Locus 4951

Sequence ID 3R_DroMel_CAF1
Location 13,022,209 – 13,022,441
Length 232
Max. P 0.961911
window8100 window8101 window8102 window8103 window8104

overview

Window 0

Location 13,022,209 – 13,022,312
Length 103
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 86.13
Mean single sequence MFE -33.98
Consensus MFE -25.94
Energy contribution -27.94
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.76
SVM decision value 0.03
SVM RNA-class probability 0.546389
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13022209 103 + 27905053
-CGGGUCCGGCUCAAAAACUUGAGGUUGGGUGAUAUCACGUCAGUUGCAGGCUUCCACCGGCUUCCAUCGGCUACCACCGACUACCACCGGACUCGUUCACCGA
-((((((((((((((....)))))((((((((....)))(((...((.(((((......))))).))..))).....))))).....)))))))))........ ( -36.60)
>DroSec_CAF1 42256 104 + 1
CCGGGACCGGCUCAAAAACUUGAGGUUGGGUGAUAUCACGUCAGUGGCAGGCUUCCACCGGCUUCCAUCGGCUACCACCGACUACCACCGGACUCGUUCACCGA
.((((.(((((((((....)))))((((((((....)))(((.((((.(((((......))))))))).))).....))))).....)))).))))........ ( -37.10)
>DroSim_CAF1 34735 103 + 1
-CGGGUCCGGCUCAAAAACUUGAGGUUGGGUGAUAUCACGUCAGUUGCAGGCUUCCACCGGCUUCCAUCGGCUACCACCGACUACCACCUGACUCGUUCACCGA
-((((((.(((((((....)))))((((((((....)))(((...((.(((((......))))).))..))).....))))).....)).))))))........ ( -30.50)
>DroEre_CAF1 42841 82 + 1
-CGGGUCCGGCUCAA-AACUUGAGGUUGGGUGAUAUCACGUCAGUUGCAGGCUUCCA----------CCGGCU----------GCCACCGGACUCGUUUACCGA
-(((((((((((((.-....))))..((((((....)))..((((((..((...)).----------.)))))----------)))))))))))))........ ( -29.30)
>DroYak_CAF1 43664 93 + 1
-CGGGUCCGGCUCAAAAACUUGAGGUUGGGUGAUAUCACGUCAGUUGCAGGCUUCCAUUGGCUUCCAUUGGCU----------ACCACCGGACUCGUUCACCGA
-((((((((((((((....)))))..((((((....)))((((((.(.(((((......)))))).)))))).----------.))))))))))))........ ( -36.40)
>consensus
_CGGGUCCGGCUCAAAAACUUGAGGUUGGGUGAUAUCACGUCAGUUGCAGGCUUCCACCGGCUUCCAUCGGCUACCACCGACUACCACCGGACUCGUUCACCGA
.((((((((((((((....)))))..((((((....)))(((...((.(((((......))))).))..)))............))))))))))))........ (-25.94 = -27.94 +   2.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 13,022,274 – 13,022,388
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 88.01
Mean single sequence MFE -36.77
Consensus MFE -29.80
Energy contribution -31.30
Covariance contribution 1.50
Combinations/Pair 1.03
Mean z-score -2.43
Structure conservation index 0.81
SVM decision value 1.53
SVM RNA-class probability 0.961911
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13022274 114 + 27905053
AUCGGCUACCACCGACUACCACCGGACUCGUUCACCGACAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCUGGAGCUAUUGCUAAAGCUAAAGCCAAAGCCAA
...((((....(((........))).............(((((((((((........))))...)))))))(.(((..((((..(((....)))..))))..))))..)))).. ( -36.10)
>DroSec_CAF1 42322 114 + 1
AUCGGCUACCACCGACUACCACCGGACUCGUUCACCGACAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCAGGAGCUGGAGCUACUGCUAAAGCUAAAGCCAA
...((((.((.(((........)))....((((..(..(((((((((((........))))...)))))))..)...)))).))((((..(((....)))..))))..)))).. ( -39.50)
>DroSim_CAF1 34800 114 + 1
AUCGGCUACCACCGACUACCACCUGACUCGUUCACCGACAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCAGGAGCUGGAGCUACUGCUAAAGCUAAAGCCAA
...((((..............((((.(((...((.(..(((((((((((........))))...)))))))..).)))))))))((((..(((....)))..))))..)))).. ( -38.80)
>DroYak_CAF1 43729 98 + 1
AUUGGCU----------ACCACCGGACUCGUUCACCGACAGUUUUUGGCACAUUUCAACCAGAUGAAACUGGAGCUGGAGCUGGAGCUGCAGCU------AUAGCUAAAGCCAA
.((((((----------......(((((.(((....))))))))(((((.........((((......))))(((((.(((....))).)))))------...))))))))))) ( -32.70)
>consensus
AUCGGCUACCACCGACUACCACCGGACUCGUUCACCGACAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCAGGAGCUGGAGCUACUGCUAAAGCUAAAGCCAA
...((((..............((((.(((...((.(..(((((((((((........))))...)))))))..).)))))))))((((..(((....)))..))))..)))).. (-29.80 = -31.30 +   1.50)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,022,312 – 13,022,428
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 88.65
Mean single sequence MFE -39.84
Consensus MFE -27.58
Energy contribution -28.78
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -2.68
Structure conservation index 0.69
SVM decision value 0.79
SVM RNA-class probability 0.850919
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13022312 116 + 27905053
CAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCUGGAGCUAUUGCUAAAGCUAAAGCCAAAGCCAAAGCUGUUGCCCAAGGAGAAGCCAUUUUGGGCUUUUUGUCC
(((((((.(((.........((((......)))).(((..((((..(((....)))..))))..)))....))))))))))..((((((((.(....).))))))))......... ( -41.20)
>DroSec_CAF1 42360 116 + 1
CAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCAGGAGCUGGAGCUACUGCUAAAGCUAAAGCCAAAGCUGUUGCCCAAGGAGAAGCCAUUUUGGCCUUUUUGUCC
(((((((.(((.........((((......))))((((..(((((.(((....))).)))))..))))...)))))))))).....(((((((..(((.....))))))))))... ( -42.70)
>DroSim_CAF1 34838 116 + 1
CAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCAGGAGCUGGAGCUACUGCUAAAGCUAAAGCCAAAGCUGUUGCCCAAGGAGAAGCCAUUUUGGCCUUUUUGUCC
(((((((.(((.........((((......))))((((..(((((.(((....))).)))))..))))...)))))))))).....(((((((..(((.....))))))))))... ( -42.70)
>DroEre_CAF1 42923 98 + 1
CAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCUGGAGCUGGAGCU------------------AAAGCUGUUGGCCAAGGAGAAGCCAUUUUGGCCUUUCUGUCC
(((((((((((........))))...)))))))(.((..(((((..(((....)))------------------..)))).)..)))..(((((.(((.....))).))))).... ( -34.10)
>DroYak_CAF1 43757 110 + 1
CAGUUUUUGGCACAUUUCAACCAGAUGAAACUGGAGCUGGAGCUGGAGCUGCAGCU------AUAGCUAAAGCCAAAGCUGUUGCCCAAGGAGAAGCCAUUUUGGCCUUUUUGUCC
(((((((.(((.........((((......))))(((((.(((((......)))))------.)))))...)))))))))).....(((((((..(((.....))))))))))... ( -38.50)
>consensus
CAGUUUUUGGCACAUUUCAGCCAGAUGAAACUGGAGCUGGAGCUGGAGCUGGAGCUA__GCUAAAGCUAAAGCCAAAGCUGUUGCCCAAGGAGAAGCCAUUUUGGCCUUUUUGUCC
(((((((.(((.........((((......))))((((..(((....)))..))))...............)))))))))).....(((((((..(((.....))))))))))... (-27.58 = -28.78 +   1.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,022,312 – 13,022,428
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 88.65
Mean single sequence MFE -34.52
Consensus MFE -23.68
Energy contribution -26.12
Covariance contribution 2.44
Combinations/Pair 1.03
Mean z-score -2.17
Structure conservation index 0.69
SVM decision value 0.23
SVM RNA-class probability 0.642606
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13022312 116 - 27905053
GGACAAAAAGCCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUGGCUUUAGCUUUAGCAAUAGCUCCAGCUCCAGCUCCAGUUUCAUCUGGCUGAAAUGUGCCAAAAACUG
(((....(((((......))))).)))((((((...((((...(((..(((....)))..)))...))))...)).))))...((((((....((((........)))).)))))) ( -35.30)
>DroSec_CAF1 42360 116 - 1
GGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGCAGUAGCUCCAGCUCCUGCUCCAGCUCCAGUUUCAUCUGGCUGAAAUGUGCCAAAAACUG
(((.....(((((.....))))).)))...((((.((..((..((...((((..(((((.(((....))).)))))..)))).(((......)))))..)).))))))........ ( -37.40)
>DroSim_CAF1 34838 116 - 1
GGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGCAGUAGCUCCAGCUCCUGCUCCAGCUCCAGUUUCAUCUGGCUGAAAUGUGCCAAAAACUG
(((.....(((((.....))))).)))...((((.((..((..((...((((..(((((.(((....))).)))))..)))).(((......)))))..)).))))))........ ( -37.40)
>DroEre_CAF1 42923 98 - 1
GGACAGAAAGGCCAAAAUGGCUUCUCCUUGGCCAACAGCUUU------------------AGCUCCAGCUCCAGCUCCAGCUCCAGUUUCAUCUGGCUGAAAUGUGCCAAAAACUG
(((((....(((((...(((((.......)))))..((((..------------------((((..(((....)))..))))..)))).....)))))....))).))........ ( -28.50)
>DroYak_CAF1 43757 110 - 1
GGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUAU------AGCUGCAGCUCCAGCUCCAGCUCCAGUUUCAUCUGGUUGAAAUGUGCCAAAAACUG
((((....(((((.....))))).....(((((..(((((.((((....)))).------)))))..)).)))).))).....((((((....((((........)))).)))))) ( -34.00)
>consensus
GGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGC__UAGCUCCAGCUCCAGCUCCAGCUCCAGUUUCAUCUGGCUGAAAUGUGCCAAAAACUG
(((.....(((((.....))))).)))..((((...((((..((((..((((........))))..))))..))))...))))((((((....((((........)))).)))))) (-23.68 = -26.12 +   2.44)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,022,348 – 13,022,441
Length 93
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 80.67
Mean single sequence MFE -31.70
Consensus MFE -20.18
Energy contribution -21.88
Covariance contribution 1.70
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.64
SVM decision value 1.43
SVM RNA-class probability 0.953493
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13022348 93 - 27905053
----------------AAGCGGAAGUCGAGGACAAAAAGCCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUGGCUUUAGCUUUAGCAAUAGCUCCAGCUCCAG
----------------((((.((((((((((.......((((((...((.....)))))))).....)))))))))).)))).((((..(((....)))..)))).... ( -31.90)
>DroSec_CAF1 42396 93 - 1
----------------AAGCGGAAGUCGAGGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGCAGUAGCUCCAGCUCCUGCUCCAG
----------------((((.((((((((((.(((..(((((.....)))))....)))(....)..)))))))))).)))).(((((.(((....))).))))).... ( -32.30)
>DroSim_CAF1 34874 93 - 1
----------------AAGCGGAAGUCGAGGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGCAGUAGCUCCAGCUCCUGCUCCAG
----------------((((.((((((((((.(((..(((((.....)))))....)))(....)..)))))))))).)))).(((((.(((....))).))))).... ( -32.30)
>DroEre_CAF1 42959 75 - 1
----------------AAGCGGAAGUCGAGGACAGAAAGGCCAAAAUGGCUUCUCCUUGGCCAACAGCUUU------------------AGCUCCAGCUCCAGCUCCAG
----------------....(((.((((((((..((..((((.....)))))))))))))).....(((..------------------(((....)))..)))))).. ( -25.30)
>DroYak_CAF1 43793 103 - 1
GAGGAAGAGGAAGGGGAAGCGGAAGUCGAGGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUAU------AGCUGCAGCUCCAGCUCCAG
..(((.....((((((((((....)).............(((.....)))))))))))((((..(((((.((((....)))).------)))))..)).))...))).. ( -36.70)
>consensus
________________AAGCGGAAGUCGAGGACAAAAAGGCCAAAAUGGCUUCUCCUUGGGCAACAGCUUUGGCUUUAGCUUUAGC__UAGCUCCAGCUCCAGCUCCAG
.................((((((.((((((((.....(((((.....))))).))))))).)....(((..((((...((....))...))))..)))))).))).... (-20.18 = -21.88 +   1.70)

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 11:42:52 2006