Locus 6266

Sequence ID 3R_DroMel_CAF1
Location 16,336,389 – 16,336,479
Length 90
Max. P 0.929276
window10220 window10221

overview

Window 0

Location 16,336,389 – 16,336,479
Length 90
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 81.71
Mean single sequence MFE -24.98
Consensus MFE -13.56
Energy contribution -15.07
Covariance contribution 1.50
Combinations/Pair 1.14
Mean z-score -2.19
Structure conservation index 0.54
SVM decision value -0.01
SVM RNA-class probability 0.530077
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16336389 90 + 27905053
UCGGCACUAUUCAACACGCGCGGCU-UUUGAAUGUCAUUUCAAAUUAAAGCAAUUGCAC---ACGCACGUGUUUAAAGCCGGCU-CUCU---GCGCUC
.((((..((...((((((.(((...-((((((......)))))).....((....))..---.))).))))))))..))))((.-....---)).... ( -25.10)
>DroSec_CAF1 38855 90 + 1
UCGGCACUAUUCAACACGCGCUGCU-UUUGAAUGUCAUUUCAAAUUGAAGCGAUUGCAC---ACGCACGUGUUGAAAGCCGGCU-CUCU---GCGCUC
.((((....(((((((((((((...-((((((......))))))....))))..(((..---..)))))))))))).))))((.-....---)).... ( -30.90)
>DroSim_CAF1 41404 90 + 1
UCGGCACUAUUCAACACGCGCUGCU-UUUGAAUGUCAUUUCAAAUUGAAGCAAUUGCAC---ACGCACGUGUUGAAAGCCGGCU-CUCU---GCGCUC
.((((....(((((((((.(((((.-.(((....(((........)))..)))..))).---..)).))))))))).))))((.-....---)).... ( -30.20)
>DroEre_CAF1 38019 91 + 1
UCGGCACUAUUCAACACGCGCUGCU-UUUGAAUGUCAUUUCAAAUUCAAGCAAUUGCAC---ACGCACGUGUUGAAAGCCGGUCUCUCU---GCGCUC
(((((....(((((((((.((((..-((((((......))))))..)).((....))..---..)).))))))))).))))).......---...... ( -28.70)
>DroYak_CAF1 55460 83 + 1
UCGGCACUAUUCAACACGCGCUGCU-UCCGAAUGUCAUUUCAAAUUGAAGCAAUUGCAC---ACGCACGUGUUAAAAGCGGGUUU-----------UC
............(((.(((((((((-((....((......))....))))))...))((---((....)))).....))).))).-----------.. ( -16.30)
>DroPer_CAF1 64238 93 + 1
UUGGCAGUCCUGA----GUGCCGCUUUUUGAAUGCCAUUUCAAAUUGAAGCAAUUUCACAGCACGCACGUGUUAGAUAUUCUCU-CUCCCACACAAUC
.(((.((....((----(((.(((((((((((......)))))...)))))........(((((....))))).).)))))...-)).)))....... ( -18.70)
>consensus
UCGGCACUAUUCAACACGCGCUGCU_UUUGAAUGUCAUUUCAAAUUGAAGCAAUUGCAC___ACGCACGUGUUGAAAGCCGGCU_CUCU___GCGCUC
.((((.......((((((.((((((.((((((......))))))....))))............)).))))))....))))................. (-13.56 = -15.07 +   1.50)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,336,389 – 16,336,479
Length 90
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 81.71
Mean single sequence MFE -29.98
Consensus MFE -23.66
Energy contribution -24.88
Covariance contribution 1.23
Combinations/Pair 1.22
Mean z-score -2.60
Structure conservation index 0.79
SVM decision value 1.20
SVM RNA-class probability 0.929276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16336389 90 - 27905053
GAGCGC---AGAG-AGCCGGCUUUAAACACGUGCGU---GUGCAAUUGCUUUAAUUUGAAAUGACAUUCAAA-AGCCGCGCGUGUUGAAUAGUGCCGA
..((..---....-.))((((....((((((((((.---((((....)).....((((((......))))))-.)))))))))))).......)))). ( -29.10)
>DroSec_CAF1 38855 90 - 1
GAGCGC---AGAG-AGCCGGCUUUCAACACGUGCGU---GUGCAAUCGCUUCAAUUUGAAAUGACAUUCAAA-AGCAGCGCGUGUUGAAUAGUGCCGA
..((..---....-.))((((.((((((((((((.(---((((....)).....((((((......))))))-.)))))))))))))))....)))). ( -33.10)
>DroSim_CAF1 41404 90 - 1
GAGCGC---AGAG-AGCCGGCUUUCAACACGUGCGU---GUGCAAUUGCUUCAAUUUGAAAUGACAUUCAAA-AGCAGCGCGUGUUGAAUAGUGCCGA
..((..---....-.))((((.((((((((((((.(---((((....)).....((((((......))))))-.)))))))))))))))....)))). ( -33.40)
>DroEre_CAF1 38019 91 - 1
GAGCGC---AGAGAGACCGGCUUUCAACACGUGCGU---GUGCAAUUGCUUGAAUUUGAAAUGACAUUCAAA-AGCAGCGCGUGUUGAAUAGUGCCGA
......---........((((.((((((((((((.(---((((....)).....((((((......))))))-.)))))))))))))))....)))). ( -32.70)
>DroYak_CAF1 55460 83 - 1
GA-----------AAACCCGCUUUUAACACGUGCGU---GUGCAAUUGCUUCAAUUUGAAAUGACAUUCGGA-AGCAGCGCGUGUUGAAUAGUGCCGA
..-----------.....(((((((((((((((((.---...)...((((((....((......))....))-)))))))))))))))).)))).... ( -28.00)
>DroPer_CAF1 64238 93 - 1
GAUUGUGUGGGAG-AGAGAAUAUCUAACACGUGCGUGCUGUGAAAUUGCUUCAAUUUGAAAUGGCAUUCAAAAAGCGGCAC----UCAGGACUGCCAA
......(((..((-(.......)))..)))((((.((((.((((..((((((.....))...))))))))...))))))))----...((....)).. ( -23.60)
>consensus
GAGCGC___AGAG_AGCCGGCUUUCAACACGUGCGU___GUGCAAUUGCUUCAAUUUGAAAUGACAUUCAAA_AGCAGCGCGUGUUGAAUAGUGCCGA
.................((((.((((((((((((((.....))....(((....((((((......)))))).))).))))))))))))....)))). (-23.66 = -24.88 +   1.23)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:17:11 2006