Locus 3193

Sequence ID 2L_DroMel_CAF1
Location 9,110,630 – 9,110,815
Length 185
Max. P 0.998994
window5074 window5075 window5076 window5077 window5078

overview

Window 4

Location 9,110,630 – 9,110,735
Length 105
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 98.10
Mean single sequence MFE -24.80
Consensus MFE -22.30
Energy contribution -22.90
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.90
SVM decision value 1.66
SVM RNA-class probability 0.970481
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110630 105 - 22407834
UUACGUUGGCCAAUUAUAAUUUUAAUUGUUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAAAGACAAUGUCUGAAAAUUACCACCACUUGCUGGGA
.((((((.(.((((((......))))))..).))))))(((.........))).........((((((.......))))))........(((.(....).))).. ( -18.80)
>DroSec_CAF1 12741 105 - 1
UUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAUGCAUAAAGACAAUGUCUGAAAAUUACCACCACUUGCUGGGA
.(((((..((((((((......))))))))..).))))((.(((.....((....))....)))))....((((...))))........(((.(....).))).. ( -22.60)
>DroSim_CAF1 12869 105 - 1
UUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAAAGACAAUGUCUGAAAAUUACCACCACUUGCUGGGA
.(((((..((((((((......))))))))..).))))(((.........))).........((((((.......))))))........(((.(....).))).. ( -25.40)
>DroEre_CAF1 12839 105 - 1
UUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAAAGACAAUGUCGGAAAAUUACCAGCACUUGCUGGGA
.(((((..((((((((......))))))))..).)))).((........((....))......(((((.......))))))).......(((((....))))).. ( -31.80)
>DroYak_CAF1 17808 105 - 1
UUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAAAGACAAUGUCUGAAAAUAACCACCACUUGCUGGGA
.(((((..((((((((......))))))))..).))))(((.........))).........((((((.......))))))........(((.(....).))).. ( -25.40)
>consensus
UUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAAAGACAAUGUCUGAAAAUUACCACCACUUGCUGGGA
.(((((..((((((((......))))))))..).))))(((.........))).........((((((.......))))))........(((.(....).))).. (-22.30 = -22.90 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,110,665 – 9,110,775
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 96.55
Mean single sequence MFE -21.82
Consensus MFE -18.50
Energy contribution -19.74
Covariance contribution 1.24
Combinations/Pair 1.04
Mean z-score -1.93
Structure conservation index 0.85
SVM decision value 1.38
SVM RNA-class probability 0.948085
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110665 110 + 22407834
UUAUGCCUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAAACAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCAGCCAGAGAAAAUC
...................(((((....((((.(((((....((((((......))))))...)))))....((((.............))))))))..)))))...... ( -22.12)
>DroSec_CAF1 12776 110 + 1
UUAUGCAUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCUUCCAGAGAAAAUC
....(((.........)))(((((.....(((.(((((...(((((((......)))))))..)))))....((((.............)))))))...)))))...... ( -23.62)
>DroSim_CAF1 12904 110 + 1
UUAUGCCUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUACCGCCUUCCAGAGAAAAUC
...................(((((.....(((.(((((...(((((((......)))))))..)))))....((.....))............)))...)))))...... ( -21.20)
>DroEre_CAF1 12874 110 + 1
UUAUGCCUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACGUAGCGCCAUCCAAAGAAAAUC
....................(((....(((((.(((((...(((((((......)))))))..)))))....((((.............)))))))))....)))..... ( -20.62)
>DroYak_CAF1 17843 110 + 1
UUAUGCCUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACGUAGCGCCAUCCAAGGAAAAUC
.....((((..((((......))))..(((((.(((((...(((((((......)))))))..)))))....((((.............)))))))))..))))...... ( -21.52)
>consensus
UUAUGCCUUUUAUAGUUGCCUCUGUUAAUGGCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCAUCCAGAGAAAAUC
...................(((((...(((((.(((((...(((((((......)))))))..)))))....((((.............))))))))).)))))...... (-18.50 = -19.74 +   1.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,110,665 – 9,110,775
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 96.55
Mean single sequence MFE -30.72
Consensus MFE -27.74
Energy contribution -28.70
Covariance contribution 0.96
Combinations/Pair 1.03
Mean z-score -2.41
Structure conservation index 0.90
SVM decision value 3.32
SVM RNA-class probability 0.998994
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110665 110 - 22407834
GAUUUUCUCUGGCUGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGUUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAA
.....((((((((((((((((......)))).))))))........((((((...(((((....))))).......))))))....)))))).................. ( -28.60)
>DroSec_CAF1 12776 110 - 1
GAUUUUCUCUGGAAGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAUGCAUAA
......(((((...(((((((......))))..........(((((..((((((((......))))))))..).))))))).....)))))(((.........))).... ( -32.20)
>DroSim_CAF1 12904 110 - 1
GAUUUUCUCUGGAAGGCGGUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAA
.....((((((((((((....(((.....)))....))))))((((..((((((((......))))))))..).))).........)))))).................. ( -29.40)
>DroEre_CAF1 12874 110 - 1
GAUUUUCUUUGGAUGGCGCUACGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAA
.....((((((((((((((((......))))..........(((((..((((((((......))))))))..).))))))))))..)))))).................. ( -31.30)
>DroYak_CAF1 17843 110 - 1
GAUUUUCCUUGGAUGGCGCUACGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAA
......((((.((((((((((......))))..........(((((..((((((((......))))))))..).)))))))))).....((....))....))))..... ( -32.10)
>consensus
GAUUUUCUCUGGAUGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGCCAUUAACAGAGGCAACUAUAAAAGGCAUAA
.....((((((((((((((((......))))..........(((((..((((((((......))))))))..).))))))))))..)))))).................. (-27.74 = -28.70 +   0.96)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,110,695 – 9,110,815
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.42
Mean single sequence MFE -24.64
Consensus MFE -21.64
Energy contribution -22.12
Covariance contribution 0.48
Combinations/Pair 1.09
Mean z-score -2.04
Structure conservation index 0.88
SVM decision value 2.36
SVM RNA-class probability 0.992970
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110695 120 + 22407834
GCCACGUUCAAACAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCAGCCAGAGAAAAUCUCUCUUUAAGCCCUGUUAAGUUUUCGCAGUGCACCCGACU
...(((((....((((((......))))))...)))))....((..(((((.(((.((.(((((...((.(((((.....)))))....))..))))).))))).)))))))........ ( -23.90)
>DroSec_CAF1 12806 120 + 1
GCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCUUCCAGAGAAAAUCUCUCUUUAAGCCCUGUUAAGUUUUCGCAGUGCACCCGACU
...(((((...(((((((......)))))))..)))))....((..(((((.(((.((.(((((.(((..(((((.....)))))..)))...))))).))))).)))))))........ ( -27.20)
>DroSim_CAF1 12934 120 + 1
GCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUACCGCCUUCCAGAGAAAAUCUCUCUUUAAGCCCUGUUAAGUUUUCGCAGUGCACCCGACU
...(((((...(((((((......)))))))..)))))....((..(((((.(((.....((.(.(((..(((((.....)))))..))).)..)).....))).)))))))........ ( -23.70)
>DroEre_CAF1 12904 119 + 1
GCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACGUAGCGCCAUCCAAAGAAAAUCUC-CUUUAAGCCCUGCUAACUUUUCGCAGUGCAUCCGACU
...(((((...(((((((......)))))))..)))))....((..(((((.(((....(((((......((((........-))))......)))))...))).)))))))........ ( -23.80)
>DroYak_CAF1 17873 120 + 1
GCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACGUAGCGCCAUCCAAGGAAAAUCUCUCUUUAAGCCCUGUUAACUUUUCGCAGUGCAGCCGACU
...(((((...(((((((......)))))))..)))))....(((.(((((.(((....(((((......(((((.......)))))......)))))...))).)))))..)))..... ( -24.60)
>consensus
GCCACGUUCAACCAAUUAAAAUUAUAAUUGGCCAACGUAAAAGCUAACUGCCAAAUACAUAGCGCCAUCCAGAGAAAAUCUCUCUUUAAGCCCUGUUAAGUUUUCGCAGUGCACCCGACU
...(((((...(((((((......)))))))..)))))....((..(((((.(((...((((.((.....(((((.....)))))....)).)))).....))).)))))))........ (-21.64 = -22.12 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,110,695 – 9,110,815
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -36.48
Consensus MFE -30.32
Energy contribution -30.76
Covariance contribution 0.44
Combinations/Pair 1.06
Mean z-score -2.23
Structure conservation index 0.83
SVM decision value 1.86
SVM RNA-class probability 0.980406
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9110695 120 - 22407834
AGUCGGGUGCACUGCGAAAACUUAACAGGGCUUAAAGAGAGAUUUUCUCUGGCUGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGUUUGAACGUGGC
.((((((((((..(((....((....))((((...((((((...))))))))))..)))..)))))))))).........(((((((.(.((((((......))))))..).))))))). ( -31.50)
>DroSec_CAF1 12806 120 - 1
AGUCGGGUGCACUGCGAAAACUUAACAGGGCUUAAAGAGAGAUUUUCUCUGGAAGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGC
.((((((((((..((.....((....))(.(((..((((((...))))))..))).)))..)))))))))).........((((((..((((((((......))))))))..).))))). ( -38.50)
>DroSim_CAF1 12934 120 - 1
AGUCGGGUGCACUGCGAAAACUUAACAGGGCUUAAAGAGAGAUUUUCUCUGGAAGGCGGUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGC
.((((((((((((((.....((.....)).(((..((((((...))))))..))))))))..))))))))).........((((((..((((((((......))))))))..).))))). ( -37.60)
>DroEre_CAF1 12904 119 - 1
AGUCGGAUGCACUGCGAAAAGUUAGCAGGGCUUAAAG-GAGAUUUUCUUUGGAUGGCGCUACGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGC
.(((((((((.((((.........)))).(((....(-(((.....))))....))).....))))))))).........((((((..((((((((......))))))))..).))))). ( -37.40)
>DroYak_CAF1 17873 120 - 1
AGUCGGCUGCACUGCGAAAAGUUAACAGGGCUUAAAGAGAGAUUUUCCUUGGAUGGCGCUACGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGC
(((..(((((..((((....((((.(((((...(((......))).)))))..))))....))))....)))))..))).((((((..((((((((......))))))))..).))))). ( -37.40)
>consensus
AGUCGGGUGCACUGCGAAAACUUAACAGGGCUUAAAGAGAGAUUUUCUCUGGAUGGCGCUAUGUAUUUGGCAGUUAGCUUUUACGUUGGCCAAUUAUAAUUUUAAUUGGUUGAACGUGGC
.(((((((((.(((...........))).(((...((((((...))))))....))).....))))))))).........((((((..((((((((......))))))))..).))))). (-30.32 = -30.76 +   0.44)

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 10:46:40 2006