Locus 7713

Sequence ID 3L_DroMel_CAF1
Location 20,613,389 – 20,613,651
Length 262
Max. P 0.974795
window12551 window12552 window12553 window12554

overview

Window 1

Location 20,613,389 – 20,613,507
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.60
Mean single sequence MFE -29.95
Consensus MFE -23.98
Energy contribution -24.50
Covariance contribution 0.52
Combinations/Pair 1.10
Mean z-score -1.76
Structure conservation index 0.80
SVM decision value 0.69
SVM RNA-class probability 0.823852
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613389 118 + 23771897
UUUGGGGCAAACAAAACUGGGCAA-AAAUUAGCUCAA-AGUUAUGCAGAAGCCAAGCGAGAUGAAAGAACAAUAUUAUUCUUUUGGGCGACGGCAAUAUUUAGCCCAAGUGUUGCUUAAG
....((((((.....(((((((..-....((((....-.)))).......(((...((...((((((((........))))))))..))..)))........)))).))).))))))... ( -28.80)
>DroSec_CAF1 58161 118 + 1
UCUGGGGCAAACAAAACUGGGCAA-AAAUUAGCUCAA-AGUUAUGCAGAAGCCAAGCGAGAUGAAAGAACAAUAUUAUUCUUUUGGGCGACGGCAAUAUUUAGCCCAAGUGUUGCUUAAG
.((..(((((.....(((((((..-....((((....-.)))).......(((...((...((((((((........))))))))..))..)))........)))).))).)))))..)) ( -29.20)
>DroAna_CAF1 80134 120 + 1
UCCCGGGCAAACAAAACUGGCUAAAAAAUUAGCUCAAAAGUUAUGCAGAAGCCAGGCGAGAAGAAAGAAUAAUAUUAUUCUUGCCGGUGACCGCAAUAUUUGGCCCAAGUGUUGCUUAAG
....((((((.((.....(((((((....(((((....)))))(((.(..(((.((((((((...............)))))))))))..).)))...)))))))....))))))))... ( -34.46)
>DroSim_CAF1 53058 118 + 1
UCUGGGGCAAACAAAACUGGGCAA-AAAUUAGCUCAA-AGUUAUGCAGAAGCCAAGCGAGAUGAAAGAACAAUAUUAUUCUUUUGGGCGACGGCAAUAUUUAGCCCAAGUGUUGCUUAAG
.((..(((((.....(((((((..-....((((....-.)))).......(((...((...((((((((........))))))))..))..)))........)))).))).)))))..)) ( -29.20)
>DroEre_CAF1 50705 118 + 1
UCUGGGGCAAACAAAACUGGGCAA-AAAUUAGCUCAA-AGUUAUGCAGAAGCCAAGCGAGAUGAAAGAACAAUAUUAUUCUUUUGAGCGACGCCAAUAUUUAGCCCAAGUGUUGCUUGAG
.((.((((((.....(((((((..-......((((..-.(((..((....))..))).....(((((((........)))))))))))(....)........)))).))).)))))).)) ( -28.10)
>consensus
UCUGGGGCAAACAAAACUGGGCAA_AAAUUAGCUCAA_AGUUAUGCAGAAGCCAAGCGAGAUGAAAGAACAAUAUUAUUCUUUUGGGCGACGGCAAUAUUUAGCCCAAGUGUUGCUUAAG
....((((((.....(((((((.......(((((....))))).......(((...((...((((((((........))))))))..))..)))........)))).))).))))))... (-23.98 = -24.50 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,613,389 – 20,613,507
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -28.66
Consensus MFE -21.66
Energy contribution -22.14
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.76
SVM decision value 0.52
SVM RNA-class probability 0.768638
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613389 118 - 23771897
CUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAAGAAUAAUAUUGUUCUUUCAUCUCGCUUGGCUUCUGCAUAACU-UUGAGCUAAUUU-UUGCCCAGUUUUGUUUGCCCCAAA
..(((((((.(((.((((.((((...((((.((....((((((((....)))))))).....))..))))....((......-....))..))))-..))))))).)))))))....... ( -25.80)
>DroSec_CAF1 58161 118 - 1
CUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAAGAAUAAUAUUGUUCUUUCAUCUCGCUUGGCUUCUGCAUAACU-UUGAGCUAAUUU-UUGCCCAGUUUUGUUUGCCCCAGA
..(((((((.(((.((((.((((...((((.((....((((((((....)))))))).....))..))))....((......-....))..))))-..))))))).)))))))....... ( -25.80)
>DroAna_CAF1 80134 120 - 1
CUUAAGCAACACUUGGGCCAAAUAUUGCGGUCACCGGCAAGAAUAAUAUUAUUCUUUCUUCUCGCCUGGCUUCUGCAUAACUUUUGAGCUAAUUUUUUAGCCAGUUUUGUUUGCCCGGGA
...........(((((((.(((((.(((((...((((((((((((....))))))).......))).))...)))))......(((.(((((....))))))))...)))))))))))). ( -34.41)
>DroSim_CAF1 53058 118 - 1
CUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAAGAAUAAUAUUGUUCUUUCAUCUCGCUUGGCUUCUGCAUAACU-UUGAGCUAAUUU-UUGCCCAGUUUUGUUUGCCCCAGA
..(((((((.(((.((((.((((...((((.((....((((((((....)))))))).....))..))))....((......-....))..))))-..))))))).)))))))....... ( -25.80)
>DroEre_CAF1 50705 118 - 1
CUCAAGCAACACUUGGGCUAAAUAUUGGCGUCGCUCAAAAGAAUAAUAUUGUUCUUUCAUCUCGCUUGGCUUCUGCAUAACU-UUGAGCUAAUUU-UUGCCCAGUUUUGUUUGCCCCAGA
..(((((((.(((.((((.(((.((((((.((((...((((((((....))))))))......))...((....))......-..)))))))).)-))))))))).)))))))....... ( -31.50)
>consensus
CUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAAGAAUAAUAUUGUUCUUUCAUCUCGCUUGGCUUCUGCAUAACU_UUGAGCUAAUUU_UUGCCCAGUUUUGUUUGCCCCAGA
..(((((((.(((.((((...................((((((((....))))))))........(((((((.............)))))))......))))))).)))))))....... (-21.66 = -22.14 +   0.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,613,467 – 20,613,576
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.95
Mean single sequence MFE -40.18
Consensus MFE -28.84
Energy contribution -27.92
Covariance contribution -0.92
Combinations/Pair 1.19
Mean z-score -1.79
Structure conservation index 0.72
SVM decision value 0.02
SVM RNA-class probability 0.546123
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613467 109 - 23771897
UUUGGCGAGUUUCGAUGAAGAGGCGGCCUUUUG-----------GGGAAUUGUGCGUAAACGCGGUGUCUUUGGGGCAGGCUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAA
...(((..(((((......))))).))).((((-----------((((.....(((....)))((((((.....))).((((((((.....)))))))).......))).)).)))))). ( -36.10)
>DroSec_CAF1 58239 109 - 1
UUUGGCGAGUUUCGAUGAAGAGACGGCCUUUUG-----------GGGCAUUGUGUGUAAACGCGGUGUCUUUGGGGCAGGCUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAA
...((((((((((......))))).(((((..(-----------(((((((((((....)))))))))))).))))).((((((((.....))))))))...........)))))..... ( -43.30)
>DroAna_CAF1 80214 120 - 1
UUUGGCGAGUUUCGAUGAAGAGGAGGCCUUUUGCGGCCCGUUCGGGGACUUGUGCGUAAACGCGGUGGCUUUGGGGCAGGCUUAAGCAACACUUGGGCCAAAUAUUGCGGUCACCGGCAA
....((((((..(......(((..((((......))))..))).)..))))))(((....)))(((((((.....(((((((((((.....))))))))......))))))))))..... ( -42.20)
>DroSim_CAF1 53136 109 - 1
UUUGGCGAGUUUCGAUGAAGAGGCGGCCUUUUG-----------GGGCAUUGUGCGUAAACGCGGUGUCUUUGGGGCAGGCUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAA
...(((((...((......))(((((((((..(-----------((((((((((......))))))))))).))))).((((((((.....))))))))......)))).)))))..... ( -41.80)
>DroEre_CAF1 50783 108 - 1
UUUGGCGAGUUUCGAUGAGGAGGAGGCCUUUUG-----------GGG-AUUGUGCGUAAACGCGGUGUCUUUGGGGCAGGCUCAAGCAACACUUGGGCUAAAUAUUGGCGUCGCUCAAAA
((((((((...((((((........(((((..(-----------((.-((((((......)))))).)))..))))).((((((((.....))))))))...))))))..)))).)))). ( -37.50)
>consensus
UUUGGCGAGUUUCGAUGAAGAGGCGGCCUUUUG___________GGGAAUUGUGCGUAAACGCGGUGUCUUUGGGGCAGGCUUAAGCAACACUUGGGCUAAAUAUUGCCGUCGCCCAAAA
...(((((((..(((..(((((.....))))).............((.((..((((....))))..)))))))..)).((((((((.....))))))))...........)))))..... (-28.84 = -27.92 +  -0.92)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,613,543 – 20,613,651
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.56
Mean single sequence MFE -26.53
Consensus MFE -20.60
Energy contribution -22.04
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -2.50
Structure conservation index 0.78
SVM decision value 1.74
SVM RNA-class probability 0.974795
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20613543 108 + 23771897
-------CAAAAGGCCGCCUCUUCAUCGAAACUCGCCAAAUACUUGGAUAAACAAAUCGGUGACCGCAAA-----AAAGCGGAAAAGAAAACAAAUCGAAUCAGACUAGGGUCUUUUGCU
-------(((((((((......(((((((......((((....)))).........)))))))((((...-----...))))...........................))))))))).. ( -28.06)
>DroSec_CAF1 58315 110 + 1
-------CAAAAGGCCGUCUCUUCAUCGAAACUCGCCAAAUACUUGGAUAAACAAAUCGGUGACCGCAAAA---AAAAGCGGAAAAGAAAACAAACCGAAUCAGACUAGGGUCUUUUGCU
-------(((((((((((((..(((((((......((((....)))).........)))))))((((....---....))))....................))))...))))))))).. ( -29.56)
>DroAna_CAF1 80294 113 + 1
CGGGCCGCAAAAGGCCUCCUCUUCAUCGAAACUCGCCAAAUGCUUGGAUAAACAAAUCGGUGACCGCAAAA----AAAUUGGAAAAGAAAACAAAUCGAAUCAGAGUGGGGUCG---ACU
.(((((......)))))((...(((((((......((((....)))).........)))))))((((....----...(((..........))).((......))))))))...---... ( -24.56)
>DroSim_CAF1 53212 113 + 1
-------CAAAAGGCCGCCUCUUCAUCGAAACUCGCCAAAUACUUGGAUAAACAAAUCGGUGACCGCAAAAAAAAAAAGCGGAAAAGAAAACAAACCGAAUCAGACUAGGGUCUUUUGCU
-------(((((((((......(((((((......((((....)))).........)))))))((((...........))))...........................))))))))).. ( -26.86)
>DroEre_CAF1 50858 108 + 1
-------CAAAAGGCCUCCUCCUCAUCGAAACUCGCCAAAUACUUGGAUAAACAAAUCCGUGACCGCAAA-----AACGCGAAAAAGACAACAAACCGAAUCAGAGUAGGGUCUUUUGCU
-------((((((((((.(((....(((..............(.(((((......))))).)..(((...-----...)))...............)))....)))..)))))))))).. ( -23.60)
>consensus
_______CAAAAGGCCGCCUCUUCAUCGAAACUCGCCAAAUACUUGGAUAAACAAAUCGGUGACCGCAAAA____AAAGCGGAAAAGAAAACAAACCGAAUCAGACUAGGGUCUUUUGCU
.......(((((((((......(((((((......((((....)))).........)))))))((((...........))))...........................))))))))).. (-20.60 = -22.04 +   1.44)

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 12:54:49 2006