Locus 5539

Sequence ID 2L_DroMel_CAF1
Location 15,798,183 – 15,798,312
Length 129
Max. P 0.998909
window8785 window8786 window8787 window8788

overview

Window 5

Location 15,798,183 – 15,798,279
Length 96
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.40
Mean single sequence MFE -27.80
Consensus MFE -25.66
Energy contribution -25.48
Covariance contribution -0.19
Combinations/Pair 1.17
Mean z-score -2.88
Structure conservation index 0.92
SVM decision value 3.07
SVM RNA-class probability 0.998339
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15798183 96 + 22407834
GGGAAUAUGUUUUAAAUGUUUCGCAA----------AAGCAAUUUUUUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACA
.(((((((.......)))))))((..----------..)).........((((...((((((.(((.((((.((((....)))).)))).))).))))))..--------------)))) ( -28.40)
>DroSec_CAF1 22107 95 + 1
GGGAUUAUGUUUUAAAUGUUUCGCAA----------AAGCAAUUU-UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACA
.......((((((.........((((----------(((.....)-))))))....((((((.(((.((((.((((....)))).)))).))).))))))))--------------)))) ( -25.90)
>DroAna_CAF1 21642 117 + 1
GGGAAUAUGUUUUAAAUAUUUCCAAAAAAAAAAAAAAAACAAAAU-UCCUGUUGUCUGCUGUCUG--UGUUUGCCUUUUGGGGCCAACAAACAAACGGCACAACAAAGCCCACCAAAACA
((((((((.......))))))))......................-...((((((..(((((.((--((((.((((....)))).)))..))).)))))))))))............... ( -28.50)
>DroSim_CAF1 13390 95 + 1
GGGAAUAUGUUUUAAAUGUUUCGCAA----------AAGCAAUUU-UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACA
.(((((((.......)))))))((..----------..)).....-...((((...((((((.(((.((((.((((....)))).)))).))).))))))..--------------)))) ( -28.40)
>consensus
GGGAAUAUGUUUUAAAUGUUUCGCAA__________AAGCAAUUU_UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA______________AACA
.(((((((.......)))))))...............(((((......)))))...((((((.(((.((((.((((....)))).)))).))).)))))).................... (-25.66 = -25.48 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,798,183 – 15,798,279
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -24.68
Consensus MFE -15.09
Energy contribution -15.22
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -2.92
Structure conservation index 0.61
SVM decision value 1.98
SVM RNA-class probability 0.984530
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15798183 96 - 22407834
UGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAAAAAAUUGCUU----------UUGCGAAACAUUUAAAACAUAUUCCC
((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).)))).......((((..----------..)))).................... ( -23.30)
>DroSec_CAF1 22107 95 - 1
UGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA-AAAUUGCUU----------UUGCGAAACAUUUAAAACAUAAUCCC
((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).))))...-...((((..----------..)))).................... ( -23.30)
>DroAna_CAF1 21642 117 - 1
UGUUUUGGUGGGCUUUGUUGUGCCGUUUGUUUGUUGGCCCCAAAAGGCAAACA--CAGACAGCAGACAACAGGA-AUUUUGUUUUUUUUUUUUUUUUGGAAAUAUUUAAAACAUAUUCCC
(((((.(.(((((........)))((((((((.(((....))).)))))))).--....)).))))))...(((-((..((((((.....((((....)))).....)))))).))))). ( -28.80)
>DroSim_CAF1 13390 95 - 1
UGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA-AAAUUGCUU----------UUGCGAAACAUUUAAAACAUAUUCCC
((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).))))...-...((((..----------..)))).................... ( -23.30)
>consensus
UGUU______________UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA_AAAUUGCUU__________UUGCGAAACAUUUAAAACAUAUUCCC
((((......................(((((((((((((......)))...(.....).)))))))))).........((((..............)))).........))))....... (-15.09 = -15.22 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,798,213 – 15,798,312
Length 99
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.16
Mean single sequence MFE -29.07
Consensus MFE -23.26
Energy contribution -23.08
Covariance contribution -0.19
Combinations/Pair 1.18
Mean z-score -3.36
Structure conservation index 0.80
SVM decision value 3.28
SVM RNA-class probability 0.998909
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15798213 99 + 22407834
AAUUUUUUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACAAUG--CUAAAAAAGG-----CAGGGACAAAGAAAGAAAGC
..((((((((.(((((((((((.(((.((((.((((....)))).)))).))).)))))...--------------.....((--((......))-----)).)))))).)))))))).. ( -34.70)
>DroSec_CAF1 22137 98 + 1
AAUUU-UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACAAUG--CUAAAAAAAG-----GAGGGACAAAGAAAGAAAGC
..(((-((((.(((((((((((.(((.((((.((((....)))).)))).))).)))))...--------------.....(.--((......))-----.).)))))).)))))))... ( -29.30)
>DroAna_CAF1 21682 117 + 1
AAAAU-UCCUGUUGUCUGCUGUCUG--UGUUUGCCUUUUGGGGCCAACAAACAAACGGCACAACAAAGCCCACCAAAACAACAACAUAAAAAAAGAAAUCCAGGGACAAAGAAAGAAAAC
....(-((.((((((..(((((.((--((((.((((....)))).)))..))).)))))))))))..((((...............................))).)...)))....... ( -22.98)
>DroSim_CAF1 13420 99 + 1
AAUUU-UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA--------------AACAAUG--CUAAAAAAAGG----GAGGGACAAAGAAAGAAAGC
..(((-((((.(((((((((((.(((.((((.((((....)))).)))).))).)))))...--------------.....(.--((......)).----)..)))))).)))))))... ( -29.30)
>consensus
AAUUU_UUUUGUUGUCUGCCGUCUGUGUGUUUGCCUUUUGGGGCCAGCAAACAAAUGGCAAA______________AACAAUG__CUAAAAAAAG_____CAGGGACAAAGAAAGAAAGC
......((((.(((((((((((.(((.((((.((((....)))).)))).))).)))))..........................((......))........))))))...)))).... (-23.26 = -23.08 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,798,213 – 15,798,312
Length 99
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.16
Mean single sequence MFE -23.59
Consensus MFE -15.35
Energy contribution -15.91
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.06
Structure conservation index 0.65
SVM decision value 0.71
SVM RNA-class probability 0.830684
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15798213 99 - 22407834
GCUUUCUUUCUUUGUCCCUG-----CCUUUUUUAG--CAUUGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAAAAAAUU
..................((-----(........)--))(((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).)))))........ ( -22.50)
>DroSec_CAF1 22137 98 - 1
GCUUUCUUUCUUUGUCCCUC-----CUUUUUUUAG--CAUUGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA-AAAUU
(((.................-----........))--).(((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).)))))..-..... ( -21.91)
>DroAna_CAF1 21682 117 - 1
GUUUUCUUUCUUUGUCCCUGGAUUUCUUUUUUUAUGUUGUUGUUUUGGUGGGCUUUGUUGUGCCGUUUGUUUGUUGGCCCCAAAAGGCAAACA--CAGACAGCAGACAACAGGA-AUUUU
......((((((((((..((((........))))...((((((((.(...(((........)))((((((((.(((....))).)))))))).--)))))))))))))).))))-).... ( -28.10)
>DroSim_CAF1 13420 99 - 1
GCUUUCUUUCUUUGUCCCUC----CCUUUUUUUAG--CAUUGUU--------------UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA-AAAUU
(((.................----.........))--).(((((--------------((((((.(((((.((...(((......)))...)).))))).)))))).)))))..-..... ( -21.87)
>consensus
GCUUUCUUUCUUUGUCCCUC_____CUUUUUUUAG__CAUUGUU______________UUUGCCAUUUGUUUGCUGGCCCCAAAAGGCAAACACACAGACGGCAGACAACAAAA_AAAUU
.......................................(((((..............((((((.(((((.((...(((......)))...)).))))).)))))).)))))........ (-15.35 = -15.91 +   0.56)

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 11:46:38 2006