Locus 7859

Sequence ID 3L_DroMel_CAF1
Location 21,005,993 – 21,006,147
Length 154
Max. P 0.999475
window12793 window12794 window12795 window12796

overview

Window 3

Location 21,005,993 – 21,006,107
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 69.91
Mean single sequence MFE -40.53
Consensus MFE -26.61
Energy contribution -27.90
Covariance contribution 1.29
Combinations/Pair 1.19
Mean z-score -1.48
Structure conservation index 0.66
SVM decision value 1.41
SVM RNA-class probability 0.951259
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21005993 114 + 23771897
CAGUUGCAGUGGCAGCACAGGUAGCGGCAGCGGAGGCAGCGGGAGUGGCAGUAGCAAGAAGGUGCCACCAGAGGUGCCCAAACGCACCAGUUCCAUUACGGCACAACAGCAGAC
..((((.(((((.(((...(((.(((......(.((((.(..(.((((((.(........).)))))))...).)))))...)))))).)))))))).))))............ ( -36.60)
>DroGri_CAF1 18376 102 + 1
CAGCUGC---GGCAGUCAGGGCAGCGGCAGUGGUGGCA---------GCAGCAGCAAGAAGGUACCACCGGAGGUGCCCAAGCGCACCUCCUCCAUCACCGCACAGCAGCAGAG
..(((((---.((.((....)).)).((.(((((((..---------((....)).....((.....))((((((((......)))))))).))))))).))...))))).... ( -44.10)
>DroWil_CAF1 2354 96 + 1
GAGCUGC------------------GGCAGCAGUGGCAGCGGCAGUGGCAGUGGCAAGAAGGUGCCACCAGAGGUACCCAAACGUACCUCAUCCAUAACGGCCCAGCAGCAGAG
..(((((------------------.((.((....)).))(((.((((..((((((......))))))..(((((((......)))))))..))))....)))..))))).... ( -40.90)
>consensus
CAGCUGC___GGCAG____GG_AGCGGCAGCGGUGGCAGCGG_AGUGGCAGUAGCAAGAAGGUGCCACCAGAGGUGCCCAAACGCACCUCAUCCAUAACGGCACAGCAGCAGAG
..(((((....((.......))....)))))(((((((.(.......((....)).....).)))))))((((((((......)))))))).........((......)).... (-26.61 = -27.90 +   1.29)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,005,993 – 21,006,107
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 69.91
Mean single sequence MFE -40.53
Consensus MFE -28.20
Energy contribution -28.27
Covariance contribution 0.07
Combinations/Pair 1.24
Mean z-score -1.04
Structure conservation index 0.70
SVM decision value 0.14
SVM RNA-class probability 0.601713
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21005993 114 - 23771897
GUCUGCUGUUGUGCCGUAAUGGAACUGGUGCGUUUGGGCACCUCUGGUGGCACCUUCUUGCUACUGCCACUCCCGCUGCCUCCGCUGCCGCUACCUGUGCUGCCACUGCAACUG
((.(((.((.(.((.(((..((...(((((((...(((((.(...(((((((............)))))))...).))))).))).))))...))..))).))))).))))).. ( -33.90)
>DroGri_CAF1 18376 102 - 1
CUCUGCUGCUGUGCGGUGAUGGAGGAGGUGCGCUUGGGCACCUCCGGUGGUACCUUCUUGCUGCUGC---------UGCCACCACUGCCGCUGCCCUGACUGCC---GCAGCUG
....(((((...(((((..(((.((((((((......))))))))((..(((.(........).)))---------..)).)))..))))).((.......)).---))))).. ( -47.80)
>DroWil_CAF1 2354 96 - 1
CUCUGCUGCUGGGCCGUUAUGGAUGAGGUACGUUUGGGUACCUCUGGUGGCACCUUCUUGCCACUGCCACUGCCGCUGCCACUGCUGCC------------------GCAGCUC
....(((((..(((.((..(((..(((((((......))))))).(((((((......))))))).............)))..)).)))------------------))))).. ( -39.90)
>consensus
CUCUGCUGCUGUGCCGUAAUGGAAGAGGUGCGUUUGGGCACCUCUGGUGGCACCUUCUUGCUACUGCCACU_CCGCUGCCACCGCUGCCGCU_CC____CUGCC___GCAGCUG
....(((((...((.((..(((.((((((((......))))))))(((((((......))))))).............)))..)).)).((..........))....))))).. (-28.20 = -28.27 +   0.07)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,006,033 – 21,006,147
Length 114
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 77.19
Mean single sequence MFE -42.74
Consensus MFE -27.57
Energy contribution -29.47
Covariance contribution 1.90
Combinations/Pair 1.19
Mean z-score -2.55
Structure conservation index 0.65
SVM decision value 2.54
SVM RNA-class probability 0.995129
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21006033 114 + 23771897
GGGAGUGGCAGUAGCAAGAAGGUGCCACCAGAGGUGCCCAAACGCACCAGUUCCAUUACGGCACAACAGCAGACACAGCUUCUUUUGCUGCAGCGCCAGACACCGCCGCCUCCU
((..(((((.(((((((((..(((((......(((((......))))).((......)))))))...(((.......)))..))))))))).((....).)...)))))..)). ( -42.70)
>DroGri_CAF1 18411 107 + 1
-------GCAGCAGCAAGAAGGUACCACCGGAGGUGCCCAAGCGCACCUCCUCCAUCACCGCACAGCAGCAGAGCCAGCUGCUGAUGAUGCAGCGACAGACGCCGCCGCCACCC
-------((.((.(((....(((......((((((((......))))))))......))).(((((((((.......))))))).)).))).(((.....))).)).))..... ( -41.20)
>DroWil_CAF1 2376 114 + 1
GGCAGUGGCAGUGGCAAGAAGGUGCCACCAGAGGUACCCAAACGUACCUCAUCCAUAACGGCCCAGCAGCAGAGUCAAUUGCUUCUCUUGCAACGACAGACACCGCCGCCGCCA
(((.(((((.(((((((((.((.(((....(((((((......))))))).........))))).(.(((((......))))).)))))))..(....).))).))))).))). ( -44.32)
>consensus
GG_AGUGGCAGUAGCAAGAAGGUGCCACCAGAGGUGCCCAAACGCACCUCAUCCAUAACGGCACAGCAGCAGAGACAGCUGCUUAUGAUGCAGCGACAGACACCGCCGCCACCA
(((.(((((.((.((.....((.....))((((((((......)))))))).................)).......(((((.......))))).......)).))))).))). (-27.57 = -29.47 +   1.90)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,006,033 – 21,006,147
Length 114
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 77.19
Mean single sequence MFE -53.65
Consensus MFE -39.03
Energy contribution -39.27
Covariance contribution 0.24
Combinations/Pair 1.29
Mean z-score -2.85
Structure conservation index 0.73
SVM decision value 3.64
SVM RNA-class probability 0.999475
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21006033 114 - 23771897
AGGAGGCGGCGGUGUCUGGCGCUGCAGCAAAAGAAGCUGUGUCUGCUGUUGUGCCGUAAUGGAACUGGUGCGUUUGGGCACCUCUGGUGGCACCUUCUUGCUACUGCCACUCCC
.((((..(((((((((((((((.((((((..............)))))).)))))......((((......)))))))))))...(((((((......)))))))))).)))). ( -49.14)
>DroGri_CAF1 18411 107 - 1
GGGUGGCGGCGGCGUCUGUCGCUGCAUCAUCAGCAGCUGGCUCUGCUGCUGUGCGGUGAUGGAGGAGGUGCGCUUGGGCACCUCCGGUGGUACCUUCUUGCUGCUGC-------
.....(((((((((((((((((((((....(((((((.......)))))))))))))))))))((((((((......))))))))((.....))....)))))))))------- ( -60.50)
>DroWil_CAF1 2376 114 - 1
UGGCGGCGGCGGUGUCUGUCGUUGCAAGAGAAGCAAUUGACUCUGCUGCUGGGCCGUUAUGGAUGAGGUACGUUUGGGUACCUCUGGUGGCACCUUCUUGCCACUGCCACUGCC
.(((((((((((.(((....(((((.......))))).))).))))))))..)))((..(((..(((((((......))))))).(((((((......))))))).)))..)). ( -51.30)
>consensus
AGGAGGCGGCGGUGUCUGUCGCUGCAACAAAAGCAGCUGACUCUGCUGCUGUGCCGUAAUGGAAGAGGUGCGUUUGGGCACCUCUGGUGGCACCUUCUUGCUACUGCCACU_CC
.(((((((((((.(((....(((((.......))))).))).))))))))..)))........((((((((......))))))))(((((((......)))))))......... (-39.03 = -39.27 +   0.24)

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 12:58:52 2006