Locus 6436

Sequence ID 2L_DroMel_CAF1
Location 18,085,026 – 18,085,484
Length 458
Max. P 0.967786
window10273 window10274 window10275 window10276 window10277 window10278 window10279 window10280

overview

Window 3

Location 18,085,026 – 18,085,125
Length 99
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 90.76
Mean single sequence MFE -18.52
Consensus MFE -15.69
Energy contribution -16.32
Covariance contribution 0.63
Combinations/Pair 1.08
Mean z-score -1.84
Structure conservation index 0.85
SVM decision value 0.79
SVM RNA-class probability 0.852633
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085026 99 + 22407834
AAUUAAUAUAAAGUUUGUAAACUGAUAG---UAGAUGGGGGGUAAUUGAAAAAAACAGUAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUAUAAA
.............((((((..((.((..---...)).))..................((((((......))))))((((.((.....)).)))).-.)))))) ( -12.20)
>DroSec_CAF1 292369 99 + 1
AAUUAAUAUAAAGUUUGUAAACUGAUAG---CAGAUGCGUGUUAAUGGA-AAAAACAGCAUGUAAUCAAAUAUGCGGCUACUAAACUAGAAGCCAAAUUUAUA
.((((((((...((((((.........)---)))))..))))))))...-.......((((((......))))))((((.(((...))).))))......... ( -20.80)
>DroSim_CAF1 294406 99 + 1
AAUUAAUAUAAAGUUUGUAAACUGAUAG---CAGAUGCGUGUUAAUUGAAAAAAACAGCAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUUUAUA
(((((((((...((((((.........)---)))))..)))))))))..........((((((......))))))((((.((.....)).)))).-....... ( -21.50)
>DroYak_CAF1 309799 100 + 1
AAUUAAUAUAAAGUUUGUAAACUGAUAGCAGCAGAUGUGUGUUAAUUGAA--AAACAGCAUGCAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUUUAUA
((((((((((..((((((............)))))).))))))))))...--.....(((((........)))))((((.((.....)).)))).-....... ( -19.60)
>consensus
AAUUAAUAUAAAGUUUGUAAACUGAUAG___CAGAUGCGUGUUAAUUGAAAAAAACAGCAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA_AUUUAUA
(((((((((...(((((..............)))))..)))))))))..........((((((......))))))((((.((.....)).))))......... (-15.69 = -16.32 +   0.63)

alignment

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secondary structure

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Window 4

Location 18,085,061 – 18,085,165
Length 104
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 85.33
Mean single sequence MFE -19.73
Consensus MFE -12.79
Energy contribution -14.85
Covariance contribution 2.06
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.65
SVM decision value 0.09
SVM RNA-class probability 0.577129
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085061 104 + 22407834
GGGGUAAUUGAAAAAAACAGUAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUAUAAAAUGAAAUAUUGCAAUUAUCGCACUGCCUUCCGAAAAUUCC
(.((((((((.........((((((......))))))((((.((.....)).)))).-..................)))))))).)................... ( -20.30)
>DroSec_CAF1 292404 95 + 1
GUGUUAAUGGA-AAAAACAGCAUGUAAUCAAAUAUGCGGCUACUAAACUAGAAGCCAAAUUUAUAAUGAAAUAUC---------GCACUGCCUUCCGAAAAUUCU
.......((((-(......((((((......))))))((((.(((...))).))))...................---------........)))))........ ( -17.30)
>DroSim_CAF1 294441 104 + 1
GUGUUAAUUGAAAAAAACAGCAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUUUAUAAUGAAAUAUCGCAGUUAUCGCACUGCCUUCCAAAAAUUCC
(((.((((((.........((((((......))))))((((.((.....)).)))).-..................)))))).)))................... ( -20.60)
>DroYak_CAF1 309837 101 + 1
GUGUUAAUUGAA--AAACAGCAUGCAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA-AUUUAUAAUGAAAUUUCGCAGUUAUU-CACUGCCUUCAAAAAAUGCC
(((((..(((((--...(((((((........)))))((((.((.....)).)))).-........)).......(((((....-.))))).)))))..))))). ( -20.70)
>consensus
GUGUUAAUUGAAAAAAACAGCAUGUAAUCAAAUAUGCGGCUACUUAGCUAGAAGCCA_AUUUAUAAUGAAAUAUCGCAGUUAUCGCACUGCCUUCCAAAAAUUCC
(((.((((((.........((((((......))))))((((.((.....)).))))....................)))))).)))................... (-12.79 = -14.85 +   2.06)

alignment

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secondary structure

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Window 5

Location 18,085,125 – 18,085,244
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.05
Mean single sequence MFE -30.55
Consensus MFE -19.83
Energy contribution -20.95
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -1.90
Structure conservation index 0.65
SVM decision value 0.23
SVM RNA-class probability 0.643023
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085125 119 + 22407834
AUGAAAUAUUGCAAUUAUCGCACUGCCUUCCGAAAAUUCCGCA-AUUAAAACUGCGCCAGGCCAACAAUCAUGGCUUUUAGCAGCUGCAAAGUUGCAUUACGCAUACGCAGUGUAUGCCG
......((.(((((((...(((((((.............((((-........))))..((((((.......))))))...)))).)))..))))))).)).((((((.....)))))).. ( -31.80)
>DroSec_CAF1 292468 111 + 1
AUGAAAUAUC---------GCACUGCCUUCCGAAAAUUCUGCAAAUUAAAACUGCGCCAGGCCAACAAUCAUGGCAUUUAGCAGCUGCAGAGUUGCAUUACGCAUACGCAGUGUAUGCCG
..........---------(((((((........(((((((((........((((.....((((.......)))).....)))).)))))))))((.....))....)))))))...... ( -32.30)
>DroSim_CAF1 294505 119 + 1
AUGAAAUAUCGCAGUUAUCGCACUGCCUUCCAAAAAUUCCGCA-AUUAAAACUGCGCCAGGCCAACAAUCAUGGCAUUUAGCAGCUGCAGAGUUGCAUUACGCAUACGCAGUGUAUGCCG
..........(((((......)))))..............(((-(((....((((.....((((.......)))).....))))......)))))).....((((((.....)))))).. ( -30.10)
>DroYak_CAF1 309899 117 + 1
AUGAAAUUUCGCAGUUAUU-CACUGCCUUCAAAAAAUGCCACA-AUUAAAACUACGCCUGGCCAACAAUCAUGGCUUUU-GCACUAACAAAGUUUCAGUACGCAUACGCGGUGUGUGCCG
.((((((((.(((((....-.))))).................-...........((..(((((.......)))))...-)).......))))))))((((((((.....)))))))).. ( -28.00)
>consensus
AUGAAAUAUCGCAGUUAUCGCACUGCCUUCCAAAAAUUCCGCA_AUUAAAACUGCGCCAGGCCAACAAUCAUGGCAUUUAGCAGCUGCAAAGUUGCAUUACGCAUACGCAGUGUAUGCCG
...................(((((((..............(((.........)))((...((((.......)))).....((((((....)))))).....))....)))))))...... (-19.83 = -20.95 +   1.12)

alignment

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secondary structure

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Window 6

Location 18,085,244 – 18,085,364
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.36
Mean single sequence MFE -36.90
Consensus MFE -28.52
Energy contribution -28.28
Covariance contribution -0.25
Combinations/Pair 1.11
Mean z-score -1.98
Structure conservation index 0.77
SVM decision value 0.35
SVM RNA-class probability 0.698655
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085244 120 - 22407834
AAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAGCCAGCUGGGGAAUGGAGCUCGCCUUUCAUAUGGCACUCGGGCUUAAUGGUCACUUCAUAAAUGCAGGCAAUUUGGGAGCU
.....((...((((((((((((((..((((..(((......))).))))..)))).....(((........)))..))))))))))...)).((((.(((((.......))))))))).. ( -34.80)
>DroSec_CAF1 292579 119 - 1
AAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAGCCAGCUGG-GAAUGGAGCUCUCAUUUCAUAUGGCACUCGGGCUUAAUGGUCACUUCAUAAAUGCAUGCAAUUUGGGAGCU
.....((...(((((((((((((((.((((..(((......))).)))-)..(((((......)))))))))))...)))))))))...)).((((.(((((.......))))))))).. ( -31.00)
>DroSim_CAF1 294624 120 - 1
AAAGAGGACUUUAAGCCUGGCCAUAACCCAAACUGAAAAGCCAGCUGGGGAAUGGAGCUUGCAUUUCAUAUGGCACUCGGGCUUAAUGGUCACUUCAUAAAUGCAGGCAAUUUGGGAGCU
......(((((((((((((((((((.((((..(((......))).))))(((((.......)))))..))))))...))))))))).)))).((((.(((((.......))))))))).. ( -36.70)
>DroYak_CAF1 310016 120 - 1
GGAGUGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAGCCAGCUUGGGAAUGGAGCCGCCAUUUUAUAUGGCAGUCGGGCUUAAUGGUCACUUCAUAAAUGCAGGCGAUUUGGACGCU
(((((((...((((((((((((((..(((((.(((......))).))))).))))....(((((.....)))))..))))))))))...))))))).........((((.......)))) ( -45.10)
>consensus
AAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAGCCAGCUGGGGAAUGGAGCUCGCAUUUCAUAUGGCACUCGGGCUUAAUGGUCACUUCAUAAAUGCAGGCAAUUUGGGAGCU
.....((...(((((((((((((((.(((...(((......)))...)))..(((((......)))))))))))...)))))))))...)).((((.(((((.......))))))))).. (-28.52 = -28.28 +  -0.25)

alignment

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secondary structure

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Window 7

Location 18,085,324 – 18,085,444
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -42.17
Consensus MFE -38.21
Energy contribution -39.02
Covariance contribution 0.81
Combinations/Pair 1.02
Mean z-score -2.44
Structure conservation index 0.91
SVM decision value 1.62
SVM RNA-class probability 0.967786
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085324 120 + 22407834
CUUUUCAGUUUGGGUUAUGACCAGGCUUAAAGUUCUCUUUUUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGU
....((((((((((((((..((.((((.((((....))))..))))(((.....)))...))(....)))))))))..((((((((.((((......)))).))))))))...)))))). ( -42.30)
>DroSec_CAF1 292658 120 + 1
CUUUUCAGUUUGGGUUAUGACCAGGCUUAAAGUUCUCUUUUUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAAGAAGAUGGUCCUAGAUGCUGGAGCAUCUUUUGUCGACUGGU
....((((((((((((((..((.((((.((((....))))..))))(((.....)))...))(....)))))))))..((((((((.(((........))).))))))))...)))))). ( -41.60)
>DroSim_CAF1 294704 120 + 1
CUUUUCAGUUUGGGUUAUGGCCAGGCUUAAAGUCCUCUUUUUAGCUGGCAGAAAGCCAUAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGU
....((((((((((((((.(((((.((.((((....))))..))))))).....(((...))).....))))))))..((((((((.((((......)))).))))))))...)))))). ( -44.50)
>DroYak_CAF1 310096 119 + 1
CUUUUCAGUUUGGGUUAUGACCAGGCUUAAAGUUCACUCCUUAGCUGGCAGAAAGCCAGUGGCACAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCU-UUGUCGACUGGU
......(((((((.......)))))))...((((.(((((((.((((((.....))))))(((........)))..)))))(((((.((((......)))).)))))-..)).))))... ( -40.30)
>consensus
CUUUUCAGUUUGGGUUAUGACCAGGCUUAAAGUUCUCUUUUUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGU
....((((((((((((((..((.((((.((((....))))..))))(((.....)))...))(....)))))))))..((((((((.((((......)))).))))))))...)))))). (-38.21 = -39.02 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,085,324 – 18,085,444
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -32.57
Consensus MFE -29.44
Energy contribution -29.38
Covariance contribution -0.06
Combinations/Pair 1.09
Mean z-score -2.16
Structure conservation index 0.90
SVM decision value 1.26
SVM RNA-class probability 0.936960
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085324 120 - 22407834
ACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAAAAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAG
..((((......(((((((....))))))).(((((((((..(((((((........))).(((((.....))))).))))..))))..........))))).........))))..... ( -30.70)
>DroSec_CAF1 292658 120 - 1
ACCAGUCGACAAAAGAUGCUCCAGCAUCUAGGACCAUCUUCUUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAAAAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAG
..((((.......((((((....))))))..((((((((.(((((((((........))))(((((.....)))))...))))))))..........))))).........))))..... ( -32.10)
>DroSim_CAF1 294704 120 - 1
ACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUAUGGCUUUCUGCCAGCUAAAAAGAGGACUUUAAGCCUGGCCAUAACCCAAACUGAAAAG
..(((((((...((((((.(((((....))))).))))))...)))((((..((((......((((.....)))).....))))(((........))))))).........))))..... ( -31.90)
>DroYak_CAF1 310096 119 - 1
ACCAGUCGACAA-AGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUGUGCCACUGGCUUUCUGCCAGCUAAGGAGUGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAG
..((((.....(-((((((....))))))).(((((((((((((.(((((.....).))).(((((.....)))))).)))))).))..........))))).........))))..... ( -35.60)
>consensus
ACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAAAAAGAGAACUUUAAGCCUGGUCAUAACCCAAACUGAAAAG
..((((......((((((.(((((....))))).))))))...(((((.........(((...))).....(((((((..((((....)))).)).))))).....)))))))))..... (-29.44 = -29.38 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,085,364 – 18,085,484
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.67
Mean single sequence MFE -39.40
Consensus MFE -35.67
Energy contribution -36.30
Covariance contribution 0.63
Combinations/Pair 1.06
Mean z-score -2.44
Structure conservation index 0.91
SVM decision value 1.23
SVM RNA-class probability 0.933666
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085364 120 + 22407834
UUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGUCGGGUAAAAACAAUUUGCCCCAGGAUAGAAACGUUAAGCG
(((((((((.....))))(.((((((..((.((((...((((((((.((((......)))).))))))))...((....))))))....))..)))))).)...........)))))... ( -39.80)
>DroSec_CAF1 292698 120 + 1
UUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAAGAAGAUGGUCCUAGAUGCUGGAGCAUCUUUUGUCGACUGGUCGGGUAAAAACAAUUUGCCCCAGGAUAGAAACGUUAAGCG
(((((((((.....))))(.((((((..((.((((...((((((((.(((........))).))))))))...((....))))))....))..)))))).)...........)))))... ( -39.10)
>DroSim_CAF1 294744 120 + 1
UUAGCUGGCAGAAAGCCAUAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGUCGGGUAAAAACAAUUUGCCCCAGGAUAGAAACGUUAAGCG
...((((((.....)))...((((((..((.((((...((((((((.((((......)))).))))))))...((....))))))....))..)))))).................))). ( -39.20)
>DroYak_CAF1 310136 118 + 1
UUAGCUGGCAGAAAGCCAGUGGCACAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCU-UUGUCGACUGGU-GGGUAAAAACAAUUUGCCCCAGGAUAGAAACGUUAAGCG
...((((((.....(((((((((....((....))....(((((((.((((......)))).)))))-))))).))))))-(((((((.....)))))))............))).))). ( -39.50)
>consensus
UUAGCUGGCAGAAAGCCAGAGGCGAAAGGUGGCCCAAAGGAAGAUGGUCCAAGAUGCUGGAGCAUCUUUUGUCGACUGGUCGGGUAAAAACAAUUUGCCCCAGGAUAGAAACGUUAAGCG
...((((((.....)))...((((((..((.((((...((((((((.((((......)))).))))))))...((....))))))....))..)))))).................))). (-35.67 = -36.30 +   0.63)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,085,364 – 18,085,484
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -30.88
Consensus MFE -26.95
Energy contribution -27.70
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.87
SVM decision value -0.00
SVM RNA-class probability 0.532852
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18085364 120 - 22407834
CGCUUAACGUUUCUAUCCUGGGGCAAAUUGUUUUUACCCGACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAA
.((................(((((..............(((....)))....(((((((....)))))))((.(((........))).)).......)))))((((.....))))))... ( -32.00)
>DroSec_CAF1 292698 120 - 1
CGCUUAACGUUUCUAUCCUGGGGCAAAUUGUUUUUACCCGACCAGUCGACAAAAGAUGCUCCAGCAUCUAGGACCAUCUUCUUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAA
.((................(((((..............(((....))).....((((((....)))))).((.(((........))).)).......)))))((((.....))))))... ( -31.30)
>DroSim_CAF1 294744 120 - 1
CGCUUAACGUUUCUAUCCUGGGGCAAAUUGUUUUUACCCGACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUAUGGCUUUCUGCCAGCUAA
.((.................((((..............(((....)))....(((((((....)))))))((.(((........))).)).......)))).((((.....))))))... ( -30.10)
>DroYak_CAF1 310136 118 - 1
CGCUUAACGUUUCUAUCCUGGGGCAAAUUGUUUUUACCC-ACCAGUCGACAA-AGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUGUGCCACUGGCUUUCUGCCAGCUAA
..................(((.((((.............-...........(-((((((....)))))))((.(((........))).))...)))).)))(((((.....))))).... ( -30.10)
>consensus
CGCUUAACGUUUCUAUCCUGGGGCAAAUUGUUUUUACCCGACCAGUCGACAAAAGAUGCUCCAGCAUCUUGGACCAUCUUCCUUUGGGCCACCUUUCGCCUCUGGCUUUCUGCCAGCUAA
.((................(((((..............(((....))).....((((((....)))))).((.(((........))).)).......)))))((((.....))))))... (-26.95 = -27.70 +   0.75)

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 12:11:10 2006