Locus 5687

Sequence ID 3L_DroMel_CAF1
Location 15,570,773 – 15,570,905
Length 132
Max. P 0.996123
window8992 window8993 window8994 window8995

overview

Window 2

Location 15,570,773 – 15,570,875
Length 102
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.03
Mean single sequence MFE -49.95
Consensus MFE -26.70
Energy contribution -28.33
Covariance contribution 1.63
Combinations/Pair 1.19
Mean z-score -3.09
Structure conservation index 0.53
SVM decision value 2.66
SVM RNA-class probability 0.996123
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15570773 102 + 23771897
CCCACGAGUUGCAGCAUCAUGUGGAGCCCAGGCAGGCGGCCAUGUUGCUGCUGCGACACUCGACACCG------------CAGCAGCAACAUCGC---AGCAGCAUGGCCUCGUCC---U
...((((((..((......))..).(((...((..((.((.((((((((((((((...........))------------)))))))))))).))---.)).))..))))))))..---. ( -45.40)
>DroEre_CAF1 33476 102 + 1
CCCAAGAGUUGCAGCAUCACGUGGAGCCCAGGCAGGCGGCAAUGUUGCUGCUGCGGCACUCGACGCCG------------CAGCAGCAGCAUCGC---AGCAGCAUGGGCUCGUCC---U
.....((((....)).)).....(((((((.((..((.((.((((((((((((((((.......))))------------)))))))))))).))---.)).)).)))))))....---. ( -56.10)
>DroYak_CAF1 53103 102 + 1
CCCACGAGUUGCAGCAUCACGUGGAGCCCAGGCAGGCGGCAAUGUUGCUGCUGCGCCACUCGACGCCG------------CAGCAGCAGCAUCGC---AGCAGCACUGGCUCGUCC---U
..((((.(.((...)).).))))(((((.((((..((.((.((((((((((((((.(.......).))------------)))))))))))).))---.)).)).)))))))....---. ( -47.80)
>DroAna_CAF1 33016 111 + 1
CCCAUGAGCUGCAACAGCAUGUGGAGCCGAG---------CAUGUUGCUGGUGCGUCACUCGACACCGAUGCUGGUGGCGCGUCAGCAGCAUCGGCUGGCCAGCAAUGCCUCCUCCUCGU
.(((((.((((...)))).)))))((((((.---------..((((((((..((((((((.(.((....))).))))))))..))))))))))))))(((.(....)))).......... ( -50.50)
>consensus
CCCACGAGUUGCAGCAUCACGUGGAGCCCAGGCAGGCGGCAAUGUUGCUGCUGCGACACUCGACACCG____________CAGCAGCAGCAUCGC___AGCAGCAUGGCCUCGUCC___U
..((((.(.((...)).).))))(((((((.((..((.((.((((((((((((...........................)))))))))))).))....)).)).)))))))........ (-26.70 = -28.33 +   1.63)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,570,773 – 15,570,875
Length 102
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.03
Mean single sequence MFE -51.80
Consensus MFE -26.96
Energy contribution -29.02
Covariance contribution 2.06
Combinations/Pair 1.16
Mean z-score -2.69
Structure conservation index 0.52
SVM decision value 1.65
SVM RNA-class probability 0.970111
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15570773 102 - 23771897
A---GGACGAGGCCAUGCUGCU---GCGAUGUUGCUGCUG------------CGGUGUCGAGUGUCGCAGCAGCAACAUGGCCGCCUGCCUGGGCUCCACAUGAUGCUGCAACUCGUGGG
.---....(((.(((.((.((.---((.((((((((((((------------(((..(...)..))))))))))))))).)).))..)).))).)))..(((((.(......)))))).. ( -51.40)
>DroEre_CAF1 33476 102 - 1
A---GGACGAGCCCAUGCUGCU---GCGAUGCUGCUGCUG------------CGGCGUCGAGUGCCGCAGCAGCAACAUUGCCGCCUGCCUGGGCUCCACGUGAUGCUGCAACUCUUGGG
(---(((.(((((((.((.((.---((((((.((((((((------------(((((.....))))))))))))).)))))).))..)).)))))))...((......))...))))... ( -56.50)
>DroYak_CAF1 53103 102 - 1
A---GGACGAGCCAGUGCUGCU---GCGAUGCUGCUGCUG------------CGGCGUCGAGUGGCGCAGCAGCAACAUUGCCGCCUGCCUGGGCUCCACGUGAUGCUGCAACUCGUGGG
.---..(((((...((((..((---.(((((((((....)------------))))))))))..)))).((((((.(((((..((((....))))..)).))).))))))..)))))... ( -53.60)
>DroAna_CAF1 33016 111 - 1
ACGAGGAGGAGGCAUUGCUGGCCAGCCGAUGCUGCUGACGCGCCACCAGCAUCGGUGUCGAGUGACGCACCAGCAACAUG---------CUCGGCUCCACAUGCUGUUGCAGCUCAUGGG
....((((..(((((((((((...((((((((((.((......)).))))))))))(((....)))...))))))..)))---------).)..)))).(((((((...))))..))).. ( -45.70)
>consensus
A___GGACGAGCCAAUGCUGCU___GCGAUGCUGCUGCUG____________CGGCGUCGAGUGACGCAGCAGCAACAUGGCCGCCUGCCUGGGCUCCACAUGAUGCUGCAACUCGUGGG
......(((((....(((.((.....((((((((..................))))))))...)).)))((((((.((((...((((....))))....)))).))))))..)))))... (-26.96 = -29.02 +   2.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,570,813 – 15,570,905
Length 92
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 76.42
Mean single sequence MFE -38.52
Consensus MFE -19.99
Energy contribution -19.24
Covariance contribution -0.75
Combinations/Pair 1.22
Mean z-score -2.40
Structure conservation index 0.52
SVM decision value 1.09
SVM RNA-class probability 0.913840
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15570813 92 + 23771897
CAUGUUGCUGCUGCGACACUCGACACCG------------CAGCAGCAACAUCGC---AGCAGCAUGGCCUCGUCC---UUGUACCAAUCCUUUGACGUGACCUCCGCCG----------
.((((((((((((((...........))------------)))))))))))).((---....))..(((...(((.---.(((..(((....)))))).)))....))).---------- ( -32.50)
>DroEre_CAF1 33516 92 + 1
AAUGUUGCUGCUGCGGCACUCGACGCCG------------CAGCAGCAGCAUCGC---AGCAGCAUGGGCUCGUCC---UUGUACCAAUCCUUUGACGUGACCUCCGCCG----------
.((((((((((((((((.......))))------------))))))))))))...---....((..((((.((((.---..(........)...)))).).)))..))..---------- ( -40.30)
>DroYak_CAF1 53143 92 + 1
AAUGUUGCUGCUGCGCCACUCGACGCCG------------CAGCAGCAGCAUCGC---AGCAGCACUGGCUCGUCC---UUGUACCAAUCCUUUGACGUGACCUCCGCCG----------
.((((((((((((((.(.......).))------------)))))))))))).((---....))...(((..(((.---.(((..(((....)))))).)))....))).---------- ( -32.50)
>DroAna_CAF1 33047 120 + 1
CAUGUUGCUGGUGCGUCACUCGACACCGAUGCUGGUGGCGCGUCAGCAGCAUCGGCUGGCCAGCAAUGCCUCCUCCUCGUUGUACCAAUCGUUCGAGGUGACCUCCACCACGCUGCCGAU
..((((((((..((((((((.(.((....))).))))))))..))))))))(((((.(((..((((((.........)))))).............((((.....))))..)))))))). ( -48.80)
>consensus
AAUGUUGCUGCUGCGACACUCGACACCG____________CAGCAGCAGCAUCGC___AGCAGCAUGGCCUCGUCC___UUGUACCAAUCCUUUGACGUGACCUCCGCCG__________
.((((((((((((...........................)))))))))))).((....)).((..((.(.((((...................)))).).))...))............ (-19.99 = -19.24 +  -0.75)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,570,813 – 15,570,905
Length 92
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 76.42
Mean single sequence MFE -43.60
Consensus MFE -22.07
Energy contribution -23.26
Covariance contribution 1.19
Combinations/Pair 1.16
Mean z-score -2.41
Structure conservation index 0.51
SVM decision value 0.96
SVM RNA-class probability 0.889702
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15570813 92 - 23771897
----------CGGCGGAGGUCACGUCAAAGGAUUGGUACAA---GGACGAGGCCAUGCUGCU---GCGAUGUUGCUGCUG------------CGGUGUCGAGUGUCGCAGCAGCAACAUG
----------((((((.((((.((((...(........)..---.)))).))))...)))))---)..((((((((((((------------(((..(...)..))))))))))))))). ( -46.40)
>DroEre_CAF1 33516 92 - 1
----------CGGCGGAGGUCACGUCAAAGGAUUGGUACAA---GGACGAGCCCAUGCUGCU---GCGAUGCUGCUGCUG------------CGGCGUCGAGUGCCGCAGCAGCAACAUU
----------((((((.((.(.((((...(........)..---.)))).).))...)))))---).((((.((((((((------------(((((.....))))))))))))).)))) ( -43.80)
>DroYak_CAF1 53143 92 - 1
----------CGGCGGAGGUCACGUCAAAGGAUUGGUACAA---GGACGAGCCAGUGCUGCU---GCGAUGCUGCUGCUG------------CGGCGUCGAGUGGCGCAGCAGCAACAUU
----------.((((.......)))).....((((((.(..---....).))))))((((((---((((((((((....)------------)))))))(.....)))))))))...... ( -39.70)
>DroAna_CAF1 33047 120 - 1
AUCGGCAGCGUGGUGGAGGUCACCUCGAACGAUUGGUACAACGAGGAGGAGGCAUUGCUGGCCAGCCGAUGCUGCUGACGCGCCACCAGCAUCGGUGUCGAGUGACGCACCAGCAACAUG
.......((.(((((...(((((.((((.....((((.((.(((.(......).))).))))))((((((((((.((......)).)))))))))).))))))))).)))))))...... ( -44.50)
>consensus
__________CGGCGGAGGUCACGUCAAAGGAUUGGUACAA___GGACGAGCCAAUGCUGCU___GCGAUGCUGCUGCUG____________CGGCGUCGAGUGACGCAGCAGCAACAUG
...........(((((.((((.((((......(((...)))....)))).))))...)))))......(((.(((((((...............(((((....)))))))))))).))). (-22.07 = -23.26 +   1.19)

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 11:56:39 2006