Locus 4418

Sequence ID 3R_DroMel_CAF1
Location 11,651,760 – 11,651,960
Length 200
Max. P 0.959059
window7217 window7218 window7219 window7220 window7221

overview

Window 7

Location 11,651,760 – 11,651,880
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.31
Mean single sequence MFE -34.98
Consensus MFE -30.84
Energy contribution -30.88
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.42
Structure conservation index 0.88
SVM decision value 0.72
SVM RNA-class probability 0.833160
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11651760 120 + 27905053
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUACAAUCGGCGAUUCGAUGCAUCCCAUGACGAUGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....).....((((((...............(.(((((((((..((((...)))).))))))))))...((((((.(((....))))))))))))))).((((((........)))))) ( -36.30)
>DroSec_CAF1 32534 120 + 1
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUAUGAUCGGCCAUUCGAUGCAUCCCAUGACGACGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....).....((((((............(((..((((((((((((......)))..)))))))))..)))..((((((........)))))))))))).((((((........)))))) ( -34.40)
>DroSim_CAF1 34739 120 + 1
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUACGAUCGGCGAUUCGAUGCAUCCCAUGACGACGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....).....((((((............(((..((((((((..(((........)))))))))))..)))..((((((........)))))))))))).((((((........)))))) ( -34.60)
>DroEre_CAF1 30565 114 + 1
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUACGAUAGGCGAUUCGAUGCAUCCCAUG------AUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....)...((.((((.((((...((((.(((..((((((((..(((........)))))))))))..))------))))).)))))).)).))......((((((........)))))) ( -34.80)
>DroYak_CAF1 33246 114 + 1
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUACGAUAGGCGAUUCGAUGCAUCCCAUG------AUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....)...((.((((.((((...((((.(((..((((((((..(((........)))))))))))..))------))))).)))))).)).))......((((((........)))))) ( -34.80)
>consensus
CGAAAGUGCCAAGAGUCGAAGACAAUCAAUUAGAGGGUGCAUUACGAUCGGCGAUUCGAUGCAUCCCAUGACGA_GAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGC
(....).....((((((...............(.((((((((..(((........)))))))))))).........((((((.....)))))))))))).((((((........)))))) (-30.84 = -30.88 +   0.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,651,760 – 11,651,880
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.31
Mean single sequence MFE -33.20
Consensus MFE -29.96
Energy contribution -30.00
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.15
Structure conservation index 0.90
SVM decision value 0.06
SVM RNA-class probability 0.561935
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11651760 120 - 27905053
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCAUCGUCAUGGGAUGCAUCGAAUCGCCGAUUGUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......))))))).........(((.(((.(((((.((((....))))))))).))).)))(((((..((.....((..((.....))..)).....))..)))))....... ( -34.00)
>DroSec_CAF1 32534 120 - 1
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCGUCGUCAUGGGAUGCAUCGAAUGGCCGAUCAUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......)))))))........(((.(((..(((((.((((....))))))))).(((((.(((.(((((................))))))))))))).......)))..))) ( -33.49)
>DroSim_CAF1 34739 120 - 1
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCGUCGUCAUGGGAUGCAUCGAAUCGCCGAUCGUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......))))))).......((((((........)))))).((((.(((.((((((((........)))..)))))))).....((((......))))....))))....... ( -33.90)
>DroEre_CAF1 30565 114 - 1
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAU------CAUGGGAUGCAUCGAAUCGCCUAUCGUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......))))))).....(((.((..((((((((((.------...(((.((((((((........)))..))))))))......))).)).)))))..)).)))........ ( -32.30)
>DroYak_CAF1 33246 114 - 1
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAU------CAUGGGAUGCAUCGAAUCGCCUAUCGUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......))))))).....(((.((..((((((((((.------...(((.((((((((........)))..))))))))......))).)).)))))..)).)))........ ( -32.30)
>consensus
GCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUC_UCGUCAUGGGAUGCAUCGAAUCGCCGAUCGUAAUGCACCCUCUAAUUGAUUGUCUUCGACUCUUGGCACUUUCG
(((((((......)))))))...(((((.((((.....))))...........(((.((((((((........)))..))))))))......)))))(((..........)))....... (-29.96 = -30.00 +   0.04)

alignment

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secondary structure

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Window 9

Location 11,651,800 – 11,651,920
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.63
Mean single sequence MFE -31.72
Consensus MFE -28.00
Energy contribution -27.64
Covariance contribution -0.36
Combinations/Pair 1.09
Mean z-score -1.63
Structure conservation index 0.88
SVM decision value 1.50
SVM RNA-class probability 0.959059
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11651800 120 + 27905053
AUUACAAUCGGCGAUUCGAUGCAUCCCAUGACGAUGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGUUUUCAAUUGAACAGUAAGUGUGUAUUACAAUCA
............((((.((((((..(.((.((((((.(((....))))))))).))....((((((........))))))..(.(((((......))))).)..)..))))))..)))). ( -32.10)
>DroSec_CAF1 32574 120 + 1
AUUAUGAUCGGCCAUUCGAUGCAUCCCAUGACGACGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGCUUUCAAUUGAACAGUAAGUGUGUAUUACAAUCA
...((((((((....))))).))).........((((((........))))))((((.((((((((........))))))(((.(((((((....))).))))..)))....)).)))). ( -28.60)
>DroSim_CAF1 34779 120 + 1
AUUACGAUCGGCGAUUCGAUGCAUCCCAUGACGACGAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGCUUUCAAUUGAACAGUAAGUGUGUAUUACAAUCA
..((((((((.((((..((.(((((.............))))).))..)))))))))...((((((........))))))(((.(((((((....))).))))..))))))......... ( -30.22)
>DroEre_CAF1 30605 114 + 1
AUUACGAUAGGCGAUUCGAUGCAUCCCAUG------AUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGCUUUCAAUUGAACAGUAAGUAUGCAUUACAAUCA
..........(((((..((.(((((.....------..))))).))..)))))((((.((((((((........))))))(((.(((((((....))).))))....)))..)).)))). ( -32.70)
>DroYak_CAF1 33286 114 + 1
AUUACGAUAGGCGAUUCGAUGCAUCCCAUG------AUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGCUUUCAAUUGAACAGUAAGUAUGCAUUGCAAUCA
..........(((((..((.(((((.....------..))))).))..)))))((((...((((((........))))))(((((((.....................))))))))))). ( -35.00)
>consensus
AUUACGAUCGGCGAUUCGAUGCAUCCCAUGACGA_GAUGAUGCUUCACAUCGUGAUUUUAGCAGCCACUUUUACGGCUGCGCAGUGCUUUCAAUUGAACAGUAAGUGUGUAUUACAAUCA
..........(((((..((.(((((.............))))).))..)))))((((.((((((((........))))))(((.(((((((....))).))))....)))..)).)))). (-28.00 = -27.64 +  -0.36)

alignment

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secondary structure

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Window 0

Location 11,651,800 – 11,651,920
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.63
Mean single sequence MFE -31.18
Consensus MFE -25.12
Energy contribution -25.24
Covariance contribution 0.12
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.81
SVM decision value 0.15
SVM RNA-class probability 0.606810
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11651800 120 - 27905053
UGAUUGUAAUACACACUUACUGUUCAAUUGAAAACACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCAUCGUCAUGGGAUGCAUCGAAUCGCCGAUUGUAAU
(((..((((.......))))...)))...........((((((((((......)))))))...((((.((((.(((.(((((.((((....))))))))).))).))))..))))))).. ( -31.80)
>DroSec_CAF1 32574 120 - 1
UGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCGUCGUCAUGGGAUGCAUCGAAUGGCCGAUCAUAAU
(((((((((.......)))).(..((.((((..(((((..(((((((......))))))).......(((((((((....))).))))))....)).))).)))).))..)))))).... ( -29.90)
>DroSim_CAF1 34779 120 - 1
UGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUCGUCGUCAUGGGAUGCAUCGAAUCGCCGAUCGUAAU
.(((((................(((....))).((.....(((((((......))))))).........(((.(((.(((((.((((....))))))))).))).))))))))))..... ( -30.80)
>DroEre_CAF1 30605 114 - 1
UGAUUGUAAUGCAUACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAU------CAUGGGAUGCAUCGAAUCGCCUAUCGUAAU
((((((((.(((...(.....)(((....))).))).)))(((((((......)))))))...)))))((((.(((.(((((..------.....))))).))).))))........... ( -30.70)
>DroYak_CAF1 33286 114 - 1
UGAUUGCAAUGCAUACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAU------CAUGGGAUGCAUCGAAUCGCCUAUCGUAAU
((((((((.(((...(.....)(((....))).))).)))(((((((......)))))))...)))))((((.(((.(((((..------.....))))).))).))))........... ( -32.70)
>consensus
UGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCAUCAUC_UCGUCAUGGGAUGCAUCGAAUCGCCGAUCGUAAU
((((((..............((((........))))..(((((((((......))))))).........(((.(((.(((((.............))))).))).))))))))))).... (-25.12 = -25.24 +   0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,651,840 – 11,651,960
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.83
Mean single sequence MFE -23.18
Consensus MFE -21.38
Energy contribution -21.98
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.92
SVM decision value 1.07
SVM RNA-class probability 0.910527
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11651840 120 - 27905053
CUCAUAAACAAAAUUAACACGGAACAUAAAUCUUUCCCAUUGAUUGUAAUACACACUUACUGUUCAAUUGAAAACACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
.(((................((((.........)))).(((((..((((.......))))...)))))))).......(((((((((......))))))).....((((...)))).)). ( -21.90)
>DroSec_CAF1 32614 120 - 1
CUCAUAAACAAAAUUAACACGGAACAUAAAUCUUUCCCAUUGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
...............................(((((..(((((..((((.......))))...))))).)))))....(((((((((......))))))).....((((...)))).)). ( -23.70)
>DroSim_CAF1 34819 120 - 1
CUCAUAAACAAAAUUAACACGGAACAUAAAUCUUUCCCAUUGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
...............................(((((..(((((..((((.......))))...))))).)))))....(((((((((......))))))).....((((...)))).)). ( -23.70)
>DroEre_CAF1 30639 120 - 1
CUCAUAAACAAAAUUAACACGGACCAUAAAUCUUUCCCACUGAUUGUAAUGCAUACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
.(((((..............(((...........)))...((((((((.(((...(.....)(((....))).))).)))(((((((......)))))))...)))))...))))).... ( -22.20)
>DroYak_CAF1 33320 120 - 1
CUCAUAAACAAAAUUAACACGGACAUUAAAUCUUUCCCAUUGAUUGCAAUGCAUACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
................................((((.(((((...(((.(((...(.....)(((....))).))).)))(((((((......)))))))........))))).)))).. ( -24.40)
>consensus
CUCAUAAACAAAAUUAACACGGAACAUAAAUCUUUCCCAUUGAUUGUAAUACACACUUACUGUUCAAUUGAAAGCACUGCGCAGCCGUAAAAGUGGCUGCUAAAAUCACGAUGUGAAGCA
...............................(((((..(((((..((((.......))))...))))).)))))....(((((((((......))))))).....((((...)))).)). (-21.38 = -21.98 +   0.60)

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 11:28:44 2006