCAACCGCUGGAUGGAUAAGACGAUUCAGCUGGUGGUGAACCCGAAUGGAAACGUUGGAUUCACCUACGAGCACUCGCCGGCCGAGGGUCAAC
..((..((.((.((((.((...)).)))).((((((((((.(......).))))))).)))((((((.((.((((....)))))).)))))).....)).))..))((((...))))... ( -46.70)
>DroYak_CAF1 5943 120 + 1
AUGGAAAGGGCAGCCAGUGCAACAGCGCCAACCGCUGGAUGGAUAAGACGAUUCAGUUGGUGGUGAACCCGAACGGAAACGUUGGAUUUACCUACGAGCACUCGCCGGCGGAGGGUCAAC
........(((..((.((((....))))...(((((((.(((((......)))))(((.((((((((.((.((((....)))))).)))))).)).))).....))))))).)))))... ( -44.70)
>consensus
AUGGAAAGGGCAGCAAGUGCAACAGUGCCAACCGCUGGAUGGAUAAGACGAUUCAGUUGGUGGUGAACCCAAAUGGACACGUUGGAUUCACCUACGAGCACUCGCCAGCCGAGGGCCAAC
.(((....(((.((.(((((..........((((((((((.(......).))))))).)))((((((.((((.((....)))))).)))))).....))))).))..))).....))).. (-39.02 = -38.90 +  -0.12)

alignment

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secondary structure

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Window 9

Location 12,965,774 – 12,965,894
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -40.13
Consensus MFE -35.47
Energy contribution -36.27
Covariance contribution 0.80
Combinations/Pair 1.13
Mean z-score -1.71
Structure conservation index 0.88
SVM decision value 1.74
SVM RNA-class probability 0.975098
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12965774 120 - 27905053
GUUGGCCCUCGGCUGGUGAGUGCUCAUAGGUGAAUCCAACGUGUCCAUUUGGGUUUACCACCAAUUGAAUUGUCUUAUCCAUCCAGCGGUUGGCACUGUUGCACUUGCUGCCCUUUCCAU
..(((.....(((.((..(((((.....(((((((((((.........))))))))))).(((((((...((.......)).....))))))).......)))))..)))))....))). ( -38.60)
>DroSec_CAF1 5803 120 - 1
GUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUUUUAUCCAUCCAGCGGUUGGCACUGUUGCACUUGCUGCCCUUUCCAU
..(((.....(((.(((((((((.....(((((((((((.........))))))))))).(((((((...................))))))).......))))))))))))....))). ( -44.51)
>DroSim_CAF1 6007 120 - 1
GUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUUUUAUCCAUCCAGCGGUUGGCACUGUUGCACUUGCUGCCCUUUCCAU
..(((.....(((.(((((((((.....(((((((((((.........))))))))))).(((((((...................))))))).......))))))))))))....))). ( -44.51)
>DroEre_CAF1 5781 120 - 1
GUUGACCCUCGGCCGGCGAGUGCUCGUAGGUGAAUCCAACGUUUCCAUUCGGGUUCACCACCAGCUGAAUCGUCUUAUCCAUCCAGCGGUUGCCACUGUUGCACUGGCUGCCCUUUCCAU
.........((((((((((..(((.((.(((((((((.............))))))))))).)))....))))).........(((((((....)))))))....))))).......... ( -39.02)
>DroYak_CAF1 5943 120 - 1
GUUGACCCUCCGCCGGCGAGUGCUCGUAGGUAAAUCCAACGUUUCCGUUCGGGUUCACCACCAACUGAAUCGUCUUAUCCAUCCAGCGGUUGGCGCUGUUGCACUGGCUGCCCUUUCCAU
.............((((.(((((.....(((.(((((((((....)))).))))).))).(((((((...................))))))).......))))).)))).......... ( -34.01)
>consensus
GUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUCUUAUCCAUCCAGCGGUUGGCACUGUUGCACUUGCUGCCCUUUCCAU
..........(((.(((((((((.....(((((((((((.........))))))))))).(((((((...................))))))).......))))))))))))........ (-35.47 = -36.27 +   0.80)

alignment

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secondary structure

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Window 0

Location 12,965,814 – 12,965,934
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -32.40
Consensus MFE -29.98
Energy contribution -30.10
Covariance contribution 0.12
Combinations/Pair 1.21
Mean z-score -1.36
Structure conservation index 0.93
SVM decision value 1.04
SVM RNA-class probability 0.904938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12965814 120 - 27905053
UUCAUCUUCUUCACUACAUAGUCCAUCAUCAUUGCGAUCGGUUGGCCCUCGGCUGGUGAGUGCUCAUAGGUGAAUCCAACGUGUCCAUUUGGGUUUACCACCAAUUGAAUUGUCUUAUCC
.................................((((((((((((..........((((....)))).(((((((((((.........))))))))))).))))))).)))))....... ( -26.30)
>DroSec_CAF1 5843 120 - 1
UUCAUCUUCUUCACCACAUAGUCCAUCAUCAUGGCGAUCGGUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUUUUAUCC
................................((((((((((((((.((((.....)))).)).....(((((((((((.........)))))))))))..)))))).))))))...... ( -35.60)
>DroSim_CAF1 6047 120 - 1
UUCAUCUUCUUCACCACAUAGUCCAUCAUCAUGGCGAUCGGUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUUUUAUCC
................................((((((((((((((.((((.....)))).)).....(((((((((((.........)))))))))))..)))))).))))))...... ( -35.60)
>DroEre_CAF1 5821 120 - 1
UUCAUCUUCUUCACCACAUAGUCCAUCAUCAUGGCGAUCGGUUGACCCUCGGCCGGCGAGUGCUCGUAGGUGAAUCCAACGUUUCCAUUCGGGUUCACCACCAGCUGAAUCGUCUUAUCC
....................(.((((....)))))....(((((.....)))))(((((..(((.((.(((((((((.............))))))))))).)))....)))))...... ( -33.82)
>DroYak_CAF1 5983 120 - 1
UUCAUCUUCUUCACCACAUAGUCCAUCAUCAUGGCGAUCGGUUGACCCUCCGCCGGCGAGUGCUCGUAGGUAAAUCCAACGUUUCCGUUCGGGUUCACCACCAACUGAAUCGUCUUAUCC
................................((((((((((((...........((((....)))).(((.(((((((((....)))).))))).)))..)))))).))))))...... ( -30.70)
>consensus
UUCAUCUUCUUCACCACAUAGUCCAUCAUCAUGGCGAUCGGUUGGCCCUCGGCUGGCGAGUGCUCGUAGGUGAAUCCAACGUGUCCAUUUGGGUUCACCACCAACUGAAUCGUCUUAUCC
................................(((((((((((((..........((((....)))).(((((((((((.........))))))))))).))))))).))))))...... (-29.98 = -30.10 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,965,934 – 12,966,054
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.50
Mean single sequence MFE -34.08
Consensus MFE -28.20
Energy contribution -28.64
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.34
Structure conservation index 0.83
SVM decision value 0.11
SVM RNA-class probability 0.590314
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12965934 120 + 27905053
GGAUGACCCUAGUUAUGGGGAAUGCGGAUCGGAAAACUUUAUUCCAGCGAAGAAAAUAAAGUUCUGUGAUGUAAGCAAAUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGA
..(((.(((((....)))))..(((.....((((.......)))).((((....(((...((((..((.((....))....))..))))....))).....)))))))......)))... ( -26.40)
>DroSec_CAF1 5963 120 + 1
GGAUGACCCUAGUUACGGGGAAUGCGGAUCGGAGGACUUUAUUCCAGCGAAGAAAAUAAUGUUCUGUGAUCUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGA
(.((..(((.......)))..)).)((((((.(((((.(((((...........))))).))))).)))))).(((...(((.....)))...))).....(((((........))))). ( -30.00)
>DroSim_CAF1 6167 120 + 1
GGAUGACCCUAGUUACGGGGAAUGCGGAUCGGAGGACUUUAUUCCAGCGAAGAAAAUAAAGUUCUGUGAUCUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGA
(.((..(((.......)))..)).)((((((.(((((((((((...........))))))))))).)))))).(((...(((.....)))...))).....(((((........))))). ( -34.10)
>DroEre_CAF1 5941 120 + 1
GGAUGACCCCAGCUACGGGGAAUGCGGAUCGGAGGCCUUUAUUCCGGCACGGAAAAUAAAGUUCUGCGAUGUUAGCAAGUGCGUGGAGCAAUGGCUGAUAAUCGCGCAGAAGAACGUGGA
..(((.((((......))))..(((((((((.((..((((((((((...))))..))))))..)).)))(((((((...(((.....)))...))))))).)).))))......)))... ( -41.30)
>DroYak_CAF1 6103 120 + 1
GGAUGACCCGAGUUACGGGGAAUGCGGAUCGGAGGACUUUACUCCAGCGCGGAAAAUAAAGUUCUGCGAGGUGAGCAAGUGCGUGGAGCAGUGGCUGAUAAUCGCGCAAAAGAACGUGGA
(.((..((((.....))))..)).)...(((.(((((((((.(((.....)))...))))))))).))).((.(((.(.(((.....))).).))).))..(((((........))))). ( -38.60)
>consensus
GGAUGACCCUAGUUACGGGGAAUGCGGAUCGGAGGACUUUAUUCCAGCGAAGAAAAUAAAGUUCUGUGAUGUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGA
......((((......))))..(((..((((.((((((((((((.......))..)))))))))).))))....)))..((((((((((....))).....)))))))............ (-28.20 = -28.64 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,965,974 – 12,966,094
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.25
Mean single sequence MFE -34.26
Consensus MFE -29.72
Energy contribution -28.80
Covariance contribution -0.92
Combinations/Pair 1.16
Mean z-score -1.96
Structure conservation index 0.87
SVM decision value 2.16
SVM RNA-class probability 0.989356
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12965974 120 + 27905053
AUUCCAGCGAAGAAAAUAAAGUUCUGUGAUGUAAGCAAAUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGACAAACUUGUCCAGGACCUGCAAAUGAAGGUUCUUAAGUUC
......((..((((.......))))(((((...(((...(((.....)))...)))....))))))).....(((.((((((....))))))((((((........))))))....))). ( -29.00)
>DroSec_CAF1 6003 120 + 1
AUUCCAGCGAAGAAAAUAAUGUUCUGUGAUCUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGACAAACUUGUCCAGGAUCUGCAAAUGAAGGUUCUUAAGUUC
......((((....(((..(((((..((..((.....))..))..)))))...))).....)))).......(((.((((((....))))))((((((........))))))....))). ( -27.40)
>DroSim_CAF1 6207 120 + 1
AUUCCAGCGAAGAAAAUAAAGUUCUGUGAUCUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGACAAACUUGUCCAGGAUCUGCAAAUGAAGGUUCUUAAGUUC
......((..((((.......))))(((((...(((...(((.....)))...)))....))))))).....(((.((((((....))))))((((((........))))))....))). ( -26.40)
>DroEre_CAF1 5981 120 + 1
AUUCCGGCACGGAAAAUAAAGUUCUGCGAUGUUAGCAAGUGCGUGGAGCAAUGGCUGAUAAUCGCGCAGAAGAACGUGGACAAACUUGUCCAGGACCUGCAAAUGAAGGUUCUCAAGUUC
.(((((...))))).......(((((((.(((((((...(((.....)))...)))))))....)))))))((((.((((((....))))))((((((........))))))....)))) ( -44.50)
>DroYak_CAF1 6143 120 + 1
ACUCCAGCGCGGAAAAUAAAGUUCUGCGAGGUGAGCAAGUGCGUGGAGCAGUGGCUGAUAAUCGCGCAAAAGAACGUGGACAAACUUGUCCGGGACCUUCAAAUGAAGGUUCUUAAGUUC
.((((..(((((((.......)))))))..).)))....((((((((((....))).....)))))))...((((..(((((....)))))(((((((((....)))))))))...)))) ( -44.00)
>consensus
AUUCCAGCGAAGAAAAUAAAGUUCUGUGAUGUAAGCAAGUGCGUGGAGCAAUGGUUGAUAAUCGCGCAAAAAAACGUGGACAAACUUGUCCAGGACCUGCAAAUGAAGGUUCUUAAGUUC
......((..((((.......))))(((((...(((...(((.....)))...)))....))))))).....(((.((((((....))))))((((((........))))))....))). (-29.72 = -28.80 +  -0.92)

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 11:42:22 2006