Locus 3011

Sequence ID 2L_DroMel_CAF1
Location 8,605,464 – 8,605,668
Length 204
Max. P 0.941440
window4790 window4791 window4792

overview

Window 0

Location 8,605,464 – 8,605,557
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.07
Mean single sequence MFE -41.42
Consensus MFE -26.49
Energy contribution -26.64
Covariance contribution 0.14
Combinations/Pair 1.21
Mean z-score -2.04
Structure conservation index 0.64
SVM decision value 1.21
SVM RNA-class probability 0.931397
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8605464 93 - 22407834
CAUUCAGGGGUUGGC------------CAUCGGUUGGCUUUUGGGUA--------------CUGGCC-CAGCAGGCUAGCCAACUUGAUGUAUUGCCGAGGGCGUAACCCCAACUGGACU
......(((((((((------------(...(((((((((((((((.--------------...)))-))).)))))))))..((((.........))))))).)))))))......... ( -41.60)
>DroSec_CAF1 33866 94 - 1
CAUUCAGGGGUUGGC------------CAUCGGUUGGCUUUUGGGUA--------------CUGGCCACAGCAGCGCAGCCAACUUGAUGGAUUGCCAAGGGCGUAACCCCAACUGGACU
......(((((((.(------------((((((((((((...(.((.--------------(((....)))..)).)))))))).))))))...(((...))).)))))))......... ( -37.00)
>DroSim_CAF1 39560 94 - 1
CAUUCAGGGGUUGGC------------CAUCGGUUGGCUUUUGGGUA--------------CUGGCCACGGCAGCGCAGGCAACUUGAUGGAUUGCCGAGGGCGUAACCCCAACUGGACU
......(((((((((------------(.(((((...((.(..(((.--------------(((((.......)).)))...)))..).))...))))).))).)))))))......... ( -37.00)
>DroEre_CAF1 35569 99 - 1
CAUUCAGGGGUUGGC------------CAUCGGUUGGCUUCUGGGUA-------CUGGGUACUGGCCACA-CAGC-AGGCCAACUUGAUGGAUUGCCGAGGGCGUAACCCCGACUGGACU
((.((.(((((((.(------------((((((((((((((((.((.-------...(((....))))).-))).-)))))))).))))))...(((...))).))))))))).)).... ( -41.10)
>DroYak_CAF1 36177 107 - 1
CAUUCAGGGGUUGGC------------CAUCGGUUGGCUUUUGGGUAUUGGGUCCUGGGUACUGGCCACAGCAGC-AGGCCAACUUGAUGGAUUGCCGAGGGCGUAACCCCAACUGGACU
......(((((((((------------(.(((((...((.(..(((....((.((((....(((....)))...)-))))).)))..).))...))))).))).)))))))......... ( -42.90)
>DroAna_CAF1 34976 107 - 1
CAUUCGGGGGGUGGUCAUCGAGGUGGUCAUCGGCUGGCUCU-GGCU--------CUGGGUCCAGACCAUU-C---UGAGCCAGCUUGAUGGAUUGCCAGGGGCGCAACCCAAACUAGAUU
.....(((..(((.((.....((..((((((((((((((((-((.(--------(((....)))))))..-.---.)))))))).)))).)))..))..)).)))..))).......... ( -48.90)
>consensus
CAUUCAGGGGUUGGC____________CAUCGGUUGGCUUUUGGGUA______________CUGGCCACAGCAGC_AAGCCAACUUGAUGGAUUGCCGAGGGCGUAACCCCAACUGGACU
......(((((((..............((((((((((((.((((((..................))).)))......))))))).)))))....(((...))).)))))))......... (-26.49 = -26.64 +   0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,605,557 – 8,605,668
Length 111
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 93.90
Mean single sequence MFE -24.28
Consensus MFE -22.38
Energy contribution -22.14
Covariance contribution -0.24
Combinations/Pair 1.05
Mean z-score -1.29
Structure conservation index 0.92
SVM decision value 0.77
SVM RNA-class probability 0.846310
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8605557 111 + 22407834
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCGGGGUCUUAGCUCCGCAGCCCAGCGACCCAUUCAAUCACGCUAUAGCGCUCCC-AAAUUUCCCAACGCUCC
.....((((((..........)))))).........(((.(((((((...(((....))).....))))).........(((....))).....-...........)).))) ( -23.80)
>DroSec_CAF1 33960 111 + 1
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCCGGGUCAUAGCUCCAGAGCCCAGCGACCCAUUCAAUCACGCUAUAGCGCCCCC-AAAUUUCCCACCGCUCC
.....((((((..........))))))....((((((....)))))).........((((.....((.....)).....(((....))).....-............)))). ( -24.40)
>DroSim_CAF1 39654 111 + 1
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCCGGGUCAUAGCUCCAGAGCCCAGCGACCCAUUCAAUCACGCUAUAGCGCCCUC-AAAUUUCCCACCGCUCC
.....((((((..........))))))....((((((....)))))).........((((.....((.....)).....(((....))).....-............)))). ( -24.40)
>DroEre_CAF1 35668 112 + 1
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCCGGGUCAUAGCUCCUGAGUCCAGCGACCCAUUCAAUCACGCCGUAGCGCCCCCGAAAAUUUCCACCGCUCC
.....((((((..........)))))).........((((.((((........)))).))))((((.............(((....))).....((.....))...)))).. ( -24.10)
>DroYak_CAF1 36284 111 + 1
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCCGGGUCAUAGCUCCAAAGUCUAGCGACCCAUUCAAUCACGCUAUAGCGCCCCC-AAAAUUUCCACCGCUCC
.....((((((..........))))))....((..(((....(((((.(((((....)).)))..))))).........(((....))).....-..........))).)). ( -24.70)
>consensus
CAUUAGCCAUAACUCUCAUUAUGUGGCAUCCGAUCCGGACCCGGGUCAUAGCUCCAGAGCCCAGCGACCCAUUCAAUCACGCUAUAGCGCCCCC_AAAUUUCCCACCGCUCC
.....((((((..........)))))).((((...))))...(((((...(((....))).....))))).........(((....)))....................... (-22.38 = -22.14 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,605,557 – 8,605,668
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 93.90
Mean single sequence MFE -39.54
Consensus MFE -32.76
Energy contribution -32.80
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.87
Structure conservation index 0.83
SVM decision value 1.32
SVM RNA-class probability 0.941440
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8605557 111 - 22407834
GGAGCGUUGGGAAAUUU-GGGAGCGCUAUAGCGUGAUUGAAUGGGUCGCUGGGCUGCGGAGCUAAGACCCCGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..(((..(((...(((.-.(..((((....))))..)..)))(((((....((((....))))..)))))..(((((...))))).)))((((((....))))))))).... ( -38.50)
>DroSec_CAF1 33960 111 - 1
GGAGCGGUGGGAAAUUU-GGGGGCGCUAUAGCGUGAUUGAAUGGGUCGCUGGGCUCUGGAGCUAUGACCCGGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..((((((.....(((.-.(..((((....))))..)..)))((((((...((((....)))).))))))..(((((...)))))))).((((((....))))))))).... ( -40.50)
>DroSim_CAF1 39654 111 - 1
GGAGCGGUGGGAAAUUU-GAGGGCGCUAUAGCGUGAUUGAAUGGGUCGCUGGGCUCUGGAGCUAUGACCCGGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..((((((.....(((.-.(..((((....))))..)..)))((((((...((((....)))).))))))..(((((...)))))))).((((((....))))))))).... ( -40.50)
>DroEre_CAF1 35668 112 - 1
GGAGCGGUGGAAAUUUUCGGGGGCGCUACGGCGUGAUUGAAUGGGUCGCUGGACUCAGGAGCUAUGACCCGGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..((((((.......(((((..((((....))))..)))))(((((((.(((.((....)))))))))))).(((((...)))))))).((((((....))))))))).... ( -41.30)
>DroYak_CAF1 36284 111 - 1
GGAGCGGUGGAAAUUUU-GGGGGCGCUAUAGCGUGAUUGAAUGGGUCGCUAGACUUUGGAGCUAUGACCCGGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..((((((......((.-.(..((((....))))..)..))(((((((.(((.((....)))))))))))).(((((...)))))))).((((((....))))))))).... ( -36.90)
>consensus
GGAGCGGUGGGAAAUUU_GGGGGCGCUAUAGCGUGAUUGAAUGGGUCGCUGGGCUCUGGAGCUAUGACCCGGGUCCGGAUCGGAUGCCACAUAAUGAGAGUUAUGGCUAAUG
..(((..(((............((((....))))........((((((.(((.((....)))))))))))..(((((...))))).)))((((((....))))))))).... (-32.76 = -32.80 +   0.04)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:07 2006