Locus 4007

Sequence ID 3L_DroMel_CAF1
Location 11,694,747 – 11,694,876
Length 129
Max. P 0.999428
window6240 window6241 window6242 window6243

overview

Window 0

Location 11,694,747 – 11,694,840
Length 93
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 77.74
Mean single sequence MFE -23.20
Consensus MFE -14.28
Energy contribution -14.12
Covariance contribution -0.16
Combinations/Pair 1.11
Mean z-score -1.97
Structure conservation index 0.62
SVM decision value 0.94
SVM RNA-class probability 0.885766
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11694747 93 + 23771897
U---------UUUCUGAAAUGUUUUCUUUUCAAUUCAAAUUUGGCGGGAAAGCCAUUUCCCGCUGUUAAGUGUGACCAAAAUCAAUUGCGAGAUGUAACAAU
.---------.........((((.((((..(((((....((((((((((((....)))))))).((((....))))))))...))))).))))...)))).. ( -21.00)
>DroSec_CAF1 12849 93 + 1
U---------UUUCAAAAAUGUUUUCUUUUCAAUUCAAAUUUAGCGGGAAAUCCAUUUCCCGCUGUUAAGUGUGACCAAAAAAAAUUGAGAGAUCCAUCGAU
.---------........(((...(((((.(((((.......(((((((((....)))))))))((((....)))).......))))))))))..))).... ( -19.90)
>DroSim_CAF1 8313 93 + 1
A---------UUUCUAAAAUGUUUUCUUUUCAAUUCAAAUUUGGCGGGAAAUCCAUUUCCCGCUGUUAAGUGCGACCAAAAAGAAUUGAGAGAUGUAUCGAU
.---------................((((((((((...((((((((((((....))))))((........))).)))))..)))))))))).......... ( -23.20)
>DroEre_CAF1 8551 86 + 1
---------------GAUAUGC-UUCUUUGCAAUUCAAAUUUGGCGGGAAAUCCUUUUCCCGCUGUACAGUGUGACCAAAGGGGUGCGCGAGAUUUGUCGGU
---------------....(((-......)))...((((((((((((((((....))))))))).....((((..((....))..)))).)))))))..... ( -27.90)
>DroYak_CAF1 8627 102 + 1
UUGUAAAAUUUAUCUGAAAUGUUUUCCGUUCUGUUCAAAUUUGGCGGGAAAUCCAUUUCCCGCUGUAUAGUGUGACCAAAAGAAAUUGUGAUAUUUCUCGAU
...........(((.((((((((.....((((..(((.(((.(((((((((....)))))))))....))).))).....)))).....))))))))..))) ( -24.00)
>consensus
U_________UUUCUGAAAUGUUUUCUUUUCAAUUCAAAUUUGGCGGGAAAUCCAUUUCCCGCUGUUAAGUGUGACCAAAAAAAAUUGAGAGAUGUAUCGAU
..........................................(((((((((....)))))))))...................................... (-14.28 = -14.12 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,694,747 – 11,694,840
Length 93
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 77.74
Mean single sequence MFE -19.63
Consensus MFE -14.30
Energy contribution -15.30
Covariance contribution 1.00
Combinations/Pair 1.19
Mean z-score -1.63
Structure conservation index 0.73
SVM decision value 0.72
SVM RNA-class probability 0.831056
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11694747 93 - 23771897
AUUGUUACAUCUCGCAAUUGAUUUUGGUCACACUUAACAGCGGGAAAUGGCUUUCCCGCCAAAUUUGAAUUGAAAAGAAAACAUUUCAGAAA---------A
..((((...(((..(((((.(.((((((........)).((((((((....))))))))))))..).)))))...))).)))).........---------. ( -18.40)
>DroSec_CAF1 12849 93 - 1
AUCGAUGGAUCUCUCAAUUUUUUUUGGUCACACUUAACAGCGGGAAAUGGAUUUCCCGCUAAAUUUGAAUUGAAAAGAAAACAUUUUUGAAA---------A
...((((..(((.(((((((....((....))......(((((((((....)))))))))......)))))))..)))...)))).......---------. ( -20.10)
>DroSim_CAF1 8313 93 - 1
AUCGAUACAUCUCUCAAUUCUUUUUGGUCGCACUUAACAGCGGGAAAUGGAUUUCCCGCCAAAUUUGAAUUGAAAAGAAAACAUUUUAGAAA---------U
.........(((.(((((((..((((((.((........))((((((....))))))))))))...)))))))..)))..............---------. ( -23.30)
>DroEre_CAF1 8551 86 - 1
ACCGACAAAUCUCGCGCACCCCUUUGGUCACACUGUACAGCGGGAAAAGGAUUUCCCGCCAAAUUUGAAUUGCAAAGAA-GCAUAUC---------------
.....(((((...(.(.(((.....)))).)........((((((((....))))))))...)))))...(((......-)))....--------------- ( -17.80)
>DroYak_CAF1 8627 102 - 1
AUCGAGAAAUAUCACAAUUUCUUUUGGUCACACUAUACAGCGGGAAAUGGAUUUCCCGCCAAAUUUGAACAGAACGGAAAACAUUUCAGAUAAAUUUUACAA
(((..(((((.......(((((((((.(((.........((((((((....))))))))......))).))))).))))...))))).)))........... ( -18.56)
>consensus
AUCGAUAAAUCUCGCAAUUCCUUUUGGUCACACUUAACAGCGGGAAAUGGAUUUCCCGCCAAAUUUGAAUUGAAAAGAAAACAUUUCAGAAA_________A
.............(((((((..((((((........)).((((((((....))))))))))))...)))))))............................. (-14.30 = -15.30 +   1.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,694,775 – 11,694,876
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 84.36
Mean single sequence MFE -35.96
Consensus MFE -23.44
Energy contribution -24.12
Covariance contribution 0.68
Combinations/Pair 1.17
Mean z-score -4.25
Structure conservation index 0.65
SVM decision value 2.61
SVM RNA-class probability 0.995726
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11694775 101 + 23771897
AAUUUGGCGGGAAAGCCAUUUCCCGCUGUUAAGUGUGACCAAAAUCAAUUGCGAGAUGUAACAAUAUUUCGCGUGCAAAAAGUUGCGACCACACUGAACUA
.....(((((((((....)))))))))(((.((((((.............(((((((((....))))))))).(((((....)))))..)))))).))).. ( -37.90)
>DroSec_CAF1 12877 101 + 1
AAUUUAGCGGGAAAUCCAUUUCCCGCUGUUAAGUGUGACCAAAAAAAAUUGAGAGAUCCAUCGAUAUUUCGGUUGCAAAGAGUUGCGACCACACUGAAUUG
....((((((((((....))))))))))...(((((..............((((.(((....))).))))((((((((....)))))))))))))...... ( -34.10)
>DroSim_CAF1 8341 101 + 1
AAUUUGGCGGGAAAUCCAUUUCCCGCUGUUAAGUGCGACCAAAAAGAAUUGAGAGAUGUAUCGAUAUUUCGGUUGCAAAGAGUUGCGACCACACUAAAUUA
.....(((((((((....)))))))))....((((.................(((((((....)))))))((((((((....)))))))).))))...... ( -33.00)
>DroEre_CAF1 8572 101 + 1
AAUUUGGCGGGAAAUCCUUUUCCCGCUGUACAGUGUGACCAAAGGGGUGCGCGAGAUUUGUCGGUAUUCCGGGUGCAAAAAGUUGCGACCACACUGAAUAA
.....(((((((((....)))))))))...((((((((((...(((((((.(((......)))))))))).)))((((....))))...)))))))..... ( -43.50)
>DroYak_CAF1 8664 101 + 1
AAUUUGGCGGGAAAUCCAUUUCCCGCUGUAUAGUGUGACCAAAAGAAAUUGUGAUAUUUCUCGAUAUUCCGGGAGAGAAAAGUUGCGACCACACUGAAUUA
.....(((((((((....)))))))))...(((((((.....((....))(..((.((((((............)))))).))..)...)))))))..... ( -31.30)
>consensus
AAUUUGGCGGGAAAUCCAUUUCCCGCUGUUAAGUGUGACCAAAAAAAAUUGAGAGAUGUAUCGAUAUUUCGGGUGCAAAAAGUUGCGACCACACUGAAUUA
.....(((((((((....)))))))))....((((((......................(((((....))))).((((....))))...))))))...... (-23.44 = -24.12 +   0.68)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,694,775 – 11,694,876
Length 101
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 84.36
Mean single sequence MFE -30.62
Consensus MFE -26.68
Energy contribution -26.36
Covariance contribution -0.32
Combinations/Pair 1.18
Mean z-score -3.37
Structure conservation index 0.87
SVM decision value 3.59
SVM RNA-class probability 0.999428
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11694775 101 - 23771897
UAGUUCAGUGUGGUCGCAACUUUUUGCACGCGAAAUAUUGUUACAUCUCGCAAUUGAUUUUGGUCACACUUAACAGCGGGAAAUGGCUUUCCCGCCAAAUU
..(((.((((((..(((((....))))..((((.((........)).))))..........)..)))))).))).((((((((....))))))))...... ( -34.80)
>DroSec_CAF1 12877 101 - 1
CAAUUCAGUGUGGUCGCAACUCUUUGCAACCGAAAUAUCGAUGGAUCUCUCAAUUUUUUUUGGUCACACUUAACAGCGGGAAAUGGAUUUCCCGCUAAAUU
......((((((..(((((....))))...(((....))).....................)..))))))....(((((((((....)))))))))..... ( -29.60)
>DroSim_CAF1 8341 101 - 1
UAAUUUAGUGUGGUCGCAACUCUUUGCAACCGAAAUAUCGAUACAUCUCUCAAUUCUUUUUGGUCGCACUUAACAGCGGGAAAUGGAUUUCCCGCCAAAUU
......((((((..(((((....))))...(((....))).....................)..)))))).....((((((((....))))))))...... ( -27.50)
>DroEre_CAF1 8572 101 - 1
UUAUUCAGUGUGGUCGCAACUUUUUGCACCCGGAAUACCGACAAAUCUCGCGCACCCCUUUGGUCACACUGUACAGCGGGAAAAGGAUUUCCCGCCAAAUU
.....(((((((..(((((....))))...(((....))).....................)..)))))))....((((((((....))))))))...... ( -32.60)
>DroYak_CAF1 8664 101 - 1
UAAUUCAGUGUGGUCGCAACUUUUCUCUCCCGGAAUAUCGAGAAAUAUCACAAUUUCUUUUGGUCACACUAUACAGCGGGAAAUGGAUUUCCCGCCAAAUU
......((((((..(.......((((.....))))....(((((((......)))))))..)..)))))).....((((((((....))))))))...... ( -28.60)
>consensus
UAAUUCAGUGUGGUCGCAACUUUUUGCACCCGAAAUAUCGAUAAAUCUCGCAAUUCCUUUUGGUCACACUUAACAGCGGGAAAUGGAUUUCCCGCCAAAUU
......((((((..(((((....))))...(((....))).....................)..)))))).....((((((((....))))))))...... (-26.68 = -26.36 +  -0.32)

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 11:12:16 2006