Locus 6479

Sequence ID 3L_DroMel_CAF1
Location 17,249,362 – 17,249,501
Length 139
Max. P 0.999906
window10444 window10445 window10446 window10447

overview

Window 4

Location 17,249,362 – 17,249,461
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.31
Mean single sequence MFE -23.02
Consensus MFE -20.70
Energy contribution -20.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.90
SVM decision value 0.36
SVM RNA-class probability 0.705245
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17249362 99 + 23771897
UCUUAUCCGGCACCACCC---------------------AACGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
........(((.......---------------------...))).....(((((...)))))((((((((((..(((((.(((((....)))..)).)))))..))))..))))))... ( -23.50)
>DroSec_CAF1 133147 99 + 1
UCUUAUCCGGCACCACCC---------------------AACGCCCGCUUUUGGCCAAGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
.(((((..((......))---------------------...((((((((.(((((((((......)))))......)))).)))))...((....))))).......)))))....... ( -23.60)
>DroSim_CAF1 127967 99 + 1
UCUUAUCCGGCACCACCC---------------------AGCGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
........(((.(((...---------------------(((....)))..)))....)))..((((((((((..(((((.(((((....)))..)).)))))..))))..))))))... ( -26.30)
>DroEre_CAF1 136388 106 + 1
UCUUAUCCGCCACCACCCA--------------CCAUACACCACCCACUGUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
........(((........--------------............((((..(((((((((......)))))......))))..))))...((....)))))................... ( -21.00)
>DroYak_CAF1 140014 120 + 1
UCUUAUCCAACACCACCCACAAUCCACAACCCACCACCCACCGCCCACUGUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
..................................................(((((...)))))((((((((((..(((((.(((((....)))..)).)))))..))))..))))))... ( -20.70)
>consensus
UCUUAUCCGGCACCACCC_____________________AACGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUU
..................................................(((((...)))))((((((((((..(((((.(((((....)))..)).)))))..))))..))))))... (-20.70 = -20.70 +  -0.00)

alignment

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secondary structure

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Window 5

Location 17,249,362 – 17,249,461
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.31
Mean single sequence MFE -33.10
Consensus MFE -26.94
Energy contribution -26.38
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.89
Structure conservation index 0.81
SVM decision value 0.97
SVM RNA-class probability 0.893070
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17249362 99 - 23771897
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGUU---------------------GGGUGGUGCCGGAUAAGA
.......(((((((((.((((((((............)))))))).))))).....((((((.(.(((...(((....)))---------------------.))).).)))))))))). ( -31.40)
>DroSec_CAF1 133147 99 - 1
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCUUGGCCAAAAGCGGGCGUU---------------------GGGUGGUGCCGGAUAAGA
.......(((((((((.((((((((............)))))))).))))).....((((((.(.(((...(((....)))---------------------.))).).)))))))))). ( -31.40)
>DroSim_CAF1 127967 99 - 1
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGCU---------------------GGGUGGUGCCGGAUAAGA
.......(((((((((.((((((((............)))))))).))))..((..((((((...)))))).)).((((((---------------------....))))))..))))). ( -34.10)
>DroEre_CAF1 136388 106 - 1
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAACAGUGGGUGGUGUAUGG--------------UGGGUGGUGGCGGAUAAGA
..((((((((((((((((..((((....))...((((..((((..((..((((...))))..)).))))..))))))..)))))).)--------------))))))))).......... ( -30.70)
>DroYak_CAF1 140014 120 - 1
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAACAGUGGGCGGUGGGUGGUGGGUUGUGGAUUGUGGGUGGUGUUGGAUAAGA
((((((((((((((((.((((((((............)))))))).))))..(((((..(.(((.(((..(....)..))).)).).)..))))).....))))))))))))........ ( -37.90)
>consensus
AAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGGU_____________________GGGUGGUGCCGGAUAAGA
..((((((((.(((((.((((((((............)))))))).))))).........(((((........)))))........................)))))))).......... (-26.94 = -26.38 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,249,381 – 17,249,501
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.42
Mean single sequence MFE -46.80
Consensus MFE -43.78
Energy contribution -43.78
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -2.82
Structure conservation index 0.94
SVM decision value 4.48
SVM RNA-class probability 0.999906
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17249381 120 + 23771897
ACGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAUGGGCGUUGUCUGGCCUUGGGUGGCGAAUGAG
.((((.((((..((((((((....(..(((((........)))))..)..(((((((..(((((((((....)).)))))))....)))))))...))))))))..))))))))...... ( -48.10)
>DroSec_CAF1 133166 120 + 1
ACGCCCGCUUUUGGCCAAGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAUGGGCGUUGUCUGGCCUUGGGUGGCGAAUGAG
.((((.((((..(((((..(....(..(((((........)))))..)..(((((((..(((((((((....)).)))))))....)))))))...)..)))))..))))))))...... ( -43.20)
>DroSim_CAF1 127986 120 + 1
GCGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAUGGGCGUUGUCUGGCCUUGGGUGGCGAAUGAG
.((((.((((..((((((((....(..(((((........)))))..)..(((((((..(((((((((....)).)))))))....)))))))...))))))))..))))))))...... ( -47.80)
>DroEre_CAF1 136414 120 + 1
CCACCCACUGUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAUGGGCGUUGUCUGGCCUUGGGUGGCGAAAGGG
(((((((.....((((((((....(..(((((........)))))..)..(((((((..(((((((((....)).)))))))....)))))))...)))))))).)))))))(....).. ( -48.80)
>DroYak_CAF1 140054 120 + 1
CCGCCCACUGUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAGGGGCGUUGUCUGGCCUUGGGUGGCGAACGAG
(((((((.....((((((((......((((((........))))))((((.(((.((((.((((((((....)).))))))))))...))).)))))))))))).)))))))........ ( -46.10)
>consensus
ACGCCCGCUUUUGGCCAGGCCAAAUUGCUUGUACUUUGCCACAAGUGACGGCUUAUGCGGCAAUAUACAUAAGUAAUAUUGCGUACCAUGGGCGUUGUCUGGCCUUGGGUGGCGAAUGAG
.((((((.....((((((((....(..(((((........)))))..)..(((((((..(((((((((....)).)))))))....)))))))...)))))))).))))))......... (-43.78 = -43.78 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,249,381 – 17,249,501
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.42
Mean single sequence MFE -40.38
Consensus MFE -37.68
Energy contribution -37.28
Covariance contribution -0.40
Combinations/Pair 1.06
Mean z-score -2.57
Structure conservation index 0.93
SVM decision value 4.10
SVM RNA-class probability 0.999798
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17249381 120 - 23771897
CUCAUUCGCCACCCAAGGCCAGACAACGCCCAUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGU
.......(((......)))......((((((...(((((((((((.((....))))))))).......((((.(....)))))...))))..((..((((((...)))))).)))))))) ( -39.40)
>DroSec_CAF1 133166 120 - 1
CUCAUUCGCCACCCAAGGCCAGACAACGCCCAUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCUUGGCCAAAAGCGGGCGU
.......(((......)))......((((((...(((((((((((.((....))))))))).......((((.(....)))))...))))..((..((((((...)))))).)))))))) ( -39.40)
>DroSim_CAF1 127986 120 - 1
CUCAUUCGCCACCCAAGGCCAGACAACGCCCAUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGC
......(((((((...(((........)))...))).(((...........(((((.((((((((............)))))))).))))).....((((((...)))))).))))))). ( -39.10)
>DroEre_CAF1 136414 120 - 1
CCCUUUCGCCACCCAAGGCCAGACAACGCCCAUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAACAGUGGGUGG
........(((((((.((((((.....(((...)))..((...(((.((..(((((.((((((((............)))))))).))))))).)))...)))))))).....))))))) ( -42.70)
>DroYak_CAF1 140054 120 - 1
CUCGUUCGCCACCCAAGGCCAGACAACGCCCCUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAACAGUGGGCGG
...(((.(((......)))..)))..(((((((((((((((((((.((....))))))))).......((((.(....)))))...)))).......(((((...)))))))).))))). ( -41.30)
>consensus
CUCAUUCGCCACCCAAGGCCAGACAACGCCCAUGGUACGCAAUAUUACUUAUGUAUAUUGCCGCAUAAGCCGUCACUUGUGGCAAAGUACAAGCAAUUUGGCCUGGCCAAAAGCGGGCGG
......(((((((...(((........)))...))).(((...........(((((.((((((((............)))))))).)))))......(((((...)))))..))))))). (-37.68 = -37.28 +  -0.40)

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 12:20:38 2006