Locus 5218

Sequence ID 2R_DroMel_CAF1
Location 16,978,417 – 16,978,592
Length 175
Max. P 0.993628
window8333 window8334 window8335

overview

Window 3

Location 16,978,417 – 16,978,518
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 95.64
Mean single sequence MFE -16.62
Consensus MFE -14.22
Energy contribution -14.50
Covariance contribution 0.28
Combinations/Pair 1.13
Mean z-score -1.98
Structure conservation index 0.86
SVM decision value 1.79
SVM RNA-class probability 0.977428
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16978417 101 + 20766785
ACCAGCUACCCAACCAUUCGCCACCCACUUACUCCCACAAACUCCUCUCGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
.((((..............(((..................((.......))..((((.....))))..............)))(....).))))....... ( -13.10)
>DroSec_CAF1 75186 101 + 1
ACCAGCCUCCCAACCAUUCGCUACCCACUUACUACCAACAACUCCUCUUGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
....(((............(((...............((((......))))..((((.....)))).........)))..((.(....).)))))...... ( -14.80)
>DroSim_CAF1 80360 101 + 1
ACCAGCCACCCAACCAUUUGCCACCCACUUACUACCAACAACUCCUCUUGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
....((((.........(((((.((..(((.......((((......))))..((((.....))))........)))...)).)))))...))))...... ( -17.90)
>DroEre_CAF1 76546 101 + 1
ACCAGCCACCCAACCAUUCGCCACCCACUUACUACCAACAACUCCUCUUGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
....((((...........(((...............((((......))))..((((.....))))..............)))(....)..))))...... ( -17.30)
>DroYak_CAF1 83390 101 + 1
AAAAGCCAGCCAACCAUUCGCCACCCACUUACUACCAACAACUCCUCUUGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
....(((((........(((((...............((((......))))..((((.....))))..............))))).....)))))...... ( -20.02)
>consensus
ACCAGCCACCCAACCAUUCGCCACCCACUUACUACCAACAACUCCUCUUGUCCACGCAACCAGCGUAAAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAA
....(((............(((...............((((......))))..((((.....))))..............)))(....)...)))...... (-14.22 = -14.50 +   0.28)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,978,417 – 16,978,518
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 95.64
Mean single sequence MFE -32.26
Consensus MFE -29.86
Energy contribution -29.90
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.81
Structure conservation index 0.93
SVM decision value 2.41
SVM RNA-class probability 0.993628
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16978417 101 - 20766785
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACGAGAGGAGUUUGUGGGAGUAAGUGGGUGGCGAAUGGUUGGGUAGCUGGU
..(((.((((...(((((((((((((((.(..(((((((.....)))))))(....).......).))))))...))))))))).)))).)))........ ( -34.20)
>DroSec_CAF1 75186 101 - 1
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACAAGAGGAGUUGUUGGUAGUAAGUGGGUAGCGAAUGGUUGGGAGGCUGGU
(((((.((((..((((((..((((((........(((((.....)))))(((((......)))))...))))))..))))))...)))).)))))...... ( -32.20)
>DroSim_CAF1 80360 101 - 1
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACAAGAGGAGUUGUUGGUAGUAAGUGGGUGGCAAAUGGUUGGGUGGCUGGU
..(((.((((...(((((((((.(((((....(((((((.....))))))).....)))))..............))))))))).)))).)))........ ( -31.66)
>DroEre_CAF1 76546 101 - 1
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACAAGAGGAGUUGUUGGUAGUAAGUGGGUGGCGAAUGGUUGGGUGGCUGGU
..(((.((((...(((((((((.(((((....(((((((.....))))))).....)))))..............))))))))).)))).)))........ ( -31.36)
>DroYak_CAF1 83390 101 - 1
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACAAGAGGAGUUGUUGGUAGUAAGUGGGUGGCGAAUGGUUGGCUGGCUUUU
...((.(((((..(((((((((.(((((....(((((((.....))))))).....)))))..............)))))))))....))))).))..... ( -31.86)
>consensus
UUUCUUGCCAGAGUUGCCGCCUUGCUUUGAAUUUUACGCUGGUUGCGUGGACAAGAGGAGUUGUUGGUAGUAAGUGGGUGGCGAAUGGUUGGGUGGCUGGU
...((.((((...(((((((((.(((((....(((((((.....))))))).....)))))..............))))))))).)))).))......... (-29.86 = -29.90 +   0.04)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,978,484 – 16,978,592
Length 108
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.18
Mean single sequence MFE -26.15
Consensus MFE -15.44
Energy contribution -16.72
Covariance contribution 1.28
Combinations/Pair 1.22
Mean z-score -1.75
Structure conservation index 0.59
SVM decision value -0.03
SVM RNA-class probability 0.517087
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16978484 108 + 20766785
AAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAAAAGAACAAAAUCUUGCUCCUAUUUCGGGCGUAAAUGAAAAUGCAAAUUUACUUUGAGCCGGGUGUCGCCAGCGG----
.........((..(((((((.(.(((((......((((......))))((.((......))))((((((..........)))))).....))))))))))))).))..---- ( -30.60)
>DroPse_CAF1 85836 107 + 1
AAAUUCAAAGAAAAACGGAAA-AAUGGCAAGGGAAA---AAAAAUCUUGCUUCCAUUUGAGGCGUAAAUGAAAAUGUAAAUUCGCUUA-AAGCGCGUGCCACGAAUCAGACC
................(((..-...(((((((....---.....)))))))))).(((((..(((..((....))(((....(((...-..)))..))).)))..))))).. ( -19.50)
>DroSim_CAF1 80427 107 + 1
AAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAAAAGAACAAAAUCUUGCUCCCAUUUCGGGCGUAAAUGAAAAUGCAAAUUCACUUU-AGCCGGGUGUCGCCAGCGG----
.........((..(((((((.(.(((((..................((((.(((.....))).)))).((((........))))....-.))))))))))))).))..---- ( -31.20)
>DroEre_CAF1 76613 107 + 1
AAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAAAGGAACAAAAUCUUGCUCCCAUUUGAGGCGUAAAUGAAAAUGCAAAUUCACUUU-AGCCUGGUGUUGCCAGCGG----
..............((((((((.(((((((((............)))))))........((((.((((((((........)))).)))-))))))).)))))).))..---- ( -28.40)
>DroYak_CAF1 83457 107 + 1
AAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAAAAGAACAAAAUCUUGCUCCCAUUUGAGGCGUAAAUGAAAAUGCAAAUUCACUUU-AGCCGGGUGACGCCAGCGG----
.........((..((((...((((.(((((((............))))))).........(((.((((((((........)))).)))-))))))))..)))).))..---- ( -27.70)
>DroPer_CAF1 88011 105 + 1
AAAUUCAAAGAAAAACGGAAA-AAUGGCAAGGGAAA-----AAAUCUUGCUUCCAUUUCAGGCGUAAAUGAAAAUGUUAAUUCGCUUA-AAGCGCGUGCCACGAAUCAGACC
..((((...((((...(((..-...(((((((....-----...)))))))))).)))).(((....((....))....((.(((...-..))).)))))..))))...... ( -19.50)
>consensus
AAAUUCAAAGCAAGGCGGCAACUCUGGCAAGAAAAAGAACAAAAUCUUGCUCCCAUUUCAGGCGUAAAUGAAAAUGCAAAUUCACUUU_AGCCGGGUGUCGCCAGCGG____
.............(((((((.....(((((((............))))))).........(((..((.((((........)))).))...)))...)))))))......... (-15.44 = -16.72 +   1.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:23 2006