Locus 2822

Sequence ID 2R_DroMel_CAF1
Location 9,821,910 – 9,822,028
Length 118
Max. P 0.999431
window4664 window4665 window4666 window4667

overview

Window 4

Location 9,821,910 – 9,822,001
Length 91
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 93.27
Mean single sequence MFE -21.68
Consensus MFE -18.96
Energy contribution -18.96
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.16
Structure conservation index 0.87
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9821910 91 + 20766785
GAGUCCUCAAGAACUCAGUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUGCUUUCCUCAUUCGUUGGCUCUUUU------
(((((..(.(((((...)))))(((((...(((...((((((...........)))))).)))....))))).......)..)))))....------ ( -20.40)
>DroSec_CAF1 59652 90 + 1
GAGUCCUCAAGAACUCAGUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUACUUUCCUCAUUCGCUGGCUCUU-U------
(((((..(.(((((...)))))(((((...(((...((((((...........)))))).)))....))))).......)..)))))..-.------ ( -18.30)
>DroSim_CAF1 61148 90 + 1
GAGUCCUCGAGAACUCAGUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUACUUUCCUCAUUCGCUGGCUCUU-U------
(((((..((((...(((((((....)))))))....((((((...........)))))).................))))..)))))..-.------ ( -21.30)
>DroEre_CAF1 64360 97 + 1
GAGUCCUCAAGAACUCAGUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUGCUUUCCUCAUUCGCUGGCUCUUUUGGCUGU
.((.((..((((.(.((((...(((((...(((...((((((...........)))))).)))....))))).......))))).))))..)))).. ( -22.60)
>DroYak_CAF1 61456 97 + 1
GAGUCCUCAAGAACUCAGUUUUGAAAGGCUGGACGCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUGCUUUCCUCAUUCGCUGGCUCUUUUGGCUGU
.((.((..((((.(.((((..((((((((.(((...((((((...........)))))).)))...)))))..)))...))))).))))..)))).. ( -25.80)
>consensus
GAGUCCUCAAGAACUCAGUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUGCUUUCCUCAUUCGCUGGCUCUUUU______
(((((..(.(((((...)))))(((((...(((...((((((...........)))))).)))....))))).......)..))))).......... (-18.96 = -18.96 +   0.00)

alignment

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secondary structure

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Window 5

Location 9,821,910 – 9,822,001
Length 91
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 93.27
Mean single sequence MFE -27.46
Consensus MFE -25.14
Energy contribution -25.54
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.25
Structure conservation index 0.92
SVM decision value 3.60
SVM RNA-class probability 0.999431
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9821910 91 - 20766785
------AAAAGAGCCAACGAAUGAGGAAAGCAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAACUGAGUUCUUGAGGACUC
------...................(((((.(..(((.(((((((.........)))))))...)))..))))))......((((((....)))))) ( -24.90)
>DroSec_CAF1 59652 90 - 1
------A-AAGAGCCAGCGAAUGAGGAAAGUAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAACUGAGUUCUUGAGGACUC
------.-(((((((((........(((((....(((.(((((((.........)))))))...)))...)))))....))).))))))........ ( -27.00)
>DroSim_CAF1 61148 90 - 1
------A-AAGAGCCAGCGAAUGAGGAAAGUAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAACUGAGUUCUCGAGGACUC
------.-..(((((.(.((((...(((((....(((.(((((((.........)))))))...)))...)))))........)))).)..)).))) ( -25.60)
>DroEre_CAF1 64360 97 - 1
ACAGCCAAAAGAGCCAGCGAAUGAGGAAAGCAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAACUGAGUUCUUGAGGACUC
..((((..(((((((((........(((((.(..(((.(((((((.........)))))))...)))..))))))....))).))))))..)).)). ( -30.10)
>DroYak_CAF1 61456 97 - 1
ACAGCCAAAAGAGCCAGCGAAUGAGGAAAGCAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGCGUCCAGCCUUUCAAAACUGAGUUCUUGAGGACUC
..((((..(((((((((........(((((....(((.(((((((.........)))))))...)))...)))))....))).))))))..)).)). ( -29.70)
>consensus
______AAAAGAGCCAGCGAAUGAGGAAAGCAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAACUGAGUUCUUGAGGACUC
........(((((((((........(((((....(((.(((((((.........)))))))...)))...)))))....))).))))))........ (-25.14 = -25.54 +   0.40)

alignment

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secondary structure

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Window 6

Location 9,821,927 – 9,822,028
Length 101
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 94.75
Mean single sequence MFE -19.30
Consensus MFE -17.41
Energy contribution -17.30
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -1.80
Structure conservation index 0.90
SVM decision value 0.15
SVM RNA-class probability 0.608222
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9821927 101 + 20766785
GUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUGCUUUCCUCAUUCGUUGGCUCUUUUAGACGCACGAUCUUCUUAUUCCC-UUUU
.....(((((...(((...((((((...........)))))).)))....))))).....((((..((((.....)).)))))).............-.... ( -17.90)
>DroSec_CAF1 59669 101 + 1
GUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUACUUUCCUCAUUCGCUGGCUCUU-UGGCCACACGAUCCUCUUAUUCCCCUUUU
.....(((((...(((...((((((...........)))))).)))....))))).....(((.(((((...-.)))))..))).................. ( -20.00)
>DroSim_CAF1 61165 101 + 1
GUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUACUUUCCUCAUUCGCUGGCUCUU-UGGCCACACGAUCUUCUUAUUCCCCUUUU
.....(((((...(((...((((((...........)))))).)))....))))).....(((.(((((...-.)))))..))).................. ( -20.00)
>consensus
GUUUUGAAAGACUGGACCCAACGGCCUUGCUUAUCAGCCGUUUUCCCUUACUUUCCUCAUUCGCUGGCUCUU_UGGCCACACGAUCUUCUUAUUCCCCUUUU
.....(((((...(((...((((((...........)))))).)))....))))).....(((.(((((.....)))))..))).................. (-17.41 = -17.30 +  -0.11)

alignment

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secondary structure

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Window 7

Location 9,821,927 – 9,822,028
Length 101
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 94.75
Mean single sequence MFE -27.07
Consensus MFE -24.52
Energy contribution -24.97
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.75
Structure conservation index 0.91
SVM decision value 1.39
SVM RNA-class probability 0.949696
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9821927 101 - 20766785
AAAA-GGGAAUAAGAAGAUCGUGCGUCUAAAAGAGCCAACGAAUGAGGAAAGCAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAAC
....-.............((((((.((.....))))..)))).....(((((.(..(((.(((((((.........)))))))...)))..))))))..... ( -23.80)
>DroSec_CAF1 59669 101 - 1
AAAAGGGGAAUAAGAGGAUCGUGUGGCCA-AAGAGCCAGCGAAUGAGGAAAGUAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAAC
..................((((.((((..-....)))))))).....(((((....(((.(((((((.........)))))))...)))...)))))..... ( -28.70)
>DroSim_CAF1 61165 101 - 1
AAAAGGGGAAUAAGAAGAUCGUGUGGCCA-AAGAGCCAGCGAAUGAGGAAAGUAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAAC
..................((((.((((..-....)))))))).....(((((....(((.(((((((.........)))))))...)))...)))))..... ( -28.70)
>consensus
AAAAGGGGAAUAAGAAGAUCGUGUGGCCA_AAGAGCCAGCGAAUGAGGAAAGUAAGGGAAAACGGCUGAUAAGCAAGGCCGUUGGGUCCAGUCUUUCAAAAC
..................((((.((((.......)))))))).....(((((....(((.(((((((.........)))))))...)))...)))))..... (-24.52 = -24.97 +   0.45)

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 10:40:20 2006