Locus 6044

Sequence ID X_DroMel_CAF1
Location 15,514,063 – 15,514,254
Length 191
Max. P 0.980261
window9819 window9820 window9821 window9822 window9823 window9824 window9825

overview

Window 9

Location 15,514,063 – 15,514,162
Length 99
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 86.61
Mean single sequence MFE -38.50
Consensus MFE -29.76
Energy contribution -30.83
Covariance contribution 1.06
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.77
SVM decision value 0.40
SVM RNA-class probability 0.723068
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514063 99 + 22224390
CUGGCGAUCUGAUCGAUCGGCGGCUGAACAGUUGCAAAAACAGCCA----GCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------
(((((((((.....)))).((((((....)))))).......))))----).........((((((((((.((((..(....)..))))..)).)))))))).------- ( -38.20)
>DroSec_CAF1 74525 99 + 1
CUGGCGAUCUGAUCGAUCGGCGGCUGAACAGUUGCAAAAACAGCCA----GCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------
(((((((((.....)))).((((((....)))))).......))))----).........((((((((((.((((..(....)..))))..)).)))))))).------- ( -38.20)
>DroSim_CAF1 86531 103 + 1
CUGGCGAUCUGAUCGAUCGGCGGCUGAACAGUUGCAAAAACAGCCA----GCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC---UUUU
(((((((((.....)))).((((((....)))))).......))))----).........((((((((((.((((..(....)..))))..)).)))))))).---.... ( -38.20)
>DroEre_CAF1 76412 103 + 1
CUGGCGAUCUGAUCGAUCGGCGGCUGAACAGUUGCAAAAACAGCCGAGGAAC-------CGGGAAACCCCGAAGGACCCAGCGAACCUGAGGGCGGGUUGAGCGGCUGAG
....(((((.....)))))((((((....)))))).....((((((.((..(-------((((....))))..)..))).((.((((((....))))))..))))))).. ( -39.40)
>consensus
CUGGCGAUCUGAUCGAUCGGCGGCUGAACAGUUGCAAAAACAGCCA____GCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC_______
.((((((((.....)))).((((((....)))))).......))))..............((((((((((.((((..........))))..)).))))))))........ (-29.76 = -30.83 +   1.06)

alignment

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secondary structure

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Window 0

Location 15,514,063 – 15,514,162
Length 99
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 86.61
Mean single sequence MFE -38.83
Consensus MFE -30.88
Energy contribution -32.00
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.80
SVM decision value 0.03
SVM RNA-class probability 0.550251
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514063 99 - 22224390
-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGC----UGGCUGUUUUUGCAACUGUUCAGCCGCCGAUCGAUCAGAUCGCCAG
-------((((((....(((.((((..(....)..)))).))).))))))(((....(((----.(((((.....((....)).))))))))((((.....))))))).. ( -40.60)
>DroSec_CAF1 74525 99 - 1
-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGC----UGGCUGUUUUUGCAACUGUUCAGCCGCCGAUCGAUCAGAUCGCCAG
-------((((((....(((.((((..(....)..)))).))).))))))(((....(((----.(((((.....((....)).))))))))((((.....))))))).. ( -40.60)
>DroSim_CAF1 86531 103 - 1
AAAA---GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGC----UGGCUGUUUUUGCAACUGUUCAGCCGCCGAUCGAUCAGAUCGCCAG
....---((((((....(((.((((..(....)..)))).))).))))))(((....(((----.(((((.....((....)).))))))))((((.....))))))).. ( -40.80)
>DroEre_CAF1 76412 103 - 1
CUCAGCCGCUCAACCCGCCCUCAGGUUCGCUGGGUCCUUCGGGGUUUCCCG-------GUUCCUCGGCUGUUUUUGCAACUGUUCAGCCGCCGAUCGAUCAGAUCGCCAG
....((.(((.(((..(((...(((...(((((((((....)))...))))-------)).))).)))(((....)))...))).))).))(((((.....))))).... ( -33.30)
>consensus
_______GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGC____UGGCUGUUUUUGCAACUGUUCAGCCGCCGAUCGAUCAGAUCGCCAG
.......((((((....(((.((((..(....)..)))).))).))))))......((((....((((((.....((....)).))))))..((((.....)))))))). (-30.88 = -32.00 +   1.12)

alignment

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secondary structure

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Window 1

Location 15,514,103 – 15,514,199
Length 96
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 93.38
Mean single sequence MFE -38.63
Consensus MFE -36.58
Energy contribution -36.36
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.73
Structure conservation index 0.95
SVM decision value 1.86
SVM RNA-class probability 0.980261
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514103 96 + 22224390
CAGCCAGCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------UUUUUCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCCA
......((..(((((.(((....)))(((((((..((.(((((.(((((.((....)))-------))))....)))))))....)))))))..))))))).. ( -37.70)
>DroSec_CAF1 74565 96 + 1
CAGCCAGCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------UUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAU
......((..(((((.(((....)))(((((((..((.(((((..((((.((.....))-------....)))))))))))....)))))))..))))))).. ( -38.80)
>DroSim_CAF1 86571 103 + 1
CAGCCAGCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCCUUUUCCCUUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAU
......((..(((((.(((....)))(((((((..((.(((((.(((((.((.....))....)))))......)))))))....)))))))..))))))).. ( -39.40)
>consensus
CAGCCAGCCAAGGACCGGGAAACCCCGCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC_______UUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAU
......((..(((((.(((....)))(((((((..((.(((((..((((..(...............)..)))))))))))....)))))))..))))))).. (-36.58 = -36.36 +  -0.22)

alignment

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secondary structure

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Window 2

Location 15,514,103 – 15,514,199
Length 96
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 93.38
Mean single sequence MFE -42.17
Consensus MFE -37.87
Energy contribution -38.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.30
Structure conservation index 0.90
SVM decision value 0.89
SVM RNA-class probability 0.874750
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514103 96 - 22224390
UGGCAGGACAUGCAGGACAUGCAGGAACCAGGAAAAA-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGCUGGCUG
.((((((((..(((((((..((..((((((((.....-------((.....))..)))..)))))))...)))))))(((....))).)))))..)))..... ( -39.60)
>DroSec_CAF1 74565 96 - 1
AUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGCUGGCUG
..(((((((..(((((((..((..(((((((((....-------((.....)).))))..)))))))...)))))))(((....))).)))))..))...... ( -43.10)
>DroSim_CAF1 86571 103 - 1
AUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAAGGGAAAAGGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGCUGGCUG
...(((..((.(((((((..((((((.((((((((.((((....((.....)).))))....))).)))))))))))(((....))).)))))..)))).))) ( -43.80)
>consensus
AUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA_______GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGCGGGGUUUCCCGGUCCUUGGCUGGCUG
..(((((((..(((((((..((..(((((((((...........((.....)).))))..)))))))...)))))))(((....))).)))))..))...... (-37.87 = -38.20 +   0.33)

alignment

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secondary structure

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Window 3

Location 15,514,129 – 15,514,220
Length 91
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 93.03
Mean single sequence MFE -32.43
Consensus MFE -29.18
Energy contribution -28.96
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.22
Structure conservation index 0.90
SVM decision value 0.81
SVM RNA-class probability 0.857083
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514129 91 + 22224390
GCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------UUUUUCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCCAGUCAGGAAGUCAACGUCACUU
(((((((..((.(((((.(((((.((....)))-------))))....)))))))....)))))))...(((((.....))))).............. ( -30.90)
>DroSec_CAF1 74591 91 + 1
GCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC-------UUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAUGUCAGGAAGUCAACGUCACUU
(((((((((.(.(((...(((((.......)))-------)))))).))).))))))...(((((((((.....)))).))))).............. ( -32.80)
>DroSim_CAF1 86597 98 + 1
GCAGGACCAAGCGAACCUGAGGGCGGUUUUCCCUUUUCCCUUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAUGUCAGGAAGUCAACGUCACUU
(((((((((.(.(((...(((((.((.....))....))))))))).))).))))))...(((((((((.....)))).))))).............. ( -33.60)
>consensus
GCAGGACCAAGCGAACCUGAGGGCGGUUUUCCC_______UUUUCCCUGGUUCCUGCAUGUCCUGCAUGUCCUGCAUGUCAGGAAGUCAACGUCACUU
(((((((..((.(((((..((((..(...............)..)))))))))))....)))))))...(((((.....))))).............. (-29.18 = -28.96 +  -0.22)

alignment

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secondary structure

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Window 4

Location 15,514,129 – 15,514,220
Length 91
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 93.03
Mean single sequence MFE -33.87
Consensus MFE -29.37
Energy contribution -29.70
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.87
SVM decision value 0.66
SVM RNA-class probability 0.814475
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514129 91 - 22224390
AAGUGACGUUGACUUCCUGACUGGCAGGACAUGCAGGACAUGCAGGAACCAGGAAAAA-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGC
..............(((((.....)))))...(((((((..((..((((((((.....-------((.....))..)))..)))))))...))))))) ( -29.80)
>DroSec_CAF1 74591 91 - 1
AAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA-------GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGC
..............(((((.....)))))...(((((((..((..(((((((((....-------((.....)).))))..)))))))...))))))) ( -34.60)
>DroSim_CAF1 86597 98 - 1
AAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAAGGGAAAAGGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGC
..............(((((.((((.....)))))))))...((((((.((((((((.((((....((.....)).))))....))).))))))))))) ( -37.20)
>consensus
AAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA_______GGGAAAACCGCCCUCAGGUUCGCUUGGUCCUGC
..............(((((.....)))))...(((((((..((..(((((((((...........((.....)).))))..)))))))...))))))) (-29.37 = -29.70 +   0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,514,162 – 15,514,254
Length 92
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 95.74
Mean single sequence MFE -29.73
Consensus MFE -28.09
Energy contribution -28.53
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.73
Structure conservation index 0.94
SVM decision value 0.33
SVM RNA-class probability 0.693059
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15514162 92 - 22224390
GUCUCCUGUUUUUGCACAUGUUGACACAUUCGCGAAGUGACGUUGACUUCCUGACUGGCAGGACAUGCAGGACAUGCAGGAACCAGGAAAAA---
...(((((((((((((...((..((....((((...)))).))..)).(((((..((......))..)))))..)))))))).)))))....--- ( -28.20)
>DroSec_CAF1 74624 92 - 1
GUCUCCUGUUUUUGCACAUGUUGACACAUUCGCGAAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA---
.((.((((((((((((...((..((....((((...)))).))..)).(((((.((((.....)))))))))..)))))))).))))))...--- ( -30.50)
>DroSim_CAF1 86634 95 - 1
GUCUCCUGUUUUUGCACAUGUUGACACAUUCGCGAAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAAGGG
.((.((((((((((((...((..((....((((...)))).))..)).(((((.((((.....)))))))))..)))))))).))))))...... ( -30.50)
>consensus
GUCUCCUGUUUUUGCACAUGUUGACACAUUCGCGAAGUGACGUUGACUUCCUGACAUGCAGGACAUGCAGGACAUGCAGGAACCAGGGAAAA___
...(((((((((((((...((..((....((((...)))).))..)).(((((.((((.....)))))))))..)))))))).)))))....... (-28.09 = -28.53 +   0.45)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:50 2006