Locus 2831

Sequence ID X_DroMel_CAF1
Location 7,558,825 – 7,559,003
Length 178
Max. P 0.965006
window4644 window4645 window4646 window4647 window4648 window4649

overview

Window 4

Location 7,558,825 – 7,558,945
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.42
Mean single sequence MFE -56.02
Consensus MFE -43.06
Energy contribution -45.34
Covariance contribution 2.28
Combinations/Pair 1.21
Mean z-score -2.00
Structure conservation index 0.77
SVM decision value 0.85
SVM RNA-class probability 0.865136
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558825 120 + 22224390
GUAGGGUGCAUAAAGUGGUGGAUACCAAACCGGUGGUGGUGGCGGCAGGACCAAAUCCUGUGGUGGCAACGAUGCCGCCGGCGGUGUAUUGUCCUGCAGGUUAGUGUCGACGGCACCACC
....(((((......((((....))))...((.((..(.((((.(((((((...(..(((((((((((....))))))).))))..)...)))))))..)))).)..)).)))))))... ( -50.20)
>DroPse_CAF1 115708 120 + 1
GUACGGGGCAUACAGCGGGGGAUACCACACGGGUGGUGGCGGUGGCAGGACCAAAUCCUGUGGCGGUAACGAUGCCGCCGGCGGUGUGUUGUCCUGCAUUGAACUGUCCACCGCUCCGCC
...((((((..((..((.((....))...)).))(((((((((.(((((((...(..(((((((((((....))))))).))))..)...))))))).....)))).))))))))))).. ( -58.80)
>DroEre_CAF1 62811 120 + 1
GUAGGGCGCGUAGAGCGGUGGAUACCAAACCGGUGGUGGUGGCGGCAGGACCAAAUCCUGUGGUGGCAACGAUGCCGCUGGCGGCGUAUUAUCCUGCAGGUUAGUGUCCACCGCACCACC
...((((((.....))(((((((((..((((.(..(.(((.((.((((((.....)))))).)).))....((((((....)))))).....))..).)))).))))))))))).))... ( -55.50)
>DroYak_CAF1 52809 120 + 1
GUAUGGCGCGUACAGCGGUGGAUACCACACCGGUGGCGGUGGCGGCAGCACCAGAUCCUGUGGCGGCAACGAUGCCGCCGGCGGUGCAUUAUCCUGCAGGCUACUGUCCACUGCACCGCC
....((((.((.((.(((((.......))))).))((((((((((.(((........(((((((((((....))))))).))))((((......)))).))).))).))))))))))))) ( -59.00)
>DroPer_CAF1 121823 120 + 1
GUACGGGGCAUACAGCGGGGGAUACCACACGGGUGGUGGCGGUGGCAGGACCAAAUCCUGUGGCGGUAAUGAUGCUGCCGGCGGUGUGUUGUCCUGCAUCGAACUGUCCACCGCUCCGCC
...((((((..((..((.((....))...)).))(((((((((.(((((((...(..(((((((((((....))))))).))))..)...))))))).....)))).))))))))))).. ( -56.60)
>consensus
GUACGGCGCAUACAGCGGUGGAUACCACACCGGUGGUGGUGGCGGCAGGACCAAAUCCUGUGGCGGCAACGAUGCCGCCGGCGGUGUAUUGUCCUGCAGGGUACUGUCCACCGCACCGCC
....(((((.......((......)).....((((((((((((.(((((((...((.(((((((((((....))))))).)))).))...)))))))..))))))).))))))))))... (-43.06 = -45.34 +   2.28)

alignment

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secondary structure

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Window 5

Location 7,558,825 – 7,558,945
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.42
Mean single sequence MFE -50.26
Consensus MFE -40.66
Energy contribution -42.50
Covariance contribution 1.84
Combinations/Pair 1.25
Mean z-score -2.27
Structure conservation index 0.81
SVM decision value 1.57
SVM RNA-class probability 0.965006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558825 120 - 22224390
GGUGGUGCCGUCGACACUAACCUGCAGGACAAUACACCGCCGGCGGCAUCGUUGCCACCACAGGAUUUGGUCCUGCCGCCACCACCACCGGUUUGGUAUCCACCACUUUAUGCACCCUAC
((((((((((.............(((((((......((...((.((((....)))).))...)).....)))))))....(((......))).))))).)))))................ ( -41.10)
>DroPse_CAF1 115708 120 - 1
GGCGGAGCGGUGGACAGUUCAAUGCAGGACAACACACCGCCGGCGGCAUCGUUACCGCCACAGGAUUUGGUCCUGCCACCGCCACCACCCGUGUGGUAUCCCCCGCUGUAUGCCCCGUAC
(((((.((((((((....))...(((((((......((...(((((........)))))...)).....))))))))))))).(((((....))))).....)))))(((((...))))) ( -49.00)
>DroEre_CAF1 62811 120 - 1
GGUGGUGCGGUGGACACUAACCUGCAGGAUAAUACGCCGCCAGCGGCAUCGUUGCCACCACAGGAUUUGGUCCUGCCGCCACCACCACCGGUUUGGUAUCCACCGCUCUACGCGCCCUAC
.((((.((((((((.(((((...(((((((......((....(.((((....)))).)....)).....)))))))....(((......)))))))).)))))))).))))......... ( -48.70)
>DroYak_CAF1 52809 120 - 1
GGCGGUGCAGUGGACAGUAGCCUGCAGGAUAAUGCACCGCCGGCGGCAUCGUUGCCGCCACAGGAUCUGGUGCUGCCGCCACCGCCACCGGUGUGGUAUCCACCGCUGUACGCGCCAUAC
(((((((((((((.(((....)))..(((((..((((((..(((((((....)))))))...((...(((((....)))))...))..))))))..))))).))))))))).)))).... ( -65.10)
>DroPer_CAF1 121823 120 - 1
GGCGGAGCGGUGGACAGUUCGAUGCAGGACAACACACCGCCGGCAGCAUCAUUACCGCCACAGGAUUUGGUCCUGCCACCGCCACCACCCGUGUGGUAUCCCCCGCUGUAUGCCCCGUAC
(((((.((((((....((((......))))....)))))).(((((.((((...((......))...)))).))))).)))))(((((....))))).......((.....))....... ( -47.40)
>consensus
GGCGGUGCGGUGGACAGUAACCUGCAGGACAAUACACCGCCGGCGGCAUCGUUGCCGCCACAGGAUUUGGUCCUGCCGCCACCACCACCGGUGUGGUAUCCACCGCUGUAUGCCCCCUAC
(((((((((((((..........(((((((......((...(((((((....)))))))...)).....))))))).(((((.((.....))))))).....))))))))).)))).... (-40.66 = -42.50 +   1.84)

alignment

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secondary structure

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Window 6

Location 7,558,865 – 7,558,973
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.45
Mean single sequence MFE -48.75
Consensus MFE -27.86
Energy contribution -27.95
Covariance contribution 0.09
Combinations/Pair 1.22
Mean z-score -1.81
Structure conservation index 0.57
SVM decision value 1.30
SVM RNA-class probability 0.939595
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558865 108 + 22224390
GGCGGCAGGACCAAAUCCUGUGGUGGCAACGAUGCCGCCGGCGGUGUAUUGUCCUGCAGGUUAGUGUCGACGGCACCACCCAGACCACCAGUCUUAUUGCCA------GCCG------UU
(((.((((((.....))))))(((((((....)))))))((((((((...(((..(((......))).))).)))))....((((.....))))....))).------))).------.. ( -43.80)
>DroPse_CAF1 115748 95 + 1
GGUGGCAGGACCAAAUCCUGUGGCGGUAACGAUGCCGCCGGCGGUGUGUUGUCCUGCAUUGAACUGUCCACCGCUCCGCCCAGGCCGCCCUU-------------------G------GU
((((((((((.....))))..(((((((....)))))))(((((.(((.((..(...........)..)).))).)))))...))))))...-------------------.------.. ( -41.60)
>DroEre_CAF1 62851 108 + 1
GGCGGCAGGACCAAAUCCUGUGGUGGCAACGAUGCCGCUGGCGGCGUAUUAUCCUGCAGGUUAGUGUCCACCGCACCACCCAGGCCACCAGCCUUGUUGCCA------CCGU------UU
....((((((.....))))))(((((((((((....(((((.((((((......))).(((..((((.....)))).)))...))).))))).)))))))))------))..------.. ( -47.40)
>DroYak_CAF1 52849 108 + 1
GGCGGCAGCACCAGAUCCUGUGGCGGCAACGAUGCCGCCGGCGGUGCAUUAUCCUGCAGGCUACUGUCCACUGCACCGCCCAAUGAGGCAGUCUUACUGCCA------GCGC------UU
(((((((((..(((...)))..))(....)..)))))))(((((((((.......((((....))))....)))))))))......(((((.....))))).------....------.. ( -50.90)
>DroAna_CAF1 54236 120 + 1
GGCGGCAGCACCAGGUCCUGUGGCGGCAGGGAGGCUGCCGGCGGGGUGUUGUCCUGCAGGACGCUGUCCACGGCCCCGCCCAGGGAGGCGUUCUUGCCGCCGUUCGCCGCCGUGGAUGUG
(((((((((..(((...))).(((((((((((.(((.((((((((.....((((....))))((((....))))))))))...)).))).)))))))))))))).))))))......... ( -69.00)
>DroPer_CAF1 121863 95 + 1
GGUGGCAGGACCAAAUCCUGUGGCGGUAAUGAUGCUGCCGGCGGUGUGUUGUCCUGCAUCGAACUGUCCACCGCUCCGCCCAGGCCGCCUUU-------------------G------GU
((((((((((.....))))..(((((((....)))))))(((((.(((.((..(...........)..)).))).)))))...))))))...-------------------.------.. ( -39.80)
>consensus
GGCGGCAGGACCAAAUCCUGUGGCGGCAACGAUGCCGCCGGCGGUGUAUUGUCCUGCAGGGUACUGUCCACCGCACCGCCCAGGCCGCCAGUCUU__UGCCA______GC_G______UU
(((((((((((......((((((((((......)))))).))))......)))))))........((.....))..))))........................................ (-27.86 = -27.95 +   0.09)

alignment

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secondary structure

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Window 7

Location 7,558,865 – 7,558,973
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 71.45
Mean single sequence MFE -46.54
Consensus MFE -26.65
Energy contribution -27.77
Covariance contribution 1.12
Combinations/Pair 1.31
Mean z-score -1.67
Structure conservation index 0.57
SVM decision value 0.98
SVM RNA-class probability 0.894605
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558865 108 - 22224390
AA------CGGC------UGGCAAUAAGACUGGUGGUCUGGGUGGUGCCGUCGACACUAACCUGCAGGACAAUACACCGCCGGCGGCAUCGUUGCCACCACAGGAUUUGGUCCUGCCGCC
..------.(((------.((((....(((..(...(((((((((((..(((...............)))....)))))))((.((((....)))).)).))))..)..))).))))))) ( -42.26)
>DroPse_CAF1 115748 95 - 1
AC------C-------------------AAGGGCGGCCUGGGCGGAGCGGUGGACAGUUCAAUGCAGGACAACACACCGCCGGCGGCAUCGUUACCGCCACAGGAUUUGGUCCUGCCACC
..------.-------------------.(((((..(((((((((.((((((....((((......))))....)))))).((((....)))).))))).)))).....)))))...... ( -39.50)
>DroEre_CAF1 62851 108 - 1
AA------ACGG------UGGCAACAAGGCUGGUGGCCUGGGUGGUGCGGUGGACACUAACCUGCAGGAUAAUACGCCGCCAGCGGCAUCGUUGCCACCACAGGAUUUGGUCCUGCCGCC
..------..((------(((((((.((((.....)))).((((.((((((((....((.((....)).)).....))))).))).))))))))))))).((((((...))))))..... ( -49.10)
>DroYak_CAF1 52849 108 - 1
AA------GCGC------UGGCAGUAAGACUGCCUCAUUGGGCGGUGCAGUGGACAGUAGCCUGCAGGAUAAUGCACCGCCGGCGGCAUCGUUGCCGCCACAGGAUCUGGUGCUGCCGCC
.(------((((------((((((.....)))))((.((((((((((((.((..(.((.....)).)..)).)))))))))(((((((....))))))).)))))...))))))...... ( -53.00)
>DroAna_CAF1 54236 120 - 1
CACAUCCACGGCGGCGAACGGCGGCAAGAACGCCUCCCUGGGCGGGGCCGUGGACAGCGUCCUGCAGGACAACACCCCGCCGGCAGCCUCCCUGCCGCCACAGGACCUGGUGCUGCCGCC
.........(((((((.((((((.......))))..(((((((((((..((.....))((((....))))....)))))))(((((.....)))))....)))).....))..))))))) ( -58.60)
>DroPer_CAF1 121863 95 - 1
AC------C-------------------AAAGGCGGCCUGGGCGGAGCGGUGGACAGUUCGAUGCAGGACAACACACCGCCGGCAGCAUCAUUACCGCCACAGGAUUUGGUCCUGCCACC
..------.-------------------...((((((((((((((.((((((....((((......))))....)))))).((.....))....))))).))))........)))))... ( -36.80)
>consensus
AA______C_GC______UGGCA__AAGAAUGGCGGCCUGGGCGGUGCGGUGGACAGUAACCUGCAGGACAACACACCGCCGGCGGCAUCGUUGCCGCCACAGGAUUUGGUCCUGCCGCC
....................................(((((((((((...((..(.((.....)).)..))...)))))))(((((((....))))))).))))...(((.....))).. (-26.65 = -27.77 +   1.12)

alignment

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secondary structure

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Window 8

Location 7,558,905 – 7,559,003
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 81.29
Mean single sequence MFE -42.80
Consensus MFE -26.96
Energy contribution -28.63
Covariance contribution 1.67
Combinations/Pair 1.15
Mean z-score -1.97
Structure conservation index 0.63
SVM decision value 0.24
SVM RNA-class probability 0.646651
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558905 98 + 22224390
GCGGUGUAUUGUCCUGCAGGUUAGUGUCGACGGCACCACCCAGACCACCAGUCUUAUUGCCAGCCGUUGGUGGUGCCGUCGUUGGCGUUGGCGGUGUU
((((.(......)))))..(((((((((((((((((((((.((((.....))))....(....)....)))))))))))))...))))))))...... ( -36.50)
>DroEre_CAF1 62891 98 + 1
GCGGCGUAUUAUCCUGCAGGUUAGUGUCCACCGCACCACCCAGGCCACCAGCCUUGUUGCCACCGUUUGGUGGUACCGUCGUUGGCGUGGGUGGUGCU
((((.(......))))).(((........)))((((((((((.((((...((..((.(((((((....))))))).))..)))))).)))))))))). ( -48.80)
>DroYak_CAF1 52889 98 + 1
GCGGUGCAUUAUCCUGCAGGCUACUGUCCACUGCACCGCCCAAUGAGGCAGUCUUACUGCCAGCGCUUGGUGGUGCCGUCGCCGGCGUUGGUGGUGUU
((((((((.......((((....))))....))))))))...............(((..((((((((.(((((.....)))))))))))))..))).. ( -43.10)
>consensus
GCGGUGUAUUAUCCUGCAGGUUAGUGUCCACCGCACCACCCAGACCACCAGUCUUAUUGCCAGCGCUUGGUGGUGCCGUCGUUGGCGUUGGUGGUGUU
((((.(......)))))...............((((((((.((((.....))))....(((((((..(((.....))).)))))))...)))))))). (-26.96 = -28.63 +   1.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,558,905 – 7,559,003
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 81.29
Mean single sequence MFE -40.57
Consensus MFE -22.20
Energy contribution -23.09
Covariance contribution 0.90
Combinations/Pair 1.16
Mean z-score -2.85
Structure conservation index 0.55
SVM decision value 0.48
SVM RNA-class probability 0.754462
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7558905 98 - 22224390
AACACCGCCAACGCCAACGACGGCACCACCAACGGCUGGCAAUAAGACUGGUGGUCUGGGUGGUGCCGUCGACACUAACCUGCAGGACAAUACACCGC
....((((....))...(((((((((((((.((.((..(........)..)).))...))))))))))))).............))............ ( -38.00)
>DroEre_CAF1 62891 98 - 1
AGCACCACCCACGCCAACGACGGUACCACCAAACGGUGGCAACAAGGCUGGUGGCCUGGGUGGUGCGGUGGACACUAACCUGCAGGAUAAUACGCCGC
.((((((((((.((((....((((.(((((....))))).......)))).)))).))))))))))((((.....((.((....)).))...)))).. ( -45.60)
>DroYak_CAF1 52889 98 - 1
AACACCACCAACGCCGGCGACGGCACCACCAAGCGCUGGCAGUAAGACUGCCUCAUUGGGCGGUGCAGUGGACAGUAGCCUGCAGGAUAAUGCACCGC
............((((....))))....((((.....(((((.....)))))...))))((((((((.((..(.((.....)).)..)).)))))))) ( -38.10)
>consensus
AACACCACCAACGCCAACGACGGCACCACCAAACGCUGGCAAUAAGACUGGUGGACUGGGUGGUGCAGUGGACACUAACCUGCAGGAUAAUACACCGC
..(((((((...((((.((..((.....))...)).))))....((((.....)))).)))))))..((((.......((....))........)))) (-22.20 = -23.09 +   0.90)

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 10:44:38 2006