Locus 2421

Sequence ID 3R_DroMel_CAF1
Location 6,762,885 – 6,763,106
Length 221
Max. P 0.954844
window3941 window3942 window3943 window3944 window3945

overview

Window 1

Location 6,762,885 – 6,762,986
Length 101
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 81.36
Mean single sequence MFE -28.93
Consensus MFE -21.90
Energy contribution -22.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.76
SVM decision value 0.77
SVM RNA-class probability 0.847118
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762885 101 - 27905053
GU-----------------AAGUCCUUCAUUAAAUUGCAUUGGUGGCACCCAAAAAAUUUGGUUAGAUCCGAGCCACAAAUUGUGAAUCUGGUCACACAAAUAAGUCCUGAUGCAAGG
..-----------------...............((((((..(.(((..((((.....))))...((((.((..(((.....)))..)).))))..........))))..)))))).. ( -25.50)
>DroSec_CAF1 27148 117 - 1
GCGGGAUGUCCCACAAAACGAGACCUUCAUUAAAUUGCAUUGGUGGCACGCAAAAAAUUUGGUUAAAUCCGAGCCAGAAAGUGUGAGUCU-AUCACACAAAGAAACCCUGAUGCAAGG
(.(((....))).)....................((((((..(.((...........(((((((.......)))))))..((((((....-.)))))).......)))..)))))).. ( -32.10)
>DroSim_CAF1 31472 118 - 1
GAGAGAUGUGUCACAAAACAAGUCCUUCAUUAAAUUGCAUUGGUGGCACGAAAAAAAUUUGGUUAAAUCCGAGCCACAAAGUGUGAAUCUGGUCACACAAAGAAACCCUGAUGCAAGG
(((.(((.(((......))).))).)))......(((((((.(((((...........((((......)))))))))...((((((......))))))...........))))))).. ( -29.20)
>consensus
GAG_GAUGU__CACAAAACAAGUCCUUCAUUAAAUUGCAUUGGUGGCACGCAAAAAAUUUGGUUAAAUCCGAGCCACAAAGUGUGAAUCUGGUCACACAAAGAAACCCUGAUGCAAGG
..................................((((((..(((((...........((((......))))))))....((((((......)))))).........)..)))))).. (-21.90 = -22.23 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,762,925 – 6,763,026
Length 101
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 83.62
Mean single sequence MFE -29.65
Consensus MFE -22.55
Energy contribution -22.55
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.76
SVM decision value 0.07
SVM RNA-class probability 0.569971
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762925 101 + 27905053
UGUGGCUCGGAUCUAACCAAAUUUUUUGGGUGCCACCAAUGCAAUUUAAUGAAGGACUU-----------------ACCAUUUAUUUCCCACAGUGCAUUGUGGCUGUGUGCCUUGAG
...(((.((.(.....((((.....))))..(((((.((((((....((((((((....-----------------.)).))))))........)))))))))))).)).)))..... ( -26.50)
>DroSec_CAF1 27187 118 + 1
UCUGGCUCGGAUUUAACCAAAUUUUUUGCGUGCCACCAAUGCAAUUUAAUGAAGGUCUCGUUUUGUGGGACAUCCCGCCAUUUAUUUCCCACAGUGCAUUGUGGCUGUAUGCCUUAAG
...(((..((......))........((((.(((((.((((((....(((((.....)))))((((((((................))))))))))))))))))))))).)))..... ( -34.09)
>DroSim_CAF1 31512 118 + 1
UGUGGCUCGGAUUUAACCAAAUUUUUUUCGUGCCACCAAUGCAAUUUAAUGAAGGACUUGUUUUGUGACACAUCUCUCCAUUUAUUUUCCACAGUGCAUUGUGGCUGUAUGCCUUAAG
.(((((.((((...............)))).)))))(((((((....(((((((((..(((........)))....))).))))))........))))))).(((.....)))..... ( -28.36)
>consensus
UGUGGCUCGGAUUUAACCAAAUUUUUUGCGUGCCACCAAUGCAAUUUAAUGAAGGACUUGUUUUGUG__ACAUC_CACCAUUUAUUUCCCACAGUGCAUUGUGGCUGUAUGCCUUAAG
...(((..((......)).............(((((.((((((....((((((((......................)).))))))........))))))))))).....)))..... (-22.55 = -22.55 +   0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,762,925 – 6,763,026
Length 101
Sequences 3
Columns 118
Reading direction reverse
Mean pairwise identity 83.62
Mean single sequence MFE -31.07
Consensus MFE -23.57
Energy contribution -23.35
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.70
Structure conservation index 0.76
SVM decision value 1.45
SVM RNA-class probability 0.954844
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762925 101 - 27905053
CUCAAGGCACACAGCCACAAUGCACUGUGGGAAAUAAAUGGU-----------------AAGUCCUUCAUUAAAUUGCAUUGGUGGCACCCAAAAAAUUUGGUUAGAUCCGAGCCACA
.....(((.....(((((((((((.((.((((..((.....)-----------------)..)))).))......)))))).)))))...........((((......)))))))... ( -26.50)
>DroSec_CAF1 27187 118 - 1
CUUAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUGGCGGGAUGUCCCACAAAACGAGACCUUCAUUAAAUUGCAUUGGUGGCACGCAAAAAAUUUGGUUAAAUCCGAGCCAGA
.....(((.....(((((((((((.(((((((.((..........)).)))))))....(((...))).......)))))).)))))...........((((......)))))))... ( -33.00)
>DroSim_CAF1 31512 118 - 1
CUUAAGGCAUACAGCCACAAUGCACUGUGGAAAAUAAAUGGAGAGAUGUGUCACAAAACAAGUCCUUCAUUAAAUUGCAUUGGUGGCACGAAAAAAAUUUGGUUAAAUCCGAGCCACA
.....(((.....(((((((((((.(((.....)))(((((((.(((.(((......))).))))))))))....)))))).)))))...........((((......)))))))... ( -33.70)
>consensus
CUUAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUGGAG_GAUGU__CACAAAACAAGUCCUUCAUUAAAUUGCAUUGGUGGCACGCAAAAAAUUUGGUUAAAUCCGAGCCACA
.....(((.....(((((((((((..(((((..................................))))).....)))))).)))))...........((((......)))))))... (-23.57 = -23.35 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,762,963 – 6,763,066
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.01
Mean single sequence MFE -30.78
Consensus MFE -20.40
Energy contribution -21.24
Covariance contribution 0.84
Combinations/Pair 1.17
Mean z-score -1.77
Structure conservation index 0.66
SVM decision value 0.53
SVM RNA-class probability 0.771553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762963 103 - 27905053
CCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCACACAGCCACAAUGCACUGUGGGAAAUAAAUGGU-----------------AAGUCCUUCAUUAAAUUGCAU
..((((..(((((......))))).(((((...((((((......(((.....))).))))))...))))).......))))-----------------..................... ( -28.90)
>DroSec_CAF1 27225 120 - 1
CCACCAGCCGCCACCCACUCGGUGACCCACUUAGCAUUGCCUUAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUGGCGGGAUGUCCCACAAAACGAGACCUUCAUUAAAUUGCAU
......((((.((((.....)))).(((((...((((((......(((.....))).))))))...))))).......))))(((....)))............................ ( -33.80)
>DroSim_CAF1 31550 120 - 1
CCACCAGCCGCCGCCCACUGGUUGACCCACUUAGCAUUGCCUUAAGGCAUACAGCCACAAUGCACUGUGGAAAAUAAAUGGAGAGAUGUGUCACAAAACAAGUCCUUCAUUAAAUUGCAU
....((((((........))))))..((((...((((((......(((.....))).))))))...))))......(((((((.(((.(((......))).))))))))))......... ( -31.30)
>DroEre_CAF1 11614 111 - 1
CCGUCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGUAUACAGUCGCAAUGCACUGUGGGAAACAAGUCGUGCGAUACAUUGCAAAAUGAUUCCUUCACA---------
.((.(...(((((......))))).(((((...(((((((..(..........)..)))))))...)))))......).))(((((....)))))...(((.....)))..--------- ( -30.40)
>DroYak_CAF1 23735 111 - 1
CCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCAUACAGCCACAAUGCACUGUGCGAAAUAAGUGGUGGGAUGUGUUGCAAAAUUAUUCCUUCAUU---------
......((.(((((((((..(....).(((((((((((((.....(((.....))).....)))..))))....))))))))))).)).)).)).................--------- ( -29.50)
>consensus
CCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUGGUGGGAUGUGUCACAAAACAAGUCCUUCAUUAAAUUGCAU
.(((((..((((........)))).(((((...((((((......(((.....))).))))))...))))).......)))))..................................... (-20.40 = -21.24 +   0.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 6,762,986 – 6,763,106
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -28.25
Consensus MFE -25.09
Energy contribution -25.21
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.55
Structure conservation index 0.89
SVM decision value 1.30
SVM RNA-class probability 0.938798
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6762986 120 - 27905053
ACCACUCAGCGGCCCCACUUCAUCAUUAAUGCACCGAAAUCCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCACACAGCCACAAUGCACUGUGGGAAAUAAAUG
........(((((.........((...........)).........)))))((((.....)))).(((((...((((((......(((.....))).))))))...)))))......... ( -29.57)
>DroSec_CAF1 27265 120 - 1
ACCACUCAGCGGCCCCACUUCAUCAUUAAUGCACCGAAAUCCACCAGCCGCCACCCACUCGGUGACCCACUUAGCAUUGCCUUAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUG
........(((((.........((...........)).........)))))((((.....)))).(((((...((((((......(((.....))).))))))...)))))......... ( -29.97)
>DroSim_CAF1 31590 120 - 1
ACCACUCAGCGGCCCCACUUCAUCAUUAAUGCACCGAAAUCCACCAGCCGCCGCCCACUGGUUGACCCACUUAGCAUUGCCUUAAGGCAUACAGCCACAAUGCACUGUGGAAAAUAAAUG
((((....(((((....................................)))))....))))....((((...((((((......(((.....))).))))))...)))).......... ( -24.92)
>DroEre_CAF1 11645 120 - 1
ACCACUCAGCGGCCCCAUUUCAUCAUUAAUGCACCGAAAUCCGUCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGUAUACAGUCGCAAUGCACUGUGGGAAACAAGUC
........(((((..((((........))))....((......)).)))))((((.....)))).(((((...(((((((..(..........)..)))))))...)))))......... ( -32.40)
>DroYak_CAF1 23766 120 - 1
ACCACUCAGCGGCCCCACUUCAUCAUUAAUGCACCGAAAUCCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCAUACAGCCACAAUGCACUGUGCGAAAUAAGUG
........(((((.........((...........)).........)))))((((.....))))...(((((((((((((.....(((.....))).....)))..))))....)))))) ( -24.37)
>consensus
ACCACUCAGCGGCCCCACUUCAUCAUUAAUGCACCGAAAUCCACCAGCCGCCGCCCACUCGGUGACCCACUUAGCAUUGCCUCAAGGCAUACAGCCACAAUGCACUGUGGGAAAUAAAUG
........(((((.........((...........)).........)))))((((.....)))).(((((...((((((......(((.....))).))))))...)))))......... (-25.09 = -25.21 +   0.12)

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 10:35:31 2006