Locus 877

Sequence ID 2R_DroMel_CAF1
Location 4,031,379 – 4,031,819
Length 440
Max. P 0.991631
window1520 window1521 window1522 window1523 window1524 window1525

overview

Window 0

Location 4,031,379 – 4,031,499
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.07
Mean single sequence MFE -33.22
Consensus MFE -27.30
Energy contribution -28.54
Covariance contribution 1.24
Combinations/Pair 1.15
Mean z-score -1.37
Structure conservation index 0.82
SVM decision value -0.04
SVM RNA-class probability 0.512259
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031379 120 - 20766785
CGGAAAAGGGAGUCGCCCGCCCACUUUUCCGGCAUUGGUAUUGACUUUGUCUGUUUACCAAACCCCUUAGGGGCACAACACCGCAAAGCAGCUUCCAAUUGUUUAAAAGGUAGUUCCUUU
((((((((((.((.....)))).))))))))(((((((..(((.((((((.((((.......((((...))))...))))..)))))))))...)))).)))...(((((.....))))) ( -33.30)
>DroSec_CAF1 14071 120 - 1
CGGAAAAGGGAGUCGCCCGCCCAUUUUUCCGGCAUUGGGAUUGACUUUGUCUGUUUACCGAAGCGCUUUGGGGCACAUCACCGCAAAGCAGUUUCAAAUUGUUUAGAAGGUAGUUCCCUU
((((((((((.(.....).)))..))))))).....((((...(((...((((..((..(((((((((((.((.......)).)))))).)))))....))..)))).)))...)))).. ( -37.60)
>DroSim_CAF1 16193 110 - 1
----------AGUCGCCCGCCCACUUUUCCGGCAUUGGUAUUGACUUUGUCUGUUUACCGAACCGCUUUGGGGCACAACACCGCAAAGCAGUUUCAAAUUGUUUAAAAGGUAGUUCCCUU
----------.((.(((((((.........))).((((((..(((...)))....)))))).........))))))((((((...(((((((.....)))))))....))).)))..... ( -26.70)
>DroEre_CAF1 13522 118 - 1
CGGAAAAAGGAGUCACCCGCCCACUUUUCCGGCAUU-GUAUUGACUUUGUAUGUUUACCGAACCGCUUUGGGGCACAAUACCACAAAGCAGCUUCAAAUUGUUUAA-AGGUAGCUCCUUU
.....(((((((..(((.(((.........)))...-...((((....(((....)))......((((((((........)).))))))....)))).........-.)))..))))))) ( -30.00)
>DroYak_CAF1 17353 119 - 1
CG-AAAAGGGAGUCACCAGCCCACUUUUCCGGGGUUGGUAUUGACUUUGUCUGUUUACCAAACCGCUUUGGGGCACAAUACCACAAAGCAGUUUCAAAUUGUUUAAAAGGUAGCUCCUUU
..-..(((((((..(((.((((.......(((..((((((..(((...)))....)))))).))).....))))...........(((((((.....)))))))....)))..))))))) ( -38.50)
>consensus
CGGAAAAGGGAGUCGCCCGCCCACUUUUCCGGCAUUGGUAUUGACUUUGUCUGUUUACCGAACCGCUUUGGGGCACAACACCGCAAAGCAGUUUCAAAUUGUUUAAAAGGUAGUUCCUUU
.....(((((((..(((.((((.......(((..((((((..(((.......))))))))).))).....))))...........(((((((.....)))))))....)))..))))))) (-27.30 = -28.54 +   1.24) 

alignment

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secondary structure

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Window 1

Location 4,031,459 – 4,031,579
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.08
Mean single sequence MFE -35.92
Consensus MFE -27.68
Energy contribution -31.20
Covariance contribution 3.52
Combinations/Pair 1.03
Mean z-score -2.14
Structure conservation index 0.77
SVM decision value 0.99
SVM RNA-class probability 0.896211
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031459 120 + 20766785
UACCAAUGCCGGAAAAGUGGGCGGGCGACUCCCUUUUCCGGUAGUGAUGCAAGGCAACAAUUGAAUUCGAAGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAU
...((.(((((((((((.((..((....))))))))))))))).))..(((((....)..((((.(((....))).)))).........))))(((((.((((.....)))).))))).. ( -39.40)
>DroSec_CAF1 14151 120 + 1
UCCCAAUGCCGGAAAAAUGGGCGGGCGACUCCCUUUUCCGGUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAC
...((.((((((((((..(((.((....))))))))))))))).))..((..(....)....((((((.(((.........))).))))))))(((((.((((.....)))).))))).. ( -40.30)
>DroSim_CAF1 16273 107 + 1
UACCAAUGCCGGAAAAGUGGGCGGGCGACU-------------GUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAC
......((((......(((.((((....))-------------))..)))..))))......((((((.(((.........))).))))))..(((((.((((.....)))).))))).. ( -26.50)
>DroEre_CAF1 13601 119 + 1
UAC-AAUGCCGGAAAAGUGGGCGGGUGACUCCUUUUUCCGGUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAC
..(-(.((((((((((..(((.((....))))))))))))))).))..((..(....)....((((((.(((.........))).))))))))(((((.((((.....)))).))))).. ( -40.30)
>DroYak_CAF1 17433 119 + 1
UACCAACCCCGGAAAAGUGGGCUGGUGACUCCCUUUU-CGGUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAC
(((((.((((......).))).)))))(((.((....-.)).)))...((..(....)....((((((.(((.........))).))))))))(((((.((((.....)))).))))).. ( -33.10)
>consensus
UACCAAUGCCGGAAAAGUGGGCGGGCGACUCCCUUUUCCGGUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAC
...((.(((((((((((.((((....).))).))))))))))).))..((..(....)....((((((.(((.........))).))))))))(((((.((((.....)))).))))).. (-27.68 = -31.20 +   3.52) 

alignment

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secondary structure

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Window 2

Location 4,031,499 – 4,031,619
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.25
Mean single sequence MFE -27.90
Consensus MFE -24.76
Energy contribution -26.28
Covariance contribution 1.52
Combinations/Pair 1.06
Mean z-score -2.00
Structure conservation index 0.89
SVM decision value 2.28
SVM RNA-class probability 0.991631
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031499 120 + 20766785
GUAGUGAUGCAAGGCAACAAUUGAAUUCGAAGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACAUAAACGAAAGAUAACAUCGAUUCAAUCUCUAUUCAAUGGAA
((((.((((((((....)..((((.(((....))).)))).........))))(((((.((((.....)))).))))).....(....)..............))).))))......... ( -22.90)
>DroSec_CAF1 14191 120 + 1
GUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACACAAACGAAAGAUAACAAAGAUUCAAUCGCUAUUCAGUGGAA
(((....)))..(....).(((((((.((((.((((((..........((((.(((((.((((.....)))).))))).))))(....)......))).))).))))..))))))).... ( -28.40)
>DroSim_CAF1 16303 117 + 1
---GUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACACAAACGAAAGAUAACAACGAUUCAAUCGCUAUUCAGUGGAA
---.(((.((..(....).(((((((.((.((................((((.(((((.((((.....)))).))))).))))(....)....)).))))))))).))...)))...... ( -25.30)
>DroEre_CAF1 13640 120 + 1
GUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACACAAACGAAAGAUAACAUCGAUUCAAUCACUAUUCAGUGGAA
((((((((....(....)...(((((.(((((................((((.(((((.((((.....)))).))))).))))(....)....))))))))))))))))))......... ( -32.80)
>DroYak_CAF1 17472 120 + 1
GUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACACAAAAGAAAGAUAACAUCGAUUCAAUCGCUAUUCAGUGGAA
((((((((....(....)...(((((.(((((...((.......))..((((.(((((.((((.....)))).))))).))))..........))))))))))))))))))......... ( -30.10)
>consensus
GUAGUGAUGCAAGGCAACAAUUGAAUUCGAUGGAACUUAAACAUGGAAUUUGCGUGUAUAUUGGCAAACGAUUUGCACACAAACGAAAGAUAACAUCGAUUCAAUCGCUAUUCAGUGGAA
((((((((....(....)...(((((.(((((................((((.(((((.((((.....)))).))))).))))(....)....))))))))))))))))))......... (-24.76 = -26.28 +   1.52) 

alignment

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secondary structure

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Window 3

Location 4,031,619 – 4,031,739
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.08
Mean single sequence MFE -32.16
Consensus MFE -23.98
Energy contribution -25.70
Covariance contribution 1.72
Combinations/Pair 1.03
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031619 120 + 20766785
GUUGAAAGUGGUGUACAAUGGUGGUGUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGAUGUGCAU
..........((((((((((((.(((((((((....))))).((((....))))....)))).))))).(((((((.(...((((((.......))))))...).))))))).))))))) ( -35.80)
>DroSec_CAF1 14311 120 + 1
GUUAAAAGUGGUGUACAAUGGUGGUCUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGCAAUUCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUUCAU
.......((.((((.((.(((((.((((((((....))))))))......))))).)))))).))....(((((((.(...((((((.......))))))...).)))))))........ ( -29.80)
>DroSim_CAF1 16420 120 + 1
GUUGAAAGUGGUGUACAAUGGUGGUCUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUUCAU
..((((.((.((((.((.(((((.((((((((....))))))))......))))).)))))).))((.((((((((.(...((((((.......))))))...).)))))))))))))). ( -34.70)
>DroEre_CAF1 13760 119 + 1
GUUGAAAGUGGCGUACAAUGGGGGUCUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGACAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGUUUACUUGUU-UGCAU
((((....((((((.(......).((((((((....)))))))).....)))))).))))......((((((((((((...((((((.......))))))...))))....)))-))))) ( -28.00)
>DroYak_CAF1 17592 120 + 1
GUUGAAAGUGGCGUACAAUGGUGGUAUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGUUGUGCAU
............((((((((((.((.((((((....))))))((((....))))......)).)))))((((((((.(...((((((.......))))))...).))))))))))))).. ( -32.50)
>consensus
GUUGAAAGUGGUGUACAAUGGUGGUCUUCAAUACUUGUUGAAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUGCAU
............((((((((((.((.((((((....))))))((((....))))......)).)))))((((((((.(...((((((.......))))))...).))))))))))))).. (-23.98 = -25.70 +   1.72) 

alignment

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secondary structure

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Window 4

Location 4,031,659 – 4,031,779
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.00
Mean single sequence MFE -29.92
Consensus MFE -24.84
Energy contribution -25.72
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -2.09
Structure conservation index 0.83
SVM decision value 1.85
SVM RNA-class probability 0.980011
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031659 120 + 20766785
AAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGAUGUGCAUUGUUUGCAUUUUCCUGCAAAAUGCCUUCCUGUGAUAUUUU
((((((.......(((((.((((......(((((((.(...((((((.......))))))...).))))))).)))))))))((((((......)))))).))))))............. ( -29.50)
>DroSec_CAF1 14351 115 + 1
AAGGUAAUAAUGCUAAUGACACGGCAAUUCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUUCAUUGUUUGCAUUUUCCUGCAAAAUGCCUUCCUGUGAU-----
((((((.......((((((.(((((((.....((((.(...((((((.......))))))...).)))))))))))))))))((((((......)))))).))))))........----- ( -30.10)
>DroSim_CAF1 16460 120 + 1
AAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUUCAUUGUUUGCAUUUUCCUGCAAAAUGCCUUCCUGUGAUAUUUU
((((((................(..((.((((((((.(...((((((.......))))))...).))))))))))..)....((((((......)))))).))))))............. ( -29.40)
>DroEre_CAF1 13800 119 + 1
AAGGUAAUAAUGCUAAUGACACGGACAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGUUUACUUGUU-UGCAUUGUUUGCAUAUUCCUGCAAAAUGCCUUCCUGUGAUAUUUU
..((((....))))((((.(((((....((((.(((((...((((((.......))))))...))))).)))).-.(((((..(((((......))))))))))....))))).)))).. ( -29.70)
>DroYak_CAF1 17632 120 + 1
AAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGUUGUGCAUUGCUUGCAUAUUCCUGCAAAAUACCUUCCUCAAAUAUUUU
((((((.....((.((((.((((.....((((((((.(...((((((.......))))))...).))))))))))))))))))(((((......)))))..))))))............. ( -30.90)
>consensus
AAGGUAAUAAUGCUAAUGACACGGCCAUGCAAAUGAACAAACCACGAUUUCAAUUUGUGGGAGGAUUAUUUGCUGUGCAUUGUUUGCAUUUUCCUGCAAAAUGCCUUCCUGUGAUAUUUU
((((((.......(((((.(((((.....(((((((.(...((((((.......))))))...).)))))))))))))))))((((((......)))))).))))))............. (-24.84 = -25.72 +   0.88) 

alignment

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secondary structure

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dotplot

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Window 5

Location 4,031,699 – 4,031,819
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.58
Mean single sequence MFE -25.96
Consensus MFE -18.06
Energy contribution -19.18
Covariance contribution 1.12
Combinations/Pair 1.11
Mean z-score -1.87
Structure conservation index 0.70
SVM decision value 0.19
SVM RNA-class probability 0.628000
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4031699 120 - 20766785
AUCAACUCCACAUUGUUCAUUACGGACUCUUGUGCCAUAGAAAAUAUCACAGGAAGGCAUUUUGCAGGAAAAUGCAAACAAUGCACAUCAAAUAAUCCUCCCACAAAUUGAAAUCGUGGU
.......((((....((((....(((.(((((((..(((.....))))))))))..((((((((((......)))))..)))))..............))).......))))...)))). ( -24.60)
>DroSec_CAF1 14391 113 - 1
AUCAACUCCACAUUGUUCUUUACGGACUCUUGUGCUAU-------AUCACAGGAAGGCAUUUUGCAGGAAAAUGCAAACAAUGAACAGCAAAUAAUCCUCCCACAAAUUGAAAUCGUGGU
..........(((((((..........(((((((....-------..)))))))..(((((((.....))))))).))))))).................((((...........)))). ( -22.70)
>DroSim_CAF1 16500 120 - 1
AUCAACUCCACAUUGUUCAUUACGGACUCUUGUGCUAUAGAAAAUAUCACAGGAAGGCAUUUUGCAGGAAAAUGCAAACAAUGAACAGCAAAUAAUCCUCCCACAAAUUGAAAUCGUGGU
.......((((.(((((((((......(((((((.(((.....))).)))))))..(((((((.....)))))))....))))))))).....................(....))))). ( -26.60)
>DroEre_CAF1 13840 119 - 1
AUGAACUCCGCAUUGUUUGUUACGCACUCUUGUGGUAUUGAAAAUAUCACAGGAAGGCAUUUUGCAGGAAUAUGCAAACAAUGCA-AACAAGUAAACCUCCCACAAAUUGAAAUCGUGGU
.........(((((((((.....((..(((((((((((.....)))))))))))..)).....(((......)))))))))))).-..............((((...........)))). ( -33.80)
>DroYak_CAF1 17672 110 - 1
----------GAUUGUUUAUUACGGACUCUUGUGGUAUUGAAAAUAUUUGAGGAAGGUAUUUUGCAGGAAUAUGCAAGCAAUGCACAACAAAUAAUCCUCCCACAAAUUGAAAUCGUGGU
----------((((((((..(((((....)))))(((((((((((((((.....)))))))))(((......)))...)))))).....))))))))...((((...........)))). ( -22.10)
>consensus
AUCAACUCCACAUUGUUCAUUACGGACUCUUGUGCUAUAGAAAAUAUCACAGGAAGGCAUUUUGCAGGAAAAUGCAAACAAUGCACAACAAAUAAUCCUCCCACAAAUUGAAAUCGUGGU
..........(((((((..........(((((((.(((.....))).)))))))..(((((((.....))))))).))))))).................((((...........)))). (-18.06 = -19.18 +   1.12) 

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 09:49:44 2006