Locus 6108

Sequence ID 2L_DroMel_CAF1
Location 17,107,540 – 17,107,694
Length 154
Max. P 0.991278
window9724 window9725 window9726 window9727

overview

Window 4

Location 17,107,540 – 17,107,654
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.05
Mean single sequence MFE -33.79
Consensus MFE -30.46
Energy contribution -30.90
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.26
Structure conservation index 0.90
SVM decision value 0.44
SVM RNA-class probability 0.736503
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107540 114 + 22407834
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCAAAGCGAAGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGGACUCACAUACGGCCACUGAGGGAGGGCCAUAC------U
.....((....(((((....((((.((.........((....)).........((((((((((((........)))))))......))))).))))))..))))).)).....------. ( -34.20)
>DroSec_CAF1 71358 114 + 1
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCAAAGCGAAGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGAACUCACAUACGGCCACUGAGGGAGGGUCAUAC------U
.((.(((....(((((....((((.((.........((....)).........((((((((((((........)))))))......))))).))))))..))))).).)).))------. ( -33.70)
>DroSim_CAF1 84937 114 + 1
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCAAAGCGAAGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGAACUCACAUACGGCCACUGAGGGAGGGUCAUAC------U
.((.(((....(((((....((((.((.........((....)).........((((((((((((........)))))))......))))).))))))..))))).).)).))------. ( -33.70)
>DroEre_CAF1 72761 119 + 1
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCAAAGCGAAGGCCAUCACAAAGUAUGCGCUUGGAGAGCCAGCCAAGCGGACUCACAUGCGGCCACU-AUGGAGGGUCAUACUCGCACU
.(((.....))).........(((((...((((........((((.......(((...(((((((........))))))).))).......)))).(.-...).))))....)))))... ( -33.24)
>DroYak_CAF1 72975 118 + 1
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCACAGCGAAGGCCAUCACAAAGUAUGCGCUUGGA--UUCAGCCAAGCGGACUCACAUACGGCAACUGAUGGAGGGUCAUACUCGAACU
.(((.....)))..........((((...((((...((....))(((((....((((((((((((.--.....)))))))......)))))(....))))))..))))....)))).... ( -34.10)
>consensus
CGUCUGCAAGACUCCUGAUAAGUGAGCAAACCCAAAGCGAAGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGGACUCACAUACGGCCACUGAGGGAGGGUCAUAC______U
.((.(((....(((((....((((.((.........((....)).........((((((((((((........)))))))......))))).))))))..))))).).)).))....... (-30.46 = -30.90 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,107,540 – 17,107,654
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -37.95
Consensus MFE -33.28
Energy contribution -33.52
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.19
Structure conservation index 0.88
SVM decision value 0.03
SVM RNA-class probability 0.547365
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107540 114 - 22407834
A------GUAUGGCCCUCCCUCAGUGGCCGUAUGUGAGUCCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCUUCGCUUUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
.------...........((..(((((((((....((((.(((((((........)))))))...))))....))))))...)))..))((((((..((((.....))))...)))))). ( -36.40)
>DroSec_CAF1 71358 114 - 1
A------GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUUCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCUUCGCUUUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
.------(((.(((((((((..(((((((((....((((.(((((((........)))))))...))))....))))))...)))..)))..............))).))).)))..... ( -37.23)
>DroSim_CAF1 84937 114 - 1
A------GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUUCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCUUCGCUUUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
.------(((.(((((((((..(((((((((....((((.(((((((........)))))))...))))....))))))...)))..)))..............))).))).)))..... ( -37.23)
>DroEre_CAF1 72761 119 - 1
AGUGCGAGUAUGACCCUCCAU-AGUGGCCGCAUGUGAGUCCGCUUGGCUGGCUCUCCAAGCGCAUACUUUGUGAUGGCCUUCGCUUUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
..((((((((.(((((.....-...(((((((((.((((.(((((((........)))))))...)))))))).)))))........))))))))))((((.....))))...))).... ( -40.19)
>DroYak_CAF1 72975 118 - 1
AGUUCGAGUAUGACCCUCCAUCAGUUGCCGUAUGUGAGUCCGCUUGGCUGAA--UCCAAGCGCAUACUUUGUGAUGGCCUUCGCUGUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
.....(((((.(((((.....((((.(((((....((((.(((((((.....--.)))))))...))))....)))))....)))).))))))))))...........(((.....))). ( -38.70)
>consensus
A______GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUCCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCUUCGCUUUGGGUUUGCUCACUUAUCAGGAGUCUUGCAGACG
.......(((.((((((.....(((((((((....((((.(((((((........)))))))...))))....))))))........(((....))))))....))).))).)))..... (-33.28 = -33.52 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,107,580 – 17,107,694
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.71
Mean single sequence MFE -33.88
Consensus MFE -29.78
Energy contribution -29.66
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -1.95
Structure conservation index 0.88
SVM decision value 2.26
SVM RNA-class probability 0.991278
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107580 114 + 22407834
AGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGGACUCACAUACGGCCACUGAGGGAGGGCCAUAC------UCGUGAAAGCCAAGCCAAGACCGUAAUGCAUAAAUUAUGAC
.(((..(((...(((((.(((((((........)))))))...........((((.((.....))))))))))------)..)))..)))..........((((((......)))))).. ( -34.80)
>DroSec_CAF1 71398 114 + 1
AGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGAACUCACAUACGGCCACUGAGGGAGGGUCAUAC------UCGUGAAAGCCAAGCCAAGACCGUAAUGCAUAAAUUAUGAC
.(((..(((...(((((.(((((((........)))))))...........((((.((.....))))))))))------)..)))..)))..........((((((......)))))).. ( -31.90)
>DroSim_CAF1 84977 114 + 1
AGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGAACUCACAUACGGCCACUGAGGGAGGGUCAUAC------UCGUGAAAGCCAAGCCAAGACCGUAAUGCAUAAAUUAUGAC
.(((..(((...(((((.(((((((........)))))))...........((((.((.....))))))))))------)..)))..)))..........((((((......)))))).. ( -31.90)
>DroEre_CAF1 72801 119 + 1
AGGCCAUCACAAAGUAUGCGCUUGGAGAGCCAGCCAAGCGGACUCACAUGCGGCCACU-AUGGAGGGUCAUACUCGCACUCGUGAAAGCCAAGUUAAGACCGUAAUGCAUAAAUUAUGAC
.(((..((((...((((((((((((........)))))))......)))))((((.((-....))))))............))))..)))..........((((((......)))))).. ( -34.30)
>DroYak_CAF1 73015 118 + 1
AGGCCAUCACAAAGUAUGCGCUUGGA--UUCAGCCAAGCGGACUCACAUACGGCAACUGAUGGAGGGUCAUACUCGAACUCGUGAAAGCCAAGCCAAGACCGUAAUGCAUAAAUUAUGAC
.(((..((((..(((((.(((((((.--.....)))))))(((((.(((..(....)..)))..)))))))))).(....)))))..)))..........((((((......)))))).. ( -36.50)
>consensus
AGGCCAUCAAAAAGUAUGCGCUUGGAGAAUCAGCCAAGCGGACUCACAUACGGCCACUGAGGGAGGGUCAUAC______UCGUGAAAGCCAAGCCAAGACCGUAAUGCAUAAAUUAUGAC
.(((..(((....((((((((((((........)))))))......)))))((((.((.....)))))).............)))..)))..........((((((......)))))).. (-29.78 = -29.66 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,107,580 – 17,107,694
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.71
Mean single sequence MFE -37.02
Consensus MFE -29.51
Energy contribution -29.75
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.92
Structure conservation index 0.80
SVM decision value 1.06
SVM RNA-class probability 0.907886
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17107580 114 - 22407834
GUCAUAAUUUAUGCAUUACGGUCUUGGCUUGGCUUUCACGA------GUAUGGCCCUCCCUCAGUGGCCGUAUGUGAGUCCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCU
((((.((..(((((.....((.(((.(((((.......)))------))((((((((.....)).))))))....))).))((((((........)))))))))))..)).))))..... ( -37.00)
>DroSec_CAF1 71398 114 - 1
GUCAUAAUUUAUGCAUUACGGUCUUGGCUUGGCUUUCACGA------GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUUCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCU
...................((((...(((((.......)))------))..))))..........((((((....((((.(((((((........)))))))...))))....)))))). ( -35.70)
>DroSim_CAF1 84977 114 - 1
GUCAUAAUUUAUGCAUUACGGUCUUGGCUUGGCUUUCACGA------GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUUCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCU
...................((((...(((((.......)))------))..))))..........((((((....((((.(((((((........)))))))...))))....)))))). ( -35.70)
>DroEre_CAF1 72801 119 - 1
GUCAUAAUUUAUGCAUUACGGUCUUAACUUGGCUUUCACGAGUGCGAGUAUGACCCUCCAU-AGUGGCCGCAUGUGAGUCCGCUUGGCUGGCUCUCCAAGCGCAUACUUUGUGAUGGCCU
(((((((..(((((.....((.((((...((((...(((..(((.(((.......))))))-.)))))))....)))).))((((((........)))))))))))..)))))))..... ( -39.40)
>DroYak_CAF1 73015 118 - 1
GUCAUAAUUUAUGCAUUACGGUCUUGGCUUGGCUUUCACGAGUUCGAGUAUGACCCUCCAUCAGUUGCCGUAUGUGAGUCCGCUUGGCUGAA--UCCAAGCGCAUACUUUGUGAUGGCCU
(((((((..(((((.....((((...(((((((((....))).))))))..))))(((((((.......).))).)))...((((((.....--.)))))))))))..)))))))..... ( -37.30)
>consensus
GUCAUAAUUUAUGCAUUACGGUCUUGGCUUGGCUUUCACGA______GUAUGACCCUCCCUCAGUGGCCGUAUGUGAGUCCGCUUGGCUGAUUCUCCAAGCGCAUACUUUUUGAUGGCCU
((((((.............((((.......))))..............))))))...........((((((....((((.(((((((........)))))))...))))....)))))). (-29.51 = -29.75 +   0.24)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:03 2006