Locus 7641

Sequence ID 3L_DroMel_CAF1
Location 20,555,384 – 20,555,524
Length 140
Max. P 0.840063
window12413 window12414 window12415 window12416

overview

Window 3

Location 20,555,384 – 20,555,501
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 92.88
Mean single sequence MFE -26.80
Consensus MFE -22.71
Energy contribution -22.60
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.42
Structure conservation index 0.85
SVM decision value 0.63
SVM RNA-class probability 0.804952
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20555384 117 + 23771897
ACAUCAUUAUUUUUCCAGUUGCUCACUUUGAAUAUUGCACUCGAUUGUUUUUCUCAAUCGCUCACCAUUUUGUGCGGCUUUUGAGUGCUUCACUCACAGGGCACACACUCUCGUGAA
...................(((((....(((.....(((((((((((.......)))))((((((......))).)))....)))))).....)))..)))))(((......))).. ( -27.40)
>DroSim_CAF1 98726 117 + 1
ACAUCACUAUUUUUCCAGUUGCUCACUUUGAAUAUUGCACUCGAUUGUUUUUCUCGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACAGGGCACACACACUCGUGAA
...................(((((....(((.....(((((((((((.......)))))((.(((......))).)).....)))))).....)))..)))))(((......))).. ( -23.50)
>DroEre_CAF1 99828 116 + 1
A-AACAAUAUUUUUCCAGUUGCUCACUUUGAAUAUUGCACUCGAUCGUUUUUCACGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACUGGUCACACACACACGUGAA
.-..((((((((....(((.....)))..)))))))).....((((((.....))))))..((((.....((((.(((...((((((...))))))...))).)))).....)))). ( -29.50)
>consensus
ACAUCAAUAUUUUUCCAGUUGCUCACUUUGAAUAUUGCACUCGAUUGUUUUUCUCGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACAGGGCACACACACUCGUGAA
...................(((((....(((.....(((((((((((.......))))).(.(((......))).)......)))))).....)))..)))))(((......))).. (-22.71 = -22.60 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,555,384 – 20,555,501
Length 117
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 92.88
Mean single sequence MFE -31.16
Consensus MFE -25.05
Energy contribution -25.17
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.26
Structure conservation index 0.80
SVM decision value 0.15
SVM RNA-class probability 0.609460
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20555384 117 - 23771897
UUCACGAGAGUGUGUGCCCUGUGAGUGAAGCACUCAAAAGCCGCACAAAAUGGUGAGCGAUUGAGAAAAACAAUCGAGUGCAAUAUUCAAAGUGAGCAACUGGAAAAAUAAUGAUGU
..(((....)))..((((((.((((((..((((((....(((((........))).))(((((.......)))))))))))..)))))).)).).)))................... ( -32.30)
>DroSim_CAF1 98726 117 - 1
UUCACGAGUGUGUGUGCCCUGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGAGAAAAACAAUCGAGUGCAAUAUUCAAAGUGAGCAACUGGAAAAAUAGUGAUGU
(((((.(.((((((.((....((((((...))))))...))))))))...).)))))..((((..........((.(((((..............)).))).)).......)))).. ( -27.47)
>DroEre_CAF1 99828 116 - 1
UUCACGUGUGUGUGUGACCAGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGUGAAAAACGAUCGAGUGCAAUAUUCAAAGUGAGCAACUGGAAAAAUAUUGUU-U
.(((((......)))))((((((((((..((((((....((((.......))))....((((((.....))))))))))))..)))))...(....).)))))............-. ( -33.70)
>consensus
UUCACGAGUGUGUGUGCCCUGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGAGAAAAACAAUCGAGUGCAAUAUUCAAAGUGAGCAACUGGAAAAAUAAUGAUGU
..(((....)))(((......((((((..((((((....((((.......))))....(((((.......)))))))))))..))))))......)))................... (-25.05 = -25.17 +   0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,555,424 – 20,555,524
Length 100
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 92.67
Mean single sequence MFE -23.37
Consensus MFE -20.46
Energy contribution -19.80
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.88
SVM decision value -0.04
SVM RNA-class probability 0.512503
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20555424 100 + 23771897
UCGAUUGUUUUUCUCAAUCGCUCACCAUUUUGUGCGGCUUUUGAGUGCUUCACUCACAGGGCACACACUCUCGUGAAUAUAUCUACUCGAAGAAUUCGUU
.((((((.......)))))).((((.....((((.(.(((.((((((...)))))).))).).)))).....)))).....(((......)))....... ( -24.20)
>DroSim_CAF1 98766 100 + 1
UCGAUUGUUUUUCUCGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACAGGGCACACACACUCGUGAAUAUAUCUACUCGAAGAAUUCGUU
.(((..(((((((..(((...((((.....((((.(.(...((((((...))))))...).).)))).....))))....))).....)))))))))).. ( -20.90)
>DroEre_CAF1 99867 100 + 1
UCGAUCGUUUUUCACGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACUGGUCACACACACACGUGAAUACAUCUACUCGAGGAAUUCGUU
..((((((.....))))))..((((.....((((.(((...((((((...))))))...))).)))).....)))).....(((......)))....... ( -25.00)
>consensus
UCGAUUGUUUUUCUCGAUCUCUCACCAUUUUGUGCGGCAUUUGAGUGCUUCACUCACAGGGCACACACACUCGUGAAUAUAUCUACUCGAAGAAUUCGUU
..(((((.......)))))..((((.....((((.(.(...((((((...))))))...).).)))).....)))).....(((......)))....... (-20.46 = -19.80 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,555,424 – 20,555,524
Length 100
Sequences 3
Columns 100
Reading direction reverse
Mean pairwise identity 92.67
Mean single sequence MFE -28.30
Consensus MFE -24.55
Energy contribution -25.00
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.37
Structure conservation index 0.87
SVM decision value 0.75
SVM RNA-class probability 0.840063
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20555424 100 - 23771897
AACGAAUUCUUCGAGUAGAUAUAUUCACGAGAGUGUGUGCCCUGUGAGUGAAGCACUCAAAAGCCGCACAAAAUGGUGAGCGAUUGAGAAAAACAAUCGA
..(((.....)))..........(((((.(...((((((.(...((((((...))))))...).))))))...).)))))((((((.......)))))). ( -27.40)
>DroSim_CAF1 98766 100 - 1
AACGAAUUCUUCGAGUAGAUAUAUUCACGAGUGUGUGUGCCCUGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGAGAAAAACAAUCGA
..(((.(((((.(((((....)))))((.(.((((((.((....((((((...))))))...))))))))...).))))))).))).............. ( -27.40)
>DroEre_CAF1 99867 100 - 1
AACGAAUUCCUCGAGUAGAUGUAUUCACGUGUGUGUGUGACCAGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGUGAAAAACGAUCGA
.........((((((((....))))).(((...((((((.(...((((((...))))))...).))))))..)))..))).((((((.....)))))).. ( -30.10)
>consensus
AACGAAUUCUUCGAGUAGAUAUAUUCACGAGUGUGUGUGCCCUGUGAGUGAAGCACUCAAAUGCCGCACAAAAUGGUGAGAGAUCGAGAAAAACAAUCGA
..(((.....)))..........(((((.(...((((((.(...((((((...))))))...).))))))...).))))).(((((.......))))).. (-24.55 = -25.00 +   0.45)

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 12:52:29 2006