Locus 5172

Sequence ID 2R_DroMel_CAF1
Location 16,832,216 – 16,832,401
Length 185
Max. P 0.693859
window8269 window8270 window8271

overview

Window 9

Location 16,832,216 – 16,832,324
Length 108
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 75.34
Mean single sequence MFE -45.33
Consensus MFE -22.54
Energy contribution -24.02
Covariance contribution 1.48
Combinations/Pair 1.45
Mean z-score -1.78
Structure conservation index 0.50
SVM decision value 0.19
SVM RNA-class probability 0.624509
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832216 108 + 20766785
---------GCCAGCAUUGUUGGACCAGCCGAGAGCAGCAACAUUGUAAGCUCCCUGCUACCAGCGUCGGUGGCCUCCAGCAGCGAGGUCGGCGGGCUUUCUUCUACGGCCCUGCAG
---------(((.((..((((((...(((.(.((((.(((....)))..)))).).))).))))))...))(((((((....).)))))))))(((((.........)))))..... ( -39.10)
>DroVir_CAF1 81 114 + 1
AGCAAAAACAGCAACAUUGUUGGCGCUGUA---AGCAGCAACAUCGUUGGCUCAUUGCUGCCAGCGUCGGUUGUGGCCAGCAGCGAAGUUGGUGGGGCCAUUUCAACGGCACUGCAG
........((((..(.((((((((((((..---..))))(((..(((((((........)))))))...)))...)))))))).)..))))(..(.(((........))).)..).. ( -45.40)
>DroPse_CAF1 1179 105 + 1
---------AGCAGCAUUGUCGGGACUGCC---AGCAGCAACAUUGUUGGCUCCCUGCUGCCGGCUUCUGUGGCCUCCAGCAGCGAAGUCGGUGGGGUAUCUUCGGAAGCCCUGCAA
---------.((((((.....((((..(((---(((((.....))))))))))))))))))(((((((.((.((.....)).)))))))))(..((((.((....)).))))..).. ( -51.70)
>DroSec_CAF1 1120 108 + 1
---------GCCAGCAUUGUUGGACCAGCUGAGAGCAGCAACAUUGUAAGCUCCCUGCUACCAGCGUCGGUGGCCUCCAGCAGCGAGGUCGGAGGGCUUUCUUCUACGGCCCUGCAG
---------..((((...))))((((.((((.((((.(((....)))..))))...((((((......))))))......))))..))))(.((((((.........)))))).).. ( -38.80)
>DroAna_CAF1 698 110 + 1
----GGAGUAGUAGCAUUGUUGGCACCGCC---AGUAGCAAUAUUGUUGGUUCCUUGCUGCCGGCGUCGGUGGCUGCCAGUAGCGAGGUUGGCGGAGUCUCGUCAACGGCCCUCCAG
----((((.....((...((((((.(((((---(((((((....)))))...(((((((((.(((((.....)).))).))))))))))))))))......)))))).)).)))).. ( -45.30)
>DroPer_CAF1 556 105 + 1
---------AGCAGCAUUGUCGGGACUGCC---AGCAGCAACAUUGUUGGCUCCCUGCUGCCGGCUUCUGUGGCCUCCAGCAGCGAAGUCGGUGGGGUAUCUUCGGAAGCCCUGCAA
---------.((((((.....((((..(((---(((((.....))))))))))))))))))(((((((.((.((.....)).)))))))))(..((((.((....)).))))..).. ( -51.70)
>consensus
_________AGCAGCAUUGUUGGAACUGCC___AGCAGCAACAUUGUUGGCUCCCUGCUGCCAGCGUCGGUGGCCUCCAGCAGCGAAGUCGGUGGGGUAUCUUCAACGGCCCUGCAG
.........(((..(.((((((((...((.....)).((.((..(((((((........)))))))...)).)).)))))))).)..))).((((((((........)))))))).. (-22.54 = -24.02 +   1.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,832,244 – 16,832,364
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.22
Mean single sequence MFE -45.55
Consensus MFE -28.69
Energy contribution -29.08
Covariance contribution 0.39
Combinations/Pair 1.38
Mean z-score -1.86
Structure conservation index 0.63
SVM decision value 0.30
SVM RNA-class probability 0.677829
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832244 120 + 20766785
GCAACAUUGUAAGCUCCCUGCUACCAGCGUCGGUGGCCUCCAGCAGCGAGGUCGGCGGGCUUUCUUCUACGGCCCUGCAGGACUUGAAUGCCCUCAAGAAGCGCAUACUCCAGCAGAAAU
((......(((.((..(((((..........(.((((((((....).))))))).)(((((.........))))).))))).(((((......)))))....)).)))....))...... ( -37.00)
>DroVir_CAF1 115 120 + 1
GCAACAUCGUUGGCUCAUUGCUGCCAGCGUCGGUUGUGGCCAGCAGCGAAGUUGGUGGGGCCAUUUCAACGGCACUGCAGGACUUAAAUGCGCUCAGGAAGCGCGUACUCCAACAGAAAU
(((((..(((((((........)))))))...))))).((((((......))))))...(((........))).(((..(((.....(((((((.....)))))))..)))..))).... ( -44.10)
>DroGri_CAF1 1280 120 + 1
GCAAUAUUGUUGGCUCAUUGCUGCCGGCGUCAGUUGUGGCCAGCAGCGAGAUUGGUGACGCCGAUUUAACGGCACUGCAAGACUUGAAUGCGCUCAGGAAGCGCAUACUACAACAGAAAU
........((((((........))))))....(((((((...((((.......(....)((((......)))).)))).........(((((((.....))))))).)))))))...... ( -41.60)
>DroMoj_CAF1 1281 120 + 1
GCAACAUCGUUGGCUCUUUACUGCCAGCGUCGGUUGUGGCCAGCAGCGAAGUUGGUGGGGCCAUUUCAACGGCACUACAGGACUUGAAUGCGCUCAAGAAGCGCAUUCUCCAACAGAAAU
(((((..(((((((........)))))))...))))).((((((......)))))).(((((........))).))...(((...(((((((((.....))))))))))))......... ( -46.90)
>DroAna_CAF1 728 120 + 1
GCAAUAUUGUUGGUUCCUUGCUGCCGGCGUCGGUGGCUGCCAGUAGCGAGGUUGGCGGAGUCUCGUCAACGGCCCUCCAGGACCUGAAUGCGCUCAAGAAGCGCAUACUUCAGCAGAAGU
...........(((((((((((((.(((((.....)).))).))))))))((((((((....)))))))).........)))))...(((((((.....)))))))(((((....))))) ( -47.30)
>DroPer_CAF1 581 120 + 1
GCAACAUUGUUGGCUCCCUGCUGCCGGCUUCUGUGGCCUCCAGCAGCGAAGUCGGUGGGGUAUCUUCGGAAGCCCUGCAAGACUCGAAUGCGCUCAAGAAGCGCAUUCUCCAGCAGAAAU
......(((((((.((.((((((..((((.....))))..)))))).))((((.(..((((.((....)).))))..)..)))).(((((((((.....))))))))).))))))).... ( -56.40)
>consensus
GCAACAUUGUUGGCUCCUUGCUGCCAGCGUCGGUGGCGGCCAGCAGCGAAGUUGGUGGGGCCUCUUCAACGGCACUGCAGGACUUGAAUGCGCUCAAGAAGCGCAUACUCCAACAGAAAU
......(((((((.((.((((((.(.(((.....))).).)))))).))((((.((((.(((........))).))))..))))...(((((((.....)))))))...))))))).... (-28.69 = -29.08 +   0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,832,284 – 16,832,401
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 80.90
Mean single sequence MFE -34.98
Consensus MFE -24.99
Energy contribution -24.05
Covariance contribution -0.94
Combinations/Pair 1.41
Mean z-score -1.50
Structure conservation index 0.71
SVM decision value 0.34
SVM RNA-class probability 0.693859
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832284 117 + 20766785
CAGCAGCGAGGUCGGCGGGCUUUCUUCUACGGCCCUGCAGGACUUGAAUGCCCUCAAGAAGCGCAUACUCCAGCAGAAAUUGCAGAUCUUGCGUAAUCUUAAAGAAAGGUGAGUUAC-
.(((.((((((((.(((((((.........)))))(((.(((...(.((((.((.....)).)))).)))).)))......)).))))))))...(((((.....)))))..)))..- ( -33.50)
>DroVir_CAF1 155 118 + 1
CAGCAGCGAAGUUGGUGGGGCCAUUUCAACGGCACUGCAGGACUUAAAUGCGCUCAGGAAGCGCGUACUCCAACAGAAAUAUCAAAUUUUGCGUAAUCUUAAGGAAAGGUAAAUAUGU
..(((((((((((((((..(((........))).(((..(((.....(((((((.....)))))))..)))..)))...)))).))))))))...(((((.....))))).....))) ( -30.00)
>DroPse_CAF1 1244 118 + 1
CAGCAGCGAAGUCGGUGGGGUAUCUUCGGAAGCCCUGCAAGACUCGAAUGCGCUCAAGAAGCGCAUUCUCCAGCAGAAAUUGCAGAUUUUGCGUACUCUUAAGGAAAGGUAUGAUUGA
.....((((((((.(..((((.((....)).))))..).......(((((((((.....)))))))))....((((...)))).))))))))((((.(((.....)))))))...... ( -43.80)
>DroGri_CAF1 1320 118 + 1
CAGCAGCGAGAUUGGUGACGCCGAUUUAACGGCACUGCAAGACUUGAAUGCGCUCAGGAAGCGCAUACUACAACAGAAAUUGCAAAUUUUGCGUAAUCUUAAGGAAAGGUAAAAAUCA
.....(((((((((....)((((......))))..(((((.......(((((((.....))))))).((.....))...)))))))))))))...(((((.....)))))........ ( -29.90)
>DroMoj_CAF1 1321 118 + 1
CAGCAGCGAAGUUGGUGGGGCCAUUUCAACGGCACUACAGGACUUGAAUGCGCUCAAGAAGCGCAUUCUCCAACAGAAAUAUCAAAUUUUGCGUAAUCUUAAGGAAAGGUAAAUACGA
.....((((((((.((((.(((........))).)))).(((...(((((((((.....)))))))))))).............))))))))((((((((.....)))))...))).. ( -35.30)
>DroAna_CAF1 768 118 + 1
CAGUAGCGAGGUUGGCGGAGUCUCGUCAACGGCCCUCCAGGACCUGAAUGCGCUCAAGAAGCGCAUACUUCAGCAGAAGUUGCAGAUCUUGCGUAAUCUUAAGGAGAGGUGAGGAAUA
..........((((((((....))))))))...(((((((((.(((.(((((((.....)))))))(((((....)))))..))).)))))....(((((.....))))))))).... ( -37.40)
>consensus
CAGCAGCGAAGUUGGUGGGGCCUCUUCAACGGCACUGCAGGACUUGAAUGCGCUCAAGAAGCGCAUACUCCAACAGAAAUUGCAAAUUUUGCGUAAUCUUAAGGAAAGGUAAAUAUGA
.....((((((((.((((.(((........))).)))).........(((((((.....)))))))..................))))))))...(((((.....)))))........ (-24.99 = -24.05 +  -0.94)

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 11:38:22 2006