Locus 5841

Sequence ID 3L_DroMel_CAF1
Location 15,763,525 – 15,763,714
Length 189
Max. P 0.986262
window9308 window9309 window9310 window9311 window9312

overview

Window 8

Location 15,763,525 – 15,763,634
Length 109
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.33
Mean single sequence MFE -16.50
Consensus MFE -11.72
Energy contribution -12.24
Covariance contribution 0.52
Combinations/Pair 1.19
Mean z-score -1.86
Structure conservation index 0.71
SVM decision value 0.86
SVM RNA-class probability 0.869650
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763525 109 - 23771897
AUUUGAUUUUCCCUCAGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUAGAGAAAAUUGAAAUUUUAUGCAUUUCCCGCAUUUACCACCAAAA-----------ACCAAACCCCAAUUUCA
.((..((((((.((.(((.....(((((.....)))))......))))).))))))..)).....((((.......))))............-----------................. ( -21.50)
>DroSec_CAF1 15100 105 - 1
AUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUACAGAAAAUUGAAAUUUUAUGCAUUUCCCC---------CCAAAAACCAA------ACCAAACCCCAAUUUCA
.((..((((((....(((.....(((((.....)))))......)))...))))))..)).................---------...........------................. ( -16.80)
>DroSim_CAF1 16095 105 - 1
AUUUCAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUACAGAAAAUUGAAAUUUUAUGCAUUUCCCC---------CCAAAAACCAA------ACCAAACCCCAAUUUCA
(((((((((((....(((.....(((((.....)))))......)))...))))).))))))...............---------...........------................. ( -15.60)
>DroEre_CAF1 15245 97 - 1
AUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUGGAGAAAAUUGAAAUUUUAUGCACAUCCCC-----------------CAA------ACCAAACCCCAAUUUCA
.((..((((((.(.((((.....(((((.....)))))......))))).))))))..)).................-----------------...------................. ( -20.80)
>DroAna_CAF1 10348 111 - 1
AUUUGAUUUUCCCUCGUCUGCCUAGAUCCCCAUACCUUGUUUAUCCUUGAGAAAAUUGAGAUUUUAUGCAUUUCCCU---------CCUCUACUCAAUCAUUUCCCAAAAACUAAGUUCA
....(((((...(......)...))))).......(((((((....(((.((((((((((.................---------......))))))..)))).))))))).))).... (  -7.80)
>consensus
AUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUAGAGAAAAUUGAAAUUUUAUGCAUUUCCCC_________CCAAAA__CAA______ACCAAACCCCAAUUUCA
.((..((((((....(((.....(((((.....)))))......)))...))))))..))............................................................ (-11.72 = -12.24 +   0.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,763,554 – 15,763,674
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.52
Mean single sequence MFE -27.49
Consensus MFE -20.76
Energy contribution -21.56
Covariance contribution 0.80
Combinations/Pair 1.15
Mean z-score -2.25
Structure conservation index 0.76
SVM decision value 1.02
SVM RNA-class probability 0.902478
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763554 120 + 23771897
AUGCGGGAAAUGCAUAAAAUUUCAAUUUUCUCUAGCAUAAACAAGCCAAAAAGGCUUUGGCAGCUGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
...(((((((((((..((((((..((((((((((((......(((((.....))))).....))).)))))))))........(((....))).))))))...)))))))..)))).... ( -32.50)
>DroSec_CAF1 15128 117 + 1
---GGGGAAAUGCAUAAAAUUUCAAUUUUCUGUAGCAUAAACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
---((..(((((((..((((((......................((((((.....)))))).(((..(((..............)))...))).))))))...)))))))..))...... ( -28.34)
>DroSim_CAF1 16123 117 + 1
---GGGGAAAUGCAUAAAAUUUCAAUUUUCUGUAGCAUAAACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUGAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
---((..(((((((....((((((.((((((...((......(((((.....))))).....))...)))))).))))))...(((....)))..........)))))))..))...... ( -31.10)
>DroEre_CAF1 15265 117 + 1
---GGGGAUGUGCAUAAAAUUUCAAUUUUCUCCAGCAUAAACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
---((..(..((((..((((((..(((((((((.((......(((((.....))))).....)).).))))))))........(((....))).))))))...))))..)..))...... ( -26.20)
>DroAna_CAF1 10382 117 + 1
---AGGGAAAUGCAUAAAAUCUCAAUUUUCUCAAGGAUAAACAAGGUAUGGGGAUCUAGGCAGACGAGGGAAAAUCAAAUCAAACCCGAAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
---.((((((................)))))).(((.(((((..(((.(((.(((((.(.....)...)))...))...))).))).....((((.......))))))))).)))..... ( -19.29)
>consensus
___GGGGAAAUGCAUAAAAUUUCAAUUUUCUCUAGCAUAAACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAU
...((..(((((((..((((((......................((((((.....)))))).(((..(((..............)))...))).))))))...)))))))..))...... (-20.76 = -21.56 +   0.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,763,554 – 15,763,674
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.52
Mean single sequence MFE -27.44
Consensus MFE -21.46
Energy contribution -22.42
Covariance contribution 0.96
Combinations/Pair 1.13
Mean z-score -2.23
Structure conservation index 0.78
SVM decision value 1.39
SVM RNA-class probability 0.949107
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763554 120 - 23771897
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCAGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUAGAGAAAAUUGAAAUUUUAUGCAUUUCCCGCAU
...(((((((....((((.......)))).....)))))))((..((((((.((.(((.....(((((.....)))))......))))).))))))..)).....((((.......)))) ( -31.00)
>DroSec_CAF1 15128 117 - 1
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUACAGAAAAUUGAAAUUUUAUGCAUUUCCCC---
...(((((((....((((.......)))).....)))))))((..((((((....(((.....(((((.....)))))......)))...))))))..)).................--- ( -26.40)
>DroSim_CAF1 16123 117 - 1
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUCAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUACAGAAAAUUGAAAUUUUAUGCAUUUCCCC---
......((..(((.(((..........(((....)))..((((((((((((....(((.....(((((.....)))))......)))...))))).)))))))...))).)))..))--- ( -26.30)
>DroEre_CAF1 15265 117 - 1
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUGGAGAAAAUUGAAAUUUUAUGCACAUCCCC---
...(((((((....((((.......)))).....)))))))((..((((((.(.((((.....(((((.....)))))......))))).))))))..)).................--- ( -30.40)
>DroAna_CAF1 10382 117 - 1
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUUCGGGUUUGAUUUGAUUUUCCCUCGUCUGCCUAGAUCCCCAUACCUUGUUUAUCCUUGAGAAAAUUGAGAUUUUAUGCAUUUCCCU---
.(((((((.(((((..(((((((((..(((....)))..))))))))).......((((....))))...........))))).)).))))).....(((((.......)))))...--- ( -23.10)
>consensus
AUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGUUUAUGCUAGAGAAAAUUGAAAUUUUAUGCAUUUCCCC___
(((((((.........(((((((((..(((....)))..)))))))))....((((((.....(((((.....)))))......))).)))....))))))).................. (-21.46 = -22.42 +   0.96)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,763,594 – 15,763,714
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -27.54
Consensus MFE -23.90
Energy contribution -23.54
Covariance contribution -0.36
Combinations/Pair 1.20
Mean z-score -1.49
Structure conservation index 0.87
SVM decision value 0.89
SVM RNA-class probability 0.875106
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763594 120 + 23771897
ACAAGCCAAAAAGGCUUUGGCAGCUGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUCAAGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((.(((((((((..(.....)...))).(((....)))............(((((....(((((......))))))))))..)))).)))))))).......... ( -26.80)
>DroSec_CAF1 15165 120 + 1
ACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUCAAGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((.((((((((.(((..............)))(((.((((.......)))).)))..(.(((((......))))).).))..)))).)))))))).......... ( -26.64)
>DroSim_CAF1 16160 120 + 1
ACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUGAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUCAAGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((.((((((((.(((....((....))..)))(((.((((.......)))).)))..(.(((((......))))).).))..)))).)))))))).......... ( -28.20)
>DroEre_CAF1 15302 120 + 1
ACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUCAAGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((.((((((((.(((..............)))(((.((((.......)))).)))..(.(((((......))))).).))..)))).)))))))).......... ( -26.64)
>DroAna_CAF1 10419 120 + 1
ACAAGGUAUGGGGAUCUAGGCAGACGAGGGAAAAUCAAAUCAAACCCGAAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUGAGGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((((((((((..(((..............)))....((((.......))))))))..(((.(((......))).)))..............)))))))))).... ( -29.44)
>consensus
ACAAGCCAAAAAGGCUUUGGCAGCCGAGGGAAAAUCAAAUCAAGCCCAGAGGCAAAAUUUAAUUGCGUUUAACCUGAAAUCAAAUUUUCAAGACGAUGCUGACCAGGCCUAGAUUCAAUC
...........((((((.((((((((.(((..............)))(((.((((.......)))).)))..(.(((((......))))).).))..)))).)))))))).......... (-23.90 = -23.54 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,763,594 – 15,763,714
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.00
Mean single sequence MFE -31.84
Consensus MFE -27.78
Energy contribution -28.70
Covariance contribution 0.92
Combinations/Pair 1.09
Mean z-score -1.89
Structure conservation index 0.87
SVM decision value 2.04
SVM RNA-class probability 0.986262
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15763594 120 - 23771897
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCUUGAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCAGCUGCCAAAGCCUUUUUGGCUUGU
..(..((...((((.(((.((((..((((((((((......)))))))....))).(((((((((..(((....)))..)))))))))........)))))))..)))).))..)..... ( -32.90)
>DroSec_CAF1 15165 120 - 1
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCUUGAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGU
...........(((..((((.((.....(((((((......)))))))......))(((((((((..(((....)))..))))))))).......))))))).(((((.....))))).. ( -33.20)
>DroSim_CAF1 16160 120 - 1
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCUUGAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUCAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGU
..(..((...((((.(((.((((..((....(((((..(((..(((((((....((((.......)))).....)))))))..))))))))...)))))))))..)))).))..)..... ( -31.80)
>DroEre_CAF1 15302 120 - 1
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCUUGAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGU
...........(((..((((.((.....(((((((......)))))))......))(((((((((..(((....)))..))))))))).......))))))).(((((.....))))).. ( -33.20)
>DroAna_CAF1 10419 120 - 1
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCCUCAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUUCGGGUUUGAUUUGAUUUUCCCUCGUCUGCCUAGAUCCCCAUACCUUGU
......((((((((..((.(.((.....(((.(((......))).)))......))(((((((((..(((....)))..))))))))).......).))))))))))............. ( -28.10)
>consensus
GAUUGAAUCUAGGCCUGGUCAGCAUCGUCUUGAAAAUUUGAUUUCAGGUUAAACGCAAUUAAAUUUUGCCUCUGGGCUUGAUUUGAUUUUCCCUCGGCUGCCAAAGCCUUUUUGGCUUGU
...........(((..((((.((.....(((((((......)))))))......))(((((((((..(((....)))..))))))))).......))))))).(((((.....))))).. (-27.78 = -28.70 +   0.92)

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 12:01:46 2006