Locus 1657

Sequence ID X_DroMel_CAF1
Location 4,672,201 – 4,672,480
Length 279
Max. P 0.697403
window2725 window2726 window2727

overview

Window 5

Location 4,672,201 – 4,672,320
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.51
Mean single sequence MFE -33.07
Consensus MFE -29.88
Energy contribution -30.12
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.67
Structure conservation index 0.90
SVM decision value 0.19
SVM RNA-class probability 0.626047
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4672201 119 - 22224390
GAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGUUGCCAAAUUUGUGUGCCAAGGUGCCAAAGUUUGCCACGCCCCGAUCCA
.............-...(((((.(((((.((((((..((((..(((......)))((...))......)))))))))).)))))(((.((((.(.....).)))).))))))))...... ( -32.90)
>DroSec_CAF1 33213 119 - 1
GAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCCGGCCAUAAACCGUUGCCAAAUUUGUGUGCCAAGGUGCCAAAGUGUGCCACGCCCCAAUCCA
.............-...(((((.......((((((..((((..(((......)))..))(((.((.....)).)))......)).))))))((..(......)..))..)))))...... ( -34.60)
>DroEre_CAF1 33644 119 - 1
GAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGAUGCCAAAUUUGUGUGCCAAGGUGCCAAAGUGUGCCACGCCCCAAUCCA
.............-...(((((.......(((((.........(((......)))(((((((((((((...........)))))).))).))))))))).(((...))))))))...... ( -33.10)
>DroYak_CAF1 30406 120 - 1
GGAAAGGCAGAAAAAAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGUGCCUGGCCAUAAACCGAUGCCAAAUUUGUGUGUCAAGGUGCCAAAGUGUGCCACGCCCCAAUCCA
.................(((((.(((((.((((((...(((.........((((.((...))))))..))).)))))).))))).......((..(......)..))..)))))...... ( -31.70)
>consensus
GAAAAGGCAGAAA_AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGAUGCCAAAUUUGUGUGCCAAGGUGCCAAAGUGUGCCACGCCCCAAUCCA
.................(((((.(((((.((((((...(((.........((((.((...))))))..))).)))))).))))).......(((((......)))))..)))))...... (-29.88 = -30.12 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,672,241 – 4,672,360
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.51
Mean single sequence MFE -31.32
Consensus MFE -30.12
Energy contribution -30.00
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -1.60
Structure conservation index 0.96
SVM decision value 0.34
SVM RNA-class probability 0.697403
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4672241 119 - 22224390
CCGGUGUAUCUGUUCGGGUCAUAAAAACAGUGAUGCCCCAGAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGUUGCCAAAU
.((((.....((..(((((((((.......(((((((((..............-...)))))......(((.....)))...))))....))))).))))..))...))))......... ( -28.23)
>DroSec_CAF1 33253 119 - 1
CCGGUGUAUCUGUUCGGGCCAUAAAAACAGUGAUGCCCCAGAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCCGGCCAUAAACCGUUGCCAAAU
.((((.....((..(((((((((.......(((((((((..............-...)))))......(((.....)))...))))....)))).)))))..))...))))......... ( -32.53)
>DroEre_CAF1 33684 119 - 1
CCGGUGUAUCUGUUCGGGCCAUAAAAACAGUGACGCCCCAGAAAAGGCAGAAA-AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGAUGCCAAAU
...(.(((((.(((..(((((.....(((.(((.(((((..............-...)))))......(((.....)))....)))....))).....)))))...))).)))))).... ( -30.83)
>DroYak_CAF1 30446 120 - 1
ACGGUGUAUCUGUUCGGGCCAUAAAAACAGUGAUGCCCCAGGAAAGGCAGAAAAAAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGUGCCUGGCCAUAAACCGAUGCCAAAU
...(.(((((.(((..(((((....(((..((.((((((..................)))))).))..)))((((..(((..........))).)))))))))...))).)))))).... ( -33.67)
>consensus
CCGGUGUAUCUGUUCGGGCCAUAAAAACAGUGAUGCCCCAGAAAAGGCAGAAA_AAAGGGGCAAUAAAGUUGGCAAAGCGGAAUCAAUAAUGUGAGCCUGGCCAUAAACCGAUGCCAAAU
.((((.....((..(((((((((.......(((((((((..................)))))......(((.....)))...))))....)))).)))))..))...))))......... (-30.12 = -30.00 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,672,360 – 4,672,480
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 98.61
Mean single sequence MFE -34.42
Consensus MFE -33.05
Energy contribution -33.30
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.96
SVM decision value 0.20
SVM RNA-class probability 0.630325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4672360 120 - 22224390
AAAACACCCAAUCGAUCGGAUCUGAUUUGAUCUGCCCGCUGCGGCCGUCCUGUCGACUGACUGCCAGGACAUAAAAACAUAAGGACAACAAUUUAUGGCACAUUUGCAGCUUCGAGGAAU
.......((..((((.((((((......))))))...(((((((..((((((.((......)).)))))).......((((((........))))))......))))))).))))))... ( -34.10)
>DroSec_CAF1 33372 120 - 1
AAAACUCCCAAUCGAUCGGAUCUGAUUUGAUCUGCCCGCUGCGGCCGUCCUGUCGACUGACUGCCAGGACAUAAAAACAUAAGGACAACAAUUUAUGGCACAUUUGCAGCUCCGAGGAAU
.....(((...(((..((((((......))))))...(((((((..((((((.((......)).)))))).......((((((........))))))......)))))))..)))))).. ( -33.80)
>DroEre_CAF1 33803 120 - 1
AAAACACCCAAUCGAUCGGAUCUGAUUUGAUCUGCCCGCUGCGGCCGUCCUGUCGACUGACUGCCAGGACAUAAAAACAUAAGGACAACAAUUUAUGGCACAUUUGCAGCUUCGAGGAAU
.......((..((((.((((((......))))))...(((((((..((((((.((......)).)))))).......((((((........))))))......))))))).))))))... ( -34.10)
>DroYak_CAF1 30566 120 - 1
AAAACUCCCCAUCGAUCGGAUCUGAUUUGAUCUGCCCGCUGCGGCCGUCCUGUCGACUGACUGCCAGGACAUAAAAACAUAAGGACAACAAUUUAUGGCACAUUUGCAGCUUCGAGGAAU
........((.((((.((((((......))))))...(((((((..((((((.((......)).)))))).......((((((........))))))......))))))).))))))... ( -35.70)
>consensus
AAAACACCCAAUCGAUCGGAUCUGAUUUGAUCUGCCCGCUGCGGCCGUCCUGUCGACUGACUGCCAGGACAUAAAAACAUAAGGACAACAAUUUAUGGCACAUUUGCAGCUUCGAGGAAU
.......((..((((.((((((......))))))...(((((((..((((((.((......)).)))))).......((((((........))))))......))))))).))))))... (-33.05 = -33.30 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:59 2006