Locus 1767

Sequence ID 3L_DroMel_CAF1
Location 5,057,542 – 5,057,761
Length 219
Max. P 0.999911
window2731 window2732 window2733 window2734 window2735 window2736 window2737

overview

Window 1

Location 5,057,542 – 5,057,641
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -23.89
Consensus MFE -19.10
Energy contribution -20.02
Covariance contribution 0.92
Combinations/Pair 1.13
Mean z-score -1.59
Structure conservation index 0.80
SVM decision value 0.44
SVM RNA-class probability 0.738269
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057542 99 + 23771897
GAAAGUUUUGGACUGUCACAUCAAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAA
....(((((....((.(((.((..((((..(((((...((((((.............))))))))))))))))))))))...)))))((.....))... ( -26.42)
>DroSec_CAF1 263995 99 + 1
GAAAGUUUUGGACCGUCACAUCAAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAAGGCAUUAAGCAAA
....((((..(.((................(((((...((((((.............)))))))))))((((....))))......)))...))))... ( -23.62)
>DroSim_CAF1 285327 99 + 1
GAAAGUUUUGGACCGUCACAUCAAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAA
....(((((.....(.(((.((..((((..(((((...((((((.............)))))))))))))))))))))....)))))((.....))... ( -24.82)
>DroEre_CAF1 270776 91 + 1
GAAAGUUUUGGGCCGUCACAUCAAGUAUACGCCGCGUUGCAUAUACCAAGUA--------UAUGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAA
....((((..(((.((.((.....))..)))))(((((((((((((...)))--------))))).((((....))))......)))))...))))... ( -23.80)
>DroYak_CAF1 274433 91 + 1
GAAAGUUUUGAACCGUCACAUCAAGUAUACGCCGCGUGGCAUACAUCAAGUA--------UUCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAA
....(((((.....(.(((.((..((((..((((((....((((.....)))--------).))))))))))))))))....)))))((.....))... ( -20.80)
>consensus
GAAAGUUUUGGACCGUCACAUCAAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAA
....(((((.....(.(((.((..((((..(((((((((.((((.....)))).)).....)))))))))))))))))....)))))((.....))... (-19.10 = -20.02 +   0.92)

alignment

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secondary structure

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Window 2

Location 5,057,542 – 5,057,641
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 90.53
Mean single sequence MFE -27.42
Consensus MFE -19.82
Energy contribution -22.26
Covariance contribution 2.44
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.72
SVM decision value 0.51
SVM RNA-class probability 0.764792
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057542 99 - 23771897
UUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUUGAUGUGACAGUCCAAAACUUUC
...((.....))(((((...(((((((((((((((((.....((((((((.....))))))))))))))..))))..)).))).))....))))).... ( -30.00)
>DroSec_CAF1 263995 99 - 1
UUUGCUUAAUGCCUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUUGAUGUGACGGUCCAAAACUUUC
.(..(((((.((.......((((....))))((((((.....((((((((.....))))))))))))))....)))))).)..)............... ( -26.00)
>DroSim_CAF1 285327 99 - 1
UUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUUGAUGUGACGGUCCAAAACUUUC
...((.....))(((((...(((((((((((((((((.....((((((((.....))))))))))))))..))))..)).))).))....))))).... ( -29.30)
>DroEre_CAF1 270776 91 - 1
UUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCAUA--------UACUUGGUAUAUGCAACGCGGCGUAUACUUGAUGUGACGGCCCAAAACUUUC
...((.....))(((((..((((....))))((((((((--------(....(((((((((......)))))))))..))))).))))..))))).... ( -28.80)
>DroYak_CAF1 274433 91 - 1
UUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGAA--------UACUUGAUGUAUGCCACGCGGCGUAUACUUGAUGUGACGGUUCAAAACUUUC
...((.....))(((((....((..((((((((((((.(--------(((.....))))....))))))(....)...))))))..))..))))).... ( -23.00)
>consensus
UUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUUGAUGUGACGGUCCAAAACUUUC
...((.....))(((((...((((((((.((((((((.....((((((((.....)))))))))))))))).....))).))).))....))))).... (-19.82 = -22.26 +   2.44)

alignment

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secondary structure

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Window 3

Location 5,057,564 – 5,057,681
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -26.09
Consensus MFE -22.22
Energy contribution -22.78
Covariance contribution 0.56
Combinations/Pair 1.17
Mean z-score -2.33
Structure conservation index 0.85
SVM decision value 2.69
SVM RNA-class probability 0.996407
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057564 117 + 23771897
AAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUG
..((....(((((...((((((.............))))))))))).(((.(((((.........)))))..))).....(((((((......)))))))............))... ( -26.82)
>DroSec_CAF1 264017 117 + 1
AAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAAGGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUG
..((....(((((...((((((.............)))))))))))((((....))))....(((((((((((...................))).))))))))........))... ( -28.73)
>DroSim_CAF1 285349 117 + 1
AAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUG
..((....(((((...((((((.............))))))))))).(((.(((((.........)))))..))).....(((((((......)))))))............))... ( -26.82)
>DroEre_CAF1 270798 109 + 1
AAGUAUACGCCGCGUUGCAUAUACCAAGUA--------UAUGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAAAGAGCCUG
..((((.(((...(((((((((((...)))--------))))))))..))).)))).........((.....))......(((((((......)))))))................. ( -24.90)
>DroYak_CAF1 274455 109 + 1
AAGUAUACGCCGCGUGGCAUACAUCAAGUA--------UUCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACGUUUAAAUUAACUUAAAUGCCUUAAUAAAGAGCCUG
((((....((((((....((((.....)))--------).)))))).(((.(((((.........)))))..)))................))))....(((((....))).))... ( -23.20)
>consensus
AAGCAUACGCCGCGUUGCAUACAUCAAGUAUACAAGUAUGCGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUG
..((....(((((((((.((((.....)))).)).....))))))).(((.(((((.........)))))..))).....(((((((......)))))))............))... (-22.22 = -22.78 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,057,564 – 5,057,681
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 92.17
Mean single sequence MFE -32.40
Consensus MFE -24.64
Energy contribution -27.44
Covariance contribution 2.80
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.76
SVM decision value 1.74
SVM RNA-class probability 0.974758
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057564 117 - 23771897
CAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUU
.((((..........((((((((((....))))))))))....((....(((((.....)))))...))((((((((.....((((((((.....))))))))))))))))..)))) ( -34.50)
>DroSec_CAF1 264017 117 - 1
CAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCCUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUU
.((((..((((..((((((((.((((.(((.........))).))))))))))))...)))).......((((((((.....((((((((.....))))))))))))))))..)))) ( -36.70)
>DroSim_CAF1 285349 117 - 1
CAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUU
.((((..........((((((((((....))))))))))....((....(((((.....)))))...))((((((((.....((((((((.....))))))))))))))))..)))) ( -34.50)
>DroEre_CAF1 270798 109 - 1
CAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCAUA--------UACUUGGUAUAUGCAACGCGGCGUAUACUU
...(((....(((((((((((((((....)))))))))......))))))(((((...(((((....)))))..(((((--------(((...))))))))))))))))........ ( -27.70)
>DroYak_CAF1 274455 109 - 1
CAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAACGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGAA--------UACUUGAUGUAUGCCACGCGGCGUAUACUU
...((.........(((((..((((((......))).)))..)))))..(((((.....)))))...))((((((((.(--------(((.....))))....))))))))...... ( -28.60)
>consensus
CAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCGCAUACUUGUAUACUUGAUGUAUGCAACGCGGCGUAUGCUU
...((.....(((((((((((((((....)))))))))......))))))((((.....))))....))((((((((.....((((((((.....))))))))))))))))...... (-24.64 = -27.44 +   2.80)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,057,604 – 5,057,721
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 98.46
Mean single sequence MFE -21.53
Consensus MFE -20.70
Energy contribution -20.54
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.49
Structure conservation index 0.96
SVM decision value 1.12
SVM RNA-class probability 0.917921
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057604 117 + 23771897
CGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((((((.........))))((((.......(((((((......)))))))........((((...((..((((....)))).))..)))))))).)))))).)))). ( -21.30)
>DroSec_CAF1 264057 117 + 1
CGCGGCAUGCGAGUGCAUAAAAAAGGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((..........(((((((((((...................))).))))))))....((((...((..((((....)))).))..)))).....)))))).)))). ( -23.81)
>DroSim_CAF1 285389 117 + 1
CGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((((((.........))))((((.......(((((((......)))))))........((((...((..((((....)))).))..)))))))).)))))).)))). ( -21.30)
>DroEre_CAF1 270830 117 + 1
UGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAAAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((((((.........))))((((.(((...(((((((......)))))))...............((..((((....)))).))..))).)))).)))))).)))). ( -20.40)
>DroYak_CAF1 274487 117 + 1
CGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACGUUUAAAUUAACUUAAAUGCCUUAAUAAAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((((((.........))))((((.(((....((((((......))))))(((..............))).................))).)))).)))))).)))). ( -20.84)
>consensus
CGCGGCAUGCGAGUGCAUAAAAAACGCAUUAAGCAAACAACAUUUAAAUUAACUUAAAUGCCUUAAUAUAGAGCCUGGCCAAAUACAUUUGACAUAUUUACUUAAUCGCAUUUCGCC
.((((.((((((((((.........))))((((.(((...(((((((......)))))))...............((..((((....)))).))..))).)))).)))))).)))). (-20.70 = -20.54 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,057,604 – 5,057,721
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 98.46
Mean single sequence MFE -33.82
Consensus MFE -33.40
Energy contribution -33.80
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.06
Structure conservation index 0.99
SVM decision value 4.50
SVM RNA-class probability 0.999911
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057604 117 - 23771897
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCG
.(((..((((((((((((((((..((((((....))))))...............((((((((((....))))))))))))))))))))(((((.....))))).))))))..))). ( -35.00)
>DroSec_CAF1 264057 117 - 1
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCCUUUUUUAUGCACUCGCAUGCCGCG
.(((..((((((((((((((((..((((((....))))))...............((((((((((....))))))))))))))))))))(((.........))).))))))..))). ( -31.40)
>DroSim_CAF1 285389 117 - 1
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCG
.(((..((((((((((((((((..((((((....))))))...............((((((((((....))))))))))))))))))))(((((.....))))).))))))..))). ( -35.00)
>DroEre_CAF1 270830 117 - 1
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCA
.(((..((((((((((((((((..((((((....))))))...............((((((((((....))))))))))))))))))))(((((.....))))).))))))..))). ( -35.00)
>DroYak_CAF1 274487 117 - 1
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAACGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCG
.(((..(((((((((((((((((.((((((....))))))...((.(((....)))))....................)))))))))))(((((.....))))).))))))..))). ( -32.70)
>consensus
GGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUGUUUGCUUAAUGCGUUUUUUAUGCACUCGCAUGCCGCG
.(((..((((((((((((((((..((((((....))))))...............((((((((((....))))))))))))))))))))(((((.....))))).))))))..))). (-33.40 = -33.80 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,057,641 – 5,057,761
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.50
Mean single sequence MFE -29.42
Consensus MFE -26.76
Energy contribution -27.40
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.70
Structure conservation index 0.91
SVM decision value 1.76
SVM RNA-class probability 0.975809
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5057641 120 - 23771897
GAGUUGUUGGCAAAGUAACGUUUGAAACUCAUACGCGUUCGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUG
((((..(((((.(((((.(((((((....(((((((.....)))...(((......)))..)))))))))))))))).)))))))))........((((((((((....)))))))))). ( -30.80)
>DroSec_CAF1 264094 120 - 1
GAGUUGUUGGCAAAGUAACGUUUGAAACUCAUACUCGUUCGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUG
((((..(((((.(((((.(((((((......((((...(((........)))...))))......)))))))))))).)))))))))........((((((((((....)))))))))). ( -30.90)
>DroSim_CAF1 285426 120 - 1
GAGUUGUUGGCAAAGUAACGUUUGAAACUCAUACUCGUUCGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUG
((((..(((((.(((((.(((((((......((((...(((........)))...))))......)))))))))))).)))))))))........((((((((((....)))))))))). ( -30.90)
>DroEre_CAF1 270867 120 - 1
CAGUUGCUGGCAAAGUAACGUUUGAAACUCAAACCCGCUCGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUG
..((((((.....))))))(((((.....)))))..((..(((.(((((((((...........)))....)))))).)))..))..........((((((((((....)))))))))). ( -30.60)
>DroYak_CAF1 274524 120 - 1
GAGUUGUUGGCAAAGUAACGUUUGAAACCCAUACCCGUACGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUUUAUUAAGGCAUUUAAGUUAAUUUAAACGUUG
((((..(((((.(((((.(((((((....(((((((....)).)...(((......)))..)))))))))))))))).)))))))))........(((.((((((....)))))).))). ( -23.90)
>consensus
GAGUUGUUGGCAAAGUAACGUUUGAAACUCAUACCCGUUCGGCGAAAUGCGAUUAAGUAAAUAUGUCAAAUGUAUUUGGCCAGGCUCUAUAUUAAGGCAUUUAAGUUAAUUUAAAUGUUG
((((..(((((.(((((.(((((((......(((....(((........)))....)))......)))))))))))).)))))))))........((((((((((....)))))))))). (-26.76 = -27.40 +   0.64)

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 10:15:50 2006