Locus 8382

Sequence ID X_DroMel_CAF1
Location 20,810,665 – 20,810,856
Length 191
Max. P 0.958428
window13766 window13767 window13768

overview

Window 6

Location 20,810,665 – 20,810,785
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.64
Mean single sequence MFE -34.40
Consensus MFE -32.38
Energy contribution -32.62
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.76
Structure conservation index 0.94
SVM decision value 1.49
SVM RNA-class probability 0.958428
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20810665 120 - 22224390
AAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUCCGAUCCGCGCGAUUUGCCCGCCAAAUCGCUGGCCAUGUAA
...((((..((((((...(((...((((((((((......))))))))))...)))....))))))......................((((((((.....))))))))))))....... ( -32.20)
>DroSim_CAF1 6273 120 - 1
AAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUCCGAGCCGCGCGAUUUGCCCGCCAAAUCGCUGGCCAUGUAA
......(((((((((...(((...((((((((((......))))))))))...)))....)))))................(.((((.((((((((.....))))))))))))))))).. ( -34.60)
>DroEre_CAF1 2642 120 - 1
AAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGAUGCGAUGUGCACUCCAAUGAUUUUCCGAGCCGCGCGAUUUGCCCGCCAAAUCGCUGGCCAUGUAA
..(((.((((((((....((....((((((((((......)))))))))).)).)))).)))))))...............(.((((.((((((((.....)))))))))))))...... ( -35.50)
>DroYak_CAF1 6897 120 - 1
AAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGAUGCGAUGUGCACUCCAAUGAUUUUCCGAGCCGCGCGAUUUGCCCCUCAAAUCGCUGGCCAUGUAA
..(((.((((((((....((....((((((((((......)))))))))).)).)))).)))))))...............(.((((.((((((((.....)))))))))))))...... ( -35.30)
>consensus
AAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUCCGAGCCGCGCGAUUUGCCCGCCAAAUCGCUGGCCAUGUAA
......(((((....(((((((...(((((((((......)))))))))(((((......))))).......)))))))....((((.((((((((.....))))))))))))))))).. (-32.38 = -32.62 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,810,705 – 20,810,817
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 92.67
Mean single sequence MFE -27.85
Consensus MFE -23.38
Energy contribution -23.38
Covariance contribution 0.00
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.84
SVM decision value 0.96
SVM RNA-class probability 0.890025
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20810705 112 - 22224390
GGGCAACAUGCAAAACA--UCGGGAAA------UUGCCAAAAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUC
.((((....((((....--........------)))).....))))...((((((...(((...((((((((((......))))))))))...)))....)))))).............. ( -24.20)
>DroSim_CAF1 6313 112 - 1
GGCCAACAUGCAAAACA--UCGGGAAA------UUGCCAAAAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUC
(((......((((....--........------))))......)))...((((((...(((...((((((((((......))))))))))...)))....)))))).............. ( -23.00)
>DroEre_CAF1 2682 112 - 1
GGCCAACAUGCAAAACA--GCGGGCCA------UGGCCAAAAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGAUGCGAUGUGCACUCCAAUGAUUUUC
(((((...(((......--))).....------)))))....(((.((((((((....((....((((((((((......)))))))))).)).)))).))))))).............. ( -30.40)
>DroYak_CAF1 6937 120 - 1
GGCCAACAUGCAAAACAUCGCGGGCCAUUGCAAUGGCCAAAAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGAUGCGAUGUGCACUCCAAUGAUUUUC
........(((...((((((((((((((....))))))...((((.....))))..........((((((((((......)))))))))).....))))))))))).............. ( -33.80)
>consensus
GGCCAACAUGCAAAACA__GCGGGAAA______UGGCCAAAAUGCCACAUGCAUAAAAGUUAACCAAGUUGAUAUUUAAUUGUCAAUUUGCACGACGCCAUGUGCACUCCAAUGAUUUUC
((...((((((..(((......(((((......)))))...((((.....))))....)))...((((((((((......))))))))))......)).)))).....)).......... (-23.38 = -23.38 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,810,745 – 20,810,856
Length 111
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.78
Mean single sequence MFE -29.68
Consensus MFE -27.40
Energy contribution -27.40
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -1.34
Structure conservation index 0.92
SVM decision value 0.06
SVM RNA-class probability 0.562062
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20810745 111 + 22224390
AUUAAAUAUCAACUUGGUUAACUUUUAUGCAUGUGGCAUUUUGGCAA------UUUCCCGA--UGUUUUGCAUGUUGCCCAGUGUUGAUUAACAGCUAAUUAAUGG-GGCAGGGCUUUAA
...............((((......((((((...((((((..((...------...)).))--)))).))))))((((((...((((((((.....)))))))).)-))))))))).... ( -24.80)
>DroSim_CAF1 6353 111 + 1
AUUAAAUAUCAACUUGGUUAACUUUUAUGCAUGUGGCAUUUUGGCAA------UUUCCCGA--UGUUUUGCAUGUUGGCCAGUGUUGAUUAACAGCUAAUUAAUGG-GGCAGGGCUUUAA
.......(((((((((((((((....(((((...((((((..((...------...)).))--)))).)))))))))))))).))))))..............(((-(((...)))))). ( -27.10)
>DroEre_CAF1 2722 111 + 1
AUUAAAUAUCAACUUGGUUAACUUUUAUGCAUGUGGCAUUUUGGCCA------UGGCCCGC--UGUUUUGCAUGUUGGCCAGUGUUGAUUAACGGCUAAUUAAUGG-GGCAGGGCUUUAA
.......(((((((((((((((....(((((.(..((.....(((..------..))).))--..)..)))))))))))))).))))))..............(((-(((...)))))). ( -30.70)
>DroYak_CAF1 6977 120 + 1
AUUAAAUAUCAACUUGGUUAACUUUUAUGCAUGUGGCAUUUUGGCCAUUGCAAUGGCCCGCGAUGUUUUGCAUGUUGGCCAGUGUUGAUUAACGGCUAAUUAAUGGGGGCAGGGCUUUAA
.......(((((((((((((((....(((((...((((((..((((((....))))))...)))))).)))))))))))))).)))))).....(((..(....)..))).......... ( -36.10)
>consensus
AUUAAAUAUCAACUUGGUUAACUUUUAUGCAUGUGGCAUUUUGGCAA______UGGCCCGA__UGUUUUGCAUGUUGGCCAGUGUUGAUUAACAGCUAAUUAAUGG_GGCAGGGCUUUAA
.......(((((((((((((((....(((((...((((....(((((......))))).....)))).)))))))))))))).))))))....((((......((....)).)))).... (-27.40 = -27.40 +   0.00)

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 13:02:36 2006