Locus 2014

Sequence ID 2R_DroMel_CAF1
Location 7,585,286 – 7,585,413
Length 127
Max. P 0.994450
window3331 window3332 window3333

overview

Window 1

Location 7,585,286 – 7,585,390
Length 104
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 80.40
Mean single sequence MFE -16.00
Consensus MFE -10.55
Energy contribution -10.18
Covariance contribution -0.38
Combinations/Pair 1.14
Mean z-score -1.94
Structure conservation index 0.66
SVM decision value 0.67
SVM RNA-class probability 0.818158
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7585286 104 + 20766785
CGUGCCAGGAUCCCUAUUCCUUCCCCACC---G----CACACACACACACACGCACACAU--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUU
.((((.((((.......))))........---(----......)........))))....--.........((.((((.((..(((....)))....)).)))).))...... ( -16.30)
>DroSec_CAF1 31190 96 + 1
CGUGCCAGGAUCCCUAUUCCUUCCCCACC---G----CACUCACACAC--------ACAC--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUUAAUGCAUCCUUUAUU
.((((.((((.......))))........---)----)))........--------....--.........((.((((.....(((....))).......)))).))...... ( -15.00)
>DroSim_CAF1 31936 88 + 1
CGUGCCAGGAUCCCUAUUCCUUCCC---------------ACACACAC--------ACAC--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUU
.(((..((((.......))))...)---------------))......--------....--.........((.((((.((..(((....)))....)).)))).))...... ( -15.80)
>DroYak_CAF1 31756 113 + 1
CGUGCCAGGAUCCCUCUUCCUUUCCCUUUCCGUUCUCCUUGCACACACAGACACACAAGCAGAUAUCCUUCGGCUGUACUUUGCGCUUUAGCAAUUUAAAUGCAUCCUUUAUU
.((((.((((.........................)))).))))..........(((.((.((......)).)))))...((((......))))................... ( -16.91)
>consensus
CGUGCCAGGAUCCCUAUUCCUUCCCCACC___G____CACACACACAC________ACAC__AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUU
......((((.......))))..................................................((.((((..((((......))))......)))).))...... (-10.55 = -10.18 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,585,317 – 7,585,413
Length 96
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -22.47
Consensus MFE -18.83
Energy contribution -19.20
Covariance contribution 0.37
Combinations/Pair 1.09
Mean z-score -2.98
Structure conservation index 0.84
SVM decision value 2.48
SVM RNA-class probability 0.994450
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7585317 96 + 20766785
ACACACACACACACGCACACAU--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUUGCAUUUUAAUUGCGGGCAACUGG
..............(((((...--.....(....)........)))))....((((((.(((((((........))))))).))))))((....)).. ( -23.19)
>DroSec_CAF1 31221 88 + 1
ACUCACACAC--------ACAC--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUUAAUGCAUCCUUUAUUGCAUUUUAAUUGCGAACAACUGG
..........--------....--........(((..((((...))))....((((((..((((((........))))))..))))))......))). ( -18.70)
>DroSim_CAF1 31961 86 + 1
--ACACACAC--------ACAC--AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUUGCAUUUUAAUUGCGGGCAACUGG
--........--------....--....((....(((((((...))))....((((((.(((((((........))))))).)))))).)))....)) ( -22.10)
>DroYak_CAF1 31794 98 + 1
UUGCACACACAGACACACAAGCAGAUAUCCUUCGGCUGUACUUUGCGCUUUAGCAAUUUAAAUGCAUCCUUUAUUGCAUUUUAAUUGCAGGCAACUGG
.........(((........((((((((.(....)..))).)))))((((..((((((.(((((((........))))))).))))))))))..))). ( -25.90)
>consensus
ACACACACAC________ACAC__AUAUCCUUCGGCUGCACUUUGUGCUUUAGCAAUUUAAAUGCAUCCUUUAUUGCAUUUUAAUUGCGGGCAACUGG
............................((....(((((((...))))....((((((.(((((((........))))))).)))))).)))....)) (-18.83 = -19.20 +   0.37)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,585,317 – 7,585,413
Length 96
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -23.38
Consensus MFE -17.38
Energy contribution -17.50
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.70
Structure conservation index 0.74
SVM decision value 0.37
SVM RNA-class probability 0.707722
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7585317 96 - 20766785
CCAGUUGCCCGCAAUUAAAAUGCAAUAAAGGAUGCAUUUAAAUUGCUAAAGCACAAAGUGCAGCCGAAGGAUAU--AUGUGUGCGUGUGUGUGUGUGU
((..(.((..((((((.(((((((........))))))).))))))....((((...)))).)).)..))((((--(((....)))))))........ ( -24.40)
>DroSec_CAF1 31221 88 - 1
CCAGUUGUUCGCAAUUAAAAUGCAAUAAAGGAUGCAUUAAAAUUGCUAAAGCACAAAGUGCAGCCGAAGGAUAU--GUGU--------GUGUGUGAGU
.......(((((((((..((((((........))))))..))))))....(((((..(..((..(....)...)--)..)--------.)))))))). ( -20.20)
>DroSim_CAF1 31961 86 - 1
CCAGUUGCCCGCAAUUAAAAUGCAAUAAAGGAUGCAUUUAAAUUGCUAAAGCACAAAGUGCAGCCGAAGGAUAU--GUGU--------GUGUGUGU--
..........((((((.(((((((........))))))).))))))....(((((..(..((..(....)...)--)..)--------...)))))-- ( -22.80)
>DroYak_CAF1 31794 98 - 1
CCAGUUGCCUGCAAUUAAAAUGCAAUAAAGGAUGCAUUUAAAUUGCUAAAGCGCAAAGUACAGCCGAAGGAUAUCUGCUUGUGUGUCUGUGUGUGCAA
....((((..((((((.(((((((........))))))).))))))....(((((.((.(((..(((.((....))..)))..))))).))))))))) ( -26.10)
>consensus
CCAGUUGCCCGCAAUUAAAAUGCAAUAAAGGAUGCAUUUAAAUUGCUAAAGCACAAAGUGCAGCCGAAGGAUAU__GUGU________GUGUGUGUGU
((..(.((..((((((.(((((((........))))))).))))))....((((...)))).)).)..))............................ (-17.38 = -17.50 +   0.12)

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 10:18:53 2006