Locus 1090

Sequence ID 2L_DroMel_CAF1
Location 3,000,157 – 3,000,356
Length 199
Max. P 0.998578
window1769 window1770 window1771 window1772

overview

Window 9

Location 3,000,157 – 3,000,277
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.66
Mean single sequence MFE -26.70
Consensus MFE -21.38
Energy contribution -22.58
Covariance contribution 1.20
Combinations/Pair 1.13
Mean z-score -1.64
Structure conservation index 0.80
SVM decision value 0.44
SVM RNA-class probability 0.739097
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3000157 120 + 22407834
AGGCUCUUCAGCUAUUGAAAAAACAUUGAAUCAAUACUUUUUUACGUGUACCAAGCCCACGUCAGUCGACUAAAAAUCCAUGGGCCUCGGCCCACGGAAAAUUAACUCAUUGCCCCCUCU
.(((...((.(((...((((((..((((...))))..))))))(((((.........))))).))).)).......(((.(((((....))))).))).............)))...... ( -25.30)
>DroSec_CAF1 7686 120 + 1
AGGCUCCUCAACUAUUGAAAAAACAUUGAAUCAAUACUUUUCUACGUGUACCAAGCCCACGUCAGUCGGCUGAAAAUCCAUGGGCCUCGGCCCACGGAAAAUUAACUCAUUGCCCCCACU
.(((........((((((............)))))).........(.((....((((.((....)).)))).....(((.(((((....))))).)))......)).)...)))...... ( -27.80)
>DroSim_CAF1 7053 120 + 1
AGGCUCUUCAACUAUUGAAAAAACAUUGAAUCAAUACUUUUCUACGUGUACCAAGCCCACGUCAGUCGGCUGAAAAUCCAUGGGCCUCGGCCCACGGAAAAUUAACUCAUUGCCCCCACU
.(((..(((...((((((............)))))).................((((.((....)).)))))))..(((.(((((....))))).))).............)))...... ( -28.20)
>DroEre_CAF1 7652 119 + 1
AGACUCUUUGGCUAUUGAA-AAACAUUGAAUCAAUACUUCUCUAUGUGUACCAAGCCCACGUCAGUCGGCUGAAAAUCCAUGGUCCUCGGCCCACGGGAAAUUAACUCAUUGCCCCCACU
.(((.....((((..((..-..((((.(((.......)))...))))....))))))...))).((.((((((..((.....))..)))))).))(((.(((......))).)))..... ( -23.70)
>DroYak_CAF1 7159 119 + 1
CGACUCUUCAGCGAUUGAA-AAACAUUGAAUCAAUACUUCUCUACGUGUACCAAGCCCACGUCAGUCGGCUGAAAAUCCAUGGGUCUCGGCCCACGGAAAAUUAACUCAUUGCCCCCACU
......((((((((((((.-....((((...)))).........((((.........)))))))))).))))))..(((.(((((....))))).)))...................... ( -28.50)
>consensus
AGGCUCUUCAGCUAUUGAAAAAACAUUGAAUCAAUACUUUUCUACGUGUACCAAGCCCACGUCAGUCGGCUGAAAAUCCAUGGGCCUCGGCCCACGGAAAAUUAACUCAUUGCCCCCACU
.(((..((((((((((((.......(((.....((((........))))..))).......))))).)))))))..(((.(((((....))))).))).............)))...... (-21.38 = -22.58 +   1.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,000,157 – 3,000,277
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.66
Mean single sequence MFE -40.46
Consensus MFE -34.86
Energy contribution -35.66
Covariance contribution 0.80
Combinations/Pair 1.10
Mean z-score -2.50
Structure conservation index 0.86
SVM decision value 3.15
SVM RNA-class probability 0.998578
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3000157 120 - 22407834
AGAGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUUAGUCGACUGACGUGGGCUUGGUACACGUAAAAAAGUAUUGAUUCAAUGUUUUUUCAAUAGCUGAAGAGCCU
.(((((((((.(((((((((..(((((((((....)))))))))..........(((.(((((..(...)..))))).....)))))))))))).)))))))))....(((....))).. ( -42.40)
>DroSec_CAF1 7686 120 - 1
AGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGAAAAGUAUUGAUUCAAUGUUUUUUCAAUAGUUGAGGAGCCU
.....((((..(((((((((((((((((..(((((.((((((.....((((....)))))))))))))))..))))..))))...))))))))).....((((((.....)))))))))) ( -42.10)
>DroSim_CAF1 7053 120 - 1
AGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGAAAAGUAUUGAUUCAAUGUUUUUUCAAUAGUUGAAGAGCCU
.....((((..(((((((((((((((((..(((((.((((((.....((((....)))))))))))))))..))))..))))...))))))))).....((((((.....)))))))))) ( -42.50)
>DroEre_CAF1 7652 119 - 1
AGUGGGGGCAAUGAGUUAAUUUCCCGUGGGCCGAGGACCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACAUAGAGAAGUAUUGAUUCAAUGUUU-UUCAAUAGCCAAAGAGUCU
..((((((.(((......))).)))(((..(((((..(((((.....((((....))))))))).)))))..)))...(((((((((((...))))))))-))).....)))........ ( -34.70)
>DroYak_CAF1 7159 119 - 1
AGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGACCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGAGAAGUAUUGAUUCAAUGUUU-UUCAAUCGCUGAAGAGUCG
((((((((((.(((((((((((((((((..(((((.((((((.....((((....)))))))))))))))..))))....)))).))))))))).)))))-.....)))))......... ( -40.60)
>consensus
AGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGAAAAGUAUUGAUUCAAUGUUUUUUCAAUAGCUGAAGAGCCU
......(((..(((((((((((((((((..(((((.((((((.....((((....)))))))))))))))..))))..))))...))))))))).....((((((.....))))))))). (-34.86 = -35.66 +   0.80)

alignment

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secondary structure

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Window 1

Location 3,000,197 – 3,000,316
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.98
Mean single sequence MFE -38.72
Consensus MFE -35.72
Energy contribution -36.20
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.92
SVM decision value 1.26
SVM RNA-class probability 0.936882
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3000197 119 - 22407834
CCCGAGGAGAAUAGAGCAAUUUUCUGGAUCGA-AGGGAAAAGAGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUUAGUCGACUGACGUGGGCUUGGUACACGUAAA
(((..(((((((......)))))))...((..-..))......))).......(((..(((.(((((((((....))))))))).....)))..))).(((((..(...)..)))))... ( -36.80)
>DroSec_CAF1 7726 120 - 1
CCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGAAAGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGA
((((((((...........)))))))).((....)).....(((...((.............(((((((((....))))))))).....((((.((....)).))))..)).)))..... ( -41.60)
>DroSim_CAF1 7093 119 - 1
CCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGA
((((((((...........)))))))).....-..((((((.....(((.....)))..))))))(((..(((((.((((((.....((((....)))))))))))))))..)))..... ( -40.50)
>DroEre_CAF1 7691 119 - 1
CCCUAAGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUCCCGUGGGCCGAGGACCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACAUAGA
(((...((((((......))))))))).....-.((((((......(((.....)))..))))))(((..(((((..(((((.....((((....))))))))).)))))..)))..... ( -34.20)
>DroYak_CAF1 7198 119 - 1
CCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGACCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGA
((((((((...........)))))))).....-..((((((.....(((.....)))..))))))(((..(((((.((((((.....((((....)))))))))))))))..)))..... ( -40.50)
>consensus
CCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA_AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCAUGGAUUUUCAGCCGACUGACGUGGGCUUGGUACACGUAGA
((((((((...........))))))))........((((((.....(((.....)))..))))))(((..(((((.((((((.....((((....)))))))))))))))..)))..... (-35.72 = -36.20 +   0.48)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,000,237 – 3,000,356
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.82
Mean single sequence MFE -36.64
Consensus MFE -31.40
Energy contribution -32.64
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.62
Structure conservation index 0.86
SVM decision value 0.72
SVM RNA-class probability 0.833043
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3000237 119 - 22407834
AAAUGGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCGAGGAGAAUAGAGCAAUUUUCUGGAUCGA-AGGGAAAAGAGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCA
...(((((..(((((((((..((((.....)))).))))))(((.(((((((((..((.((((((...((..-..))...)))))).....))..)).))))))).))))))...))))) ( -39.00)
>DroSec_CAF1 7766 120 - 1
AAAUGGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGAAAGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCA
...(((((..(((..((...(((((.((...)).)))))(((((((((...........))))))))).(....)((((((.....(((.....)))..))))))))..)))...))))) ( -40.50)
>DroSim_CAF1 7133 119 - 1
AAAUGGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCA
...(((((..(((..((...(((((.((...)).)))))(((((((((...........)))))))))....-..((((((.....(((.....)))..))))))))..)))...))))) ( -39.90)
>DroEre_CAF1 7731 119 - 1
AAAUAGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCUAAGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUCCCGUGGGCCGAGGACCA
.....(((....((((..(((((((.((...)).)))((((((...((((((......))))))....((..-..))......)))))).....))))....))))...)))........ ( -31.40)
>DroYak_CAF1 7238 119 - 1
AAAUAGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA-AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGACCCA
............(((((...(.(((.((........((.(((((((((...........))))))))).)).-..((((((.....(((.....)))..)))))))).))))..).)))) ( -32.40)
>consensus
AAAUGGGCAAGGUGGGCGUAGCGCUGACAAAGUGGGCGUUCCCGAGGAGAAUAGAGCAAUUUUCGGGAUCGA_AGGGAAAAGUGGGGGCAAUGAGUUAAUUUUCCGUGGGCCGAGGCCCA
...(((((..(((..((...(((((.((...)).)))))(((((((((...........))))))))).......((((((.....(((.....)))..))))))))..)))...))))) (-31.40 = -32.64 +   1.24)

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 09:53:22 2006