Locus 1406

Sequence ID 3R_DroMel_CAF1
Location 4,094,662 – 4,094,902
Length 240
Max. P 0.998560
window2322 window2323 window2324

overview

Window 2

Location 4,094,662 – 4,094,782
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -43.90
Consensus MFE -41.68
Energy contribution -41.76
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.72
Structure conservation index 0.95
SVM decision value 2.45
SVM RNA-class probability 0.994057
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094662 120 - 27905053
ACCCGCCACCGUUAUUGGAAAGGUAAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAGGCCCUGCCGCCUCUUUUGCCCAAACGCACAGUGCUAGGAAUCCACGGAAA
..(((..(((((((((.....)))))))))...........((((.(((((((((.....((((((.(((((......)))))....)))))).))))))).))))))......)))... ( -46.70)
>DroSec_CAF1 6580 120 - 1
ACCCACCACCGAUAUUGGAAAGGUAAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAGGUCCUGCCGCCUCUUUUGCCCAAACGCACAGUGCUAGGAAUCCACGGAAA
........(((.....(((((((........)))))))...((((.(((((((((.....((((((.(((((......)))))....)))))).))))))).))))))......)))... ( -42.50)
>DroSim_CAF1 6617 120 - 1
ACCCGCCACCGAUAGUGGAAAGGUAAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAGGCCCUGCCGCCUCUUUUGCCCAAACGCACAGUGCUAGGAAUCCACGGAAA
..(((((((.....))))...((...(((.........)))((((.(((((((((.....((((((.(((((......)))))....)))))).))))))).))))))...)).)))... ( -45.10)
>DroEre_CAF1 6624 120 - 1
ACCCGAAACCGAUAUUGGUAAGGUGAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAAGCCCUGCCGCCUCUUCUGCCCAAACGCACAGUGCUAGGAAUCCACGGAAA
..(((..((((....)))).(((((..((.......)).)))))((((.((((((.....((((((.((((...........)))).)))))).))))))))))..........)))... ( -38.10)
>DroYak_CAF1 6581 120 - 1
CCCCGCCACCGAUGUUGGAAAGGUGAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAGGCCCUGCCGCCUCUUCUGCCCAAACGCACAGUGCUGGGAAUCCACGGAAA
..(((.((((...........)))).(((.....(((((.....((((.((((((.....((((((.(((((......)))))....)))))).)))))))))).))))).))))))... ( -47.10)
>consensus
ACCCGCCACCGAUAUUGGAAAGGUAAUGGUCUUUUUCCCCACCUGCGCCUGUGUGGAGUAUUGGGCUGAGGCCCUGCCGCCUCUUUUGCCCAAACGCACAGUGCUAGGAAUCCACGGAAA
........(((.....(((((((........)))))))...((((.(((((((((.....((((((.(((((......)))))....)))))).))))))).))))))......)))... (-41.68 = -41.76 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,094,742 – 4,094,862
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -42.72
Consensus MFE -40.46
Energy contribution -40.50
Covariance contribution 0.04
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.95
SVM decision value 3.14
SVM RNA-class probability 0.998560
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094742 120 + 27905053
GGGGAAAAAGACCAUUACCUUUCCAAUAACGGUGGCGGGUGAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGU
.((........)).((((((..(((.......))).))))))........((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))) ( -43.60)
>DroSec_CAF1 6660 120 + 1
GGGGAAAAAGACCAUUACCUUUCCAAUAUCGGUGGUGGGUGAACUGAGGAAUUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGU
...........((((((((...........))))))))............((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))) ( -42.60)
>DroSim_CAF1 6697 120 + 1
GGGGAAAAAGACCAUUACCUUUCCACUAUCGGUGGCGGGUGAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGU
.((........)).((((((..((((.....)))).))))))........((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))) ( -47.60)
>DroEre_CAF1 6704 120 + 1
GGGGAAAAAGACCAUCACCUUACCAAUAUCGGUUUCGGGUGAACUCAGGAACUCCAGCAGGGCUACAAACUUCAGUUCUGGCUCGACAAUCCUGUAGAAAUUCUGCAGGCGGGCUGGCGU
.((........)).((((((.(((......)))...))))))........((.(((((.((((((..(((....))).))))))..(...(((((((.....)))))))..)))))).)) ( -40.40)
>DroYak_CAF1 6661 120 + 1
GGGGAAAAAGACCAUCACCUUUCCAACAUCGGUGGCGGGGGAACUAAGGAACUCCAGCAGGGCCACAAACUUGAGUUCUGGCUCGACAAUCCUGUAGAAAUUCUGCAGGCGGGCUGGCGU
.((........)).((.(((..(((.......)))..)))))........((.(((((.((((((..(((....))).))))))..(...(((((((.....)))))))..)))))).)) ( -39.40)
>consensus
GGGGAAAAAGACCAUUACCUUUCCAAUAUCGGUGGCGGGUGAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGU
.((........)).((((((..((......))....))))))........((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))) (-40.46 = -40.50 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,094,782 – 4,094,902
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -39.48
Consensus MFE -36.92
Energy contribution -37.08
Covariance contribution 0.16
Combinations/Pair 1.11
Mean z-score -1.14
Structure conservation index 0.94
SVM decision value 0.32
SVM RNA-class probability 0.688585
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4094782 120 + 27905053
GAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGUGUUUACGGAUGCCUUCUCUUUGACUGAUACGAGAACAGGA
...(((..((((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))).))..)))...(((((((............))))..))). ( -42.40)
>DroSec_CAF1 6700 120 + 1
GAACUGAGGAAUUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGUGUUUACGGAUGCCUUCUCUUUGACUGAUACGAGCACAGGA
...(((..((((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))).))..)))...(((.(((............)))...))). ( -38.10)
>DroSim_CAF1 6737 120 + 1
GAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGUGUUUACGGAUGCCUUCUCUUUGACUGAUACGAGCACAGGA
...(((..((((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))).))..)))...(((.(((............)))...))). ( -40.40)
>DroEre_CAF1 6744 120 + 1
GAACUCAGGAACUCCAGCAGGGCUACAAACUUCAGUUCUGGCUCGACAAUCCUGUAGAAAUUCUGCAGGCGGGCUGGCGUGUUCACGGAGGCCUUCUCCUUAACUGAAACGAGUACGGGA
(.((((..((((.(((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))...))))..((((.....))))...........)))).).... ( -40.50)
>DroYak_CAF1 6701 120 + 1
GAACUAAGGAACUCCAGCAGGGCCACAAACUUGAGUUCUGGCUCGACAAUCCUGUAGAAAUUCUGCAGGCGGGCUGGCGUGUUUACGGAGGCCUUCUCUUUAACUGAAACGAGUACAGGA
...((...((((.(((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))...))))....)).(((.((((((.....))).)))...))). ( -36.00)
>consensus
GAACUGAGGAACUCCAGCAGGGCCACAAACUUUAGUUCUGGCUCGACAAUCCUGUAGAAGUUCUGCAGGCGGGCUGGAGUGUUUACGGAUGCCUUCUCUUUGACUGAUACGAGCACAGGA
...(((.(((((((((((.((((((..(((....))).))))))..(...(((((((.....)))))))..))))))))).))).)))...(((.(((............)))...))). (-36.92 = -37.08 +   0.16)

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 10:09:25 2006