Locus 1214

Sequence ID 2L_DroMel_CAF1
Location 3,247,767 – 3,247,925
Length 158
Max. P 0.994454
window1986 window1987 window1988 window1989

overview

Window 6

Location 3,247,767 – 3,247,887
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.33
Mean single sequence MFE -29.50
Consensus MFE -25.80
Energy contribution -26.44
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.87
SVM decision value 2.48
SVM RNA-class probability 0.994454
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3247767 120 + 22407834
CUAGCACUGACAGUUACAAUUGCUGGUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAG
...(((.(((((((.......))).))))...(((((((......((((((((((..(((.(((....))).))).)))))))))).........))))))).))).............. ( -30.26)
>DroSec_CAF1 81815 120 + 1
CUAGCAUGGACAGAUACAAUUGCUGGUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGAAGAAUCAAAAG
((((((((........))..)))))).....((((.(((((((..((((((((((..(((.(((....))).))).))))))))))...........)))))))...))))......... ( -31.82)
>DroSim_CAF1 84947 120 + 1
CUAGCAUGGACAGAUACAAUUGCUGGUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAG
............(((....((((((..(((..(((((((......((((((((((..(((.(((....))).))).)))))))))).........)))))))))))))))).)))..... ( -29.66)
>DroEre_CAF1 78584 120 + 1
CUAGCACUGACAGAUACAAUUGCUGCUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCGAAAUGGGCAGCCAGAAACCGCAACAAAGUUCUAUGGAAAUGCAGCAGAAUCAAAAG
............(((....((((((((((((....(((((.....((((((((((..(((.((......)).))).))))))))))...))))).)))))....))))))).)))..... ( -27.10)
>DroYak_CAF1 77841 120 + 1
CUAGCACUGACAGAUACAAUUGCUGGUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCCCAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAG
............(((....((((((..(((..(((((((......((((((((((..(((.(((....))).))).)))))))))).........)))))))))))))))).)))..... ( -28.66)
>consensus
CUAGCACUGACAGAUACAAUUGCUGGUCAUACUUCAAUUUCAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAG
...................((((((..(((..(((((((......((((((((((..(((.(((....))).))).)))))))))).........))))))))))))))))......... (-25.80 = -26.44 +   0.64)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,247,767 – 3,247,887
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -29.76
Consensus MFE -25.70
Energy contribution -26.74
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.28
Structure conservation index 0.86
SVM decision value -0.03
SVM RNA-class probability 0.516714
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3247767 120 - 22407834
CUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGACCAGCAAUUGUAACUGUCAGUGCUAG
...........((((((.((((((((.........(((((((((((...(((....)))...)).)))))))))(((((......)))))........)))))).)).)).))))..... ( -30.50)
>DroSec_CAF1 81815 120 - 1
CUUUUGAUUCUUCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGACCAGCAAUUGUAUCUGUCCAUGCUAG
...................((((((.......((.(((((((((((...(((....)))...)).))))))))))).....))))))((((((..(((.........)))..)))))).. ( -29.50)
>DroSim_CAF1 84947 120 - 1
CUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGACCAGCAAUUGUAUCUGUCCAUGCUAG
..........(((((.(((((((((.......((.(((((((((((...(((....)))...)).))))))))))).....))))))))).....)))))...((((......))))... ( -30.20)
>DroEre_CAF1 78584 120 - 1
CUUUUGAUUCUGCUGCAUUUCCAUAGAACUUUGUUGCGGUUUCUGGCUGCCCAUUUCGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGAGCAGCAAUUGUAUCUGUCAGUGCUAG
..............(((((...(((((((.((((((((((((((((.........))))))))).......((.(((((......))))).)).)))))))..)).))))).)))))... ( -28.40)
>DroYak_CAF1 77841 120 - 1
CUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUGGGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGACCAGCAAUUGUAUCUGUCAGUGCUAG
..........(((((.(((((((((.......((.(((((((((((...(((....)))...)).))))))))))).....))))))))).....)))))...((((......))))... ( -30.20)
>consensus
CUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUGAAAUUGAAGUAUGACCAGCAAUUGUAUCUGUCAGUGCUAG
..........(((((.(((((((((.......((.(((((((((((...(((....)))...)).))))))))))).....))))))))).....)))))...((((......))))... (-25.70 = -26.74 +   1.04)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,247,807 – 3,247,925
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.27
Mean single sequence MFE -22.02
Consensus MFE -19.64
Energy contribution -19.88
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.40
Structure conservation index 0.89
SVM decision value 0.85
SVM RNA-class probability 0.867445
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3247807 118 + 22407834
CAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAGAAAAAUCACCCAAAUACC--AGUGGCAUAGAGAAAAAUGC
.....((((((((((..(((.(((....))).))).))))))))))................((((.......((....)).....(((.........--.)))))))............ ( -22.30)
>DroSec_CAF1 81855 118 + 1
CAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGAAGAAUCAAAAGAAAAAUCACCCAAAUACC--AGUGGCAUAGAGAAAAAUGC
.....((((((((((..(((.(((....))).))).))))))))))................((((.((....))...........(((.........--.)))))))............ ( -22.40)
>DroSim_CAF1 84987 117 + 1
CAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAGAAAAAUCACCCAAAUAAC--AGUGGCAUAGAGAA-AAUGC
.....((((((((((..(((.(((....))).))).))))))))))................((((.......((....)).....(((.........--.)))))))......-..... ( -22.30)
>DroEre_CAF1 78624 117 + 1
CAAAGUGCGGUUUUUUAGUUUCCGAAAUGGGCAGCCAGAAACCGCAACAAAGUUCUAUGGAAAUGCAGCAGAAUCAAAAGAAAAAUCGUCCAAAUACC--AGUGGCAUAGAAA-AAAUGC
.....((((((((((..(((.((......)).))).))))))))))......(((((((....................((....))..(((......--..)))))))))).-...... ( -22.70)
>DroYak_CAF1 77881 119 + 1
CAAAGUGCGGUUUUUUAGUUUCCCCAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAGAAAAAUCACACAAAUACCCAAAUGGCAUAGAAA-AAAUGC
.....((((((((((..(((.(((....))).))).)))))))))).....((((..(((.....)))..))))..............................((((.....-..)))) ( -20.40)
>consensus
CAAAGUGCGGUUUUUUAGUUUCCCAAAUGGGCAGCCAAAAACCGCAACAAAGUUCAAUUGAAAUGCAGCAGAAUCAAAAGAAAAAUCACCCAAAUACC__AGUGGCAUAGAGAAAAAUGC
.....((((((((((..(((.(((....))).))).)))))))))).....((((..(((.....)))..))))..............................((((........)))) (-19.64 = -19.88 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,247,807 – 3,247,925
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.27
Mean single sequence MFE -26.14
Consensus MFE -21.94
Energy contribution -22.54
Covariance contribution 0.60
Combinations/Pair 1.07
Mean z-score -1.29
Structure conservation index 0.84
SVM decision value 0.00
SVM RNA-class probability 0.535228
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3247807 118 - 22407834
GCAUUUUUCUCUAUGCCACU--GGUAUUUGGGUGAUUUUUCUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUG
((((........))))((((--.(....).))))....(((..((((............))))..)))......((((((((((((...(((....)))...)).))))))))))..... ( -27.90)
>DroSec_CAF1 81855 118 - 1
GCAUUUUUCUCUAUGCCACU--GGUAUUUGGGUGAUUUUUCUUUUGAUUCUUCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUG
((((........))))((((--.(....).))))....(((..((((............))))..)))......((((((((((((...(((....)))...)).))))))))))..... ( -27.90)
>DroSim_CAF1 84987 117 - 1
GCAUU-UUCUCUAUGCCACU--GUUAUUUGGGUGAUUUUUCUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUG
((((.-......))))((((--........))))....(((..((((............))))..)))......((((((((((((...(((....)))...)).))))))))))..... ( -26.40)
>DroEre_CAF1 78624 117 - 1
GCAUUU-UUUCUAUGCCACU--GGUAUUUGGACGAUUUUUCUUUUGAUUCUGCUGCAUUUCCAUAGAACUUUGUUGCGGUUUCUGGCUGCCCAUUUCGGAAACUAAAAAACCGCACUUUG
(((...-.(((((((.....--.(((...((((((........))).)))...))).....)))))))...)))((((((((.(((....)))....(....)....))))))))..... ( -22.30)
>DroYak_CAF1 77881 119 - 1
GCAUUU-UUUCUAUGCCAUUUGGGUAUUUGUGUGAUUUUUCUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUGGGGAAACUAAAAAACCGCACUUUG
((((..-.....(((((.....)))))..)))).....(((..((((............))))..)))......((((((((((((...(((....)))...)).))))))))))..... ( -26.20)
>consensus
GCAUUUUUCUCUAUGCCACU__GGUAUUUGGGUGAUUUUUCUUUUGAUUCUGCUGCAUUUCAAUUGAACUUUGUUGCGGUUUUUGGCUGCCCAUUUGGGAAACUAAAAAACCGCACUUUG
........(((.(((((.....)))))..)))......(((..((((............))))..)))......((((((((((((...(((....)))...)).))))))))))..... (-21.94 = -22.54 +   0.60)

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 09:56:49 2006