Locus 1232

Sequence ID 3R_DroMel_CAF1
Location 3,709,173 – 3,709,344
Length 171
Max. P 0.987759
window2011 window2012 window2013 window2014

overview

Window 1

Location 3,709,173 – 3,709,270
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -28.90
Consensus MFE -22.79
Energy contribution -24.48
Covariance contribution 1.69
Combinations/Pair 1.15
Mean z-score -2.41
Structure conservation index 0.79
SVM decision value 0.80
SVM RNA-class probability 0.853032
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3709173 97 + 27905053
AACUUAGAAACACGGCAAAGAGUGGAAACUAUGUUGUGCAUGGAAGUGGCCAACUCCUGGCAGUUUUCUGCAUCCAGAAGAUAGCCGAGCAACAAAG
.((((.....(((((((...(((....))).))))))).....))))......(((..(((.((((((((....)))))))).))))))........ ( -27.10)
>DroSec_CAF1 67048 97 + 1
AACUUGGUAACACGGCAAAGAGUGGAAACUAUGUUGUGCAUGGAAGUGGCCAACUCCUGGCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAG
..((((((...((((((...(((....))).))))))(((.(((((..((((.....))))..))))))))............))))))........ ( -31.20)
>DroSim_CAF1 70245 97 + 1
AACUUGGUAACACGGCAAAGAGUGGAAACUAUGUUGUGCAUGGAAGUGGCCAACUCCUGGCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAG
..((((((...((((((...(((....))).))))))(((.(((((..((((.....))))..))))))))............))))))........ ( -31.20)
>DroYak_CAF1 66000 97 + 1
AACUUGGUUACACGGCAAAGAGUUUAAACUAUGCUGUGUAUAAAAGUGGCCAACUCUUCGCAGUUUCCUGCAUCCAUAAGAUAGCCAAGCAACAAAG
.((((...(((((((((...(((....))).)))))))))...))))(((.........((((....))))(((.....))).)))........... ( -26.10)
>consensus
AACUUGGUAACACGGCAAAGAGUGGAAACUAUGUUGUGCAUGGAAGUGGCCAACUCCUGGCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAG
..((((((...((((((...(((....))).))))))(((.(((((..((((.....))))..))))))))............))))))........ (-22.79 = -24.48 +   1.69)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,709,173 – 3,709,270
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 92.78
Mean single sequence MFE -28.86
Consensus MFE -26.71
Energy contribution -27.02
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.42
Structure conservation index 0.93
SVM decision value 2.09
SVM RNA-class probability 0.987759
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3709173 97 - 27905053
CUUUGUUGCUCGGCUAUCUUCUGGAUGCAGAAAACUGCCAGGAGUUGGCCACUUCCAUGCACAACAUAGUUUCCACUCUUUGCCGUGUUUCUAAGUU
...........(((((.((((((...((((....)))))))))).)))))((((....((((..((.((........)).))..))))....)))). ( -25.80)
>DroSec_CAF1 67048 97 - 1
CUUUGUUGCUCGGCUAUCUUCUGGAUGCAGGAAACUGCCAGGAGUUGGCCACUUCCAUGCACAACAUAGUUUCCACUCUUUGCCGUGUUACCAAGUU
...........(((((.((((((...((((....)))))))))).)))))((((....((((..((.((........)).))..))))....)))). ( -30.10)
>DroSim_CAF1 70245 97 - 1
CUUUGUUGCUCGGCUAUCUUCUGGAUGCAGGAAACUGCCAGGAGUUGGCCACUUCCAUGCACAACAUAGUUUCCACUCUUUGCCGUGUUACCAAGUU
...........(((((.((((((...((((....)))))))))).)))))((((....((((..((.((........)).))..))))....)))). ( -30.10)
>DroYak_CAF1 66000 97 - 1
CUUUGUUGCUUGGCUAUCUUAUGGAUGCAGGAAACUGCGAAGAGUUGGCCACUUUUAUACACAGCAUAGUUUAAACUCUUUGCCGUGUAACCAAGUU
(((.(((((.((((............((((....))))((((((((....(((..............)))...)))))))))))).))))).))).. ( -29.44)
>consensus
CUUUGUUGCUCGGCUAUCUUCUGGAUGCAGGAAACUGCCAGGAGUUGGCCACUUCCAUGCACAACAUAGUUUCCACUCUUUGCCGUGUUACCAAGUU
...........(((((.((((((...((((....)))))))))).)))))((((....((((..((.((........)).))..))))....)))). (-26.71 = -27.02 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,709,207 – 3,709,304
Length 97
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 69.63
Mean single sequence MFE -38.40
Consensus MFE -10.86
Energy contribution -12.28
Covariance contribution 1.42
Combinations/Pair 1.35
Mean z-score -2.46
Structure conservation index 0.28
SVM decision value 1.27
SVM RNA-class probability 0.938552
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3709207 97 - 27905053
UUCCGCUG-GAUUGUGUAGAACGCGAGGCGGCUG-CCUUUGUUGCUCGGC-UAUCUUCUGGAUGCAGAAAACUGCCAGGA---------------GUUGGCCACUUCCAUGCACA
....((((-(((((((.....)))))((((((..-.....)))))).(((-((.((((((...((((....)))))))))---------------).)))))...)))).))... ( -36.00)
>DroPse_CAF1 69776 105 - 1
UGUGGCUGUGACUGUGGGGC---UGCUGCUGCUGUCUUUUGUUCCUCGUCUUAUCUUAUGGGAGCAGGAAGCUGUGGGGAUAAGGAUGAGGAUGAGUCGUCC-------UGCCUG
...(((.((((((..(((((---.((....)).)))))....(((((((((((((((......((((....)))).))))))).))))))))..))))).).-------.))).. ( -37.60)
>DroSec_CAF1 67082 97 - 1
UUCCGCUG-GAUUGUGUAGAAGGCGAGGCGCCUG-CCUUUGUUGCUCGGC-UAUCUUCUGGAUGCAGGAAACUGCCAGGA---------------GUUGGCCACUUCCAUGCACA
....((((-((..(.(((((((((.((....)))-)))))..))).)(((-((.((((((...((((....)))))))))---------------).)))))...)))).))... ( -41.70)
>DroSim_CAF1 70279 97 - 1
UUCCGCUG-GAUUGUGUAGAAGGCGAGGCGGCUG-CCUUUGUUGCUCGGC-UAUCUUCUGGAUGCAGGAAACUGCCAGGA---------------GUUGGCCACUUCCAUGCACA
....((((-((..(.(((((((((.((....)))-)))))..))).)(((-((.((((((...((((....)))))))))---------------).)))))...)))).))... ( -40.20)
>DroYak_CAF1 66034 97 - 1
UUCUACUG-GAUUGUAUAGAAGGCGAGGCGGUUG-CCUUUGUUGCUUGGC-UAUCUUAUGGAUGCAGGAAACUGCGAAGA---------------GUUGGCCACUUUUAUACACA
........-...(((((((((((((((((....)-))))....)).((((-((.(((.....(((((....)))))..))---------------).)))))))))))))))).. ( -34.60)
>DroPer_CAF1 75626 105 - 1
UGUGGCUGUGGCUGUGGGGC---UGCUGCUGCUGUCUUUUGUUCCUCGUCUUAUCUUAUGGGAGCAGGAAACUGUGGGGAUAAGGAUGAGGAUGAGUCGUCC-------UGCCUG
.(..((.(..(((....)))---..).))..).(.(((....(((((((((((((((......((((....)))).))))))).)))))))).))).)....-------...... ( -40.30)
>consensus
UUCCGCUG_GAUUGUGUAGAAGGCGAGGCGGCUG_CCUUUGUUGCUCGGC_UAUCUUAUGGAUGCAGGAAACUGCCAGGA_______________GUUGGCCACUUCCAUGCACA
.............((((.((((.(((.(((((........))))))))...............((((....))))............................)))).))))... (-10.86 = -12.28 +   1.42)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,709,232 – 3,709,344
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 92.86
Mean single sequence MFE -34.23
Consensus MFE -31.41
Energy contribution -30.97
Covariance contribution -0.44
Combinations/Pair 1.15
Mean z-score -1.65
Structure conservation index 0.92
SVM decision value 0.72
SVM RNA-class probability 0.831602
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3709232 112 + 27905053
GCAGUUUUCUGCAUCCAGAAGAUAGCCGAGCAACAAAGGCAGCCGCCUCGCGUUCUACACAAUCCAGCGGAAGACAUUGCGGAUGGUUAUAGAUGGAGGAAACAAUAGUCCG
((((....)))).((((....((((((((((.....((((....))))...))))......((((.((((......))))))))))))))...))))(((........))). ( -33.20)
>DroSec_CAF1 67107 112 + 1
GCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAGGCAGGCGCCUCGCCUUCUACACAAUCCAGCGGAAGACAUUGCGGAUGGUUAUAGAUGGAGGAAACAAUAUUGUG
...(((((((.((((......(((((((.((((...((((....)))).(.((((..(........)..)))).).))))...))))))).)))).)))))))......... ( -35.10)
>DroSim_CAF1 70304 112 + 1
GCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAGGCAGCCGCCUCGCCUUCUACACAAUCCAGCGGAAGACAUUGCGGAUGGUUAUAGAUGGAGGAAACAAUAGUGCG
((((((((((.((((......(((((((.((((...((((....)))).(.((((..(........)..)))).).))))...))))))).)))).))))))).....))). ( -35.90)
>DroYak_CAF1 66059 112 + 1
GCAGUUUCCUGCAUCCAUAAGAUAGCCAAGCAACAAAGGCAACCGCCUCGCCUUCUAUACAAUCCAGUAGAAGACAUUGCGGAUGGUUAUAGAUGUGCGAAACAAUAGGGCG
...(((((.((((((......(((((((.((((...((((....)))).(.(((((((........))))))).).))))...))))))).)))))).)))))......... ( -32.70)
>consensus
GCAGUUUCCUGCAUCCAGAAGAUAGCCGAGCAACAAAGGCAGCCGCCUCGCCUUCUACACAAUCCAGCGGAAGACAUUGCGGAUGGUUAUAGAUGGAGGAAACAAUAGUGCG
...(((((((.((((......(((((((.((((...((((....)))).(.(((((.(........).))))).).))))...))))))).)))).)))))))......... (-31.41 = -30.97 +  -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 10:04:15 2006