Locus 243

Sequence ID 3L_DroMel_CAF1
Location 660,625 – 660,754
Length 129
Max. P 0.995849
window361 window362 window363 window364

overview

Window 1

Location 660,625 – 660,740
Length 115
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 91.65
Mean single sequence MFE -26.99
Consensus MFE -19.36
Energy contribution -19.36
Covariance contribution -0.00
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.72
SVM decision value 0.06
SVM RNA-class probability 0.564482
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 660625 115 + 23771897
UA---UUAAAUCAUAGAUAAAUGUGGAAACGGCCAAGUAGGCAUCUCUAUAUACAUGAUGAUGCCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUGCAAUGCCCAUUU
..---.............(((((.(....)(((......((((((((.........)).))))))......((((((............))))))(((......)))...)))))))) ( -27.90)
>DroSec_CAF1 16395 118 + 1
UAUUAUUGAAUCAUAGAUAAAUGUGGAAACGGCCAAGUAGGCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCGUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUU
...(((((((...(((((......(....)(((...((.((((((((.........)).))))))..))...)))(((((............))))))))))..)))))))....... ( -27.50)
>DroSim_CAF1 16324 115 + 1
UA---UUGAAUCAUAGAUAAAUGUGGAAACGGCCAAGUAGGCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCGUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUU
((---(((((...(((((......(....)(((...((.((((((((.........)).))))))..))...)))(((((............))))))))))..)))))))....... ( -27.30)
>DroEre_CAF1 16699 115 + 1
UA---UUAAAUCCUAGAUAAAUCUGGAAAUGGCCAAGUAGUCAUCUCUAUAUAUAAAAUGAUGGCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUU
..---.......(((((....)))))((((((.((....((((((..............))))))(((......((((((............))))))......)))..)).)))))) ( -25.34)
>DroYak_CAF1 17010 115 + 1
CA---UUAAAUCAUAGAUAAAUCUGGAAAUGGCCAGGUAGUCAUCUCUAUAUAGAUGAUGAAGCCGAACCGAGUUGCUGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUU
..---........((((....)))).((((((.(((((.(((((((......)))))))...))).......((.(((((.........))))).))............)).)))))) ( -26.90)
>consensus
UA___UUAAAUCAUAGAUAAAUGUGGAAACGGCCAAGUAGGCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUU
.......................(((.............((((((..............))))))......((((((............))))))(((((.......))))))))... (-19.36 = -19.36 +  -0.00) 

alignment

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secondary structure

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dotplot

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Window 2

Location 660,625 – 660,740
Length 115
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 91.65
Mean single sequence MFE -28.94
Consensus MFE -23.14
Energy contribution -23.74
Covariance contribution 0.60
Combinations/Pair 1.08
Mean z-score -1.66
Structure conservation index 0.80
SVM decision value 0.58
SVM RNA-class probability 0.789857
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 660625 115 - 23771897
AAAUGGGCAUUGCAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGGCAUCAUCAUGUAUAUAGAGAUGCCUACUUGGCCGUUUCCACAUUUAUCUAUGAUUUAA---UA
....((((((((((......))))).)))))...((((((((.(((...)))))))))))(((((.(((..((((((((.....)).))))))......))).))))).....---.. ( -29.30)
>DroSec_CAF1 16395 118 - 1
AAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGACGCUGCAGCUUGGUUCGGCAUCAUCGUGUAUAUAGAGAUGCCUACUUGGCCGUUUCCACAUUUAUCUAUGAUUCAAUAAUA
((((((.((..(((......((((((..(......)..))))))......)))((((((.((.........))))))))....)).))))))...(((......)))........... ( -30.20)
>DroSim_CAF1 16324 115 - 1
AAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGACGCUGCAGCUUGGUUCGGCAUCAUCGUGUAUAUAGAGAUGCCUACUUGGCCGUUUCCACAUUUAUCUAUGAUUCAA---UA
((((((.((..(((......((((((..(......)..))))))......)))((((((.((.........))))))))....)).))))))...(((......)))......---.. ( -30.20)
>DroEre_CAF1 16699 115 - 1
AAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGCCAUCAUUUUAUAUAUAGAGAUGACUACUUGGCCAUUUCCAGAUUUAUCUAGGAUUUAA---UA
.(((((.((..(((......((((((............))))))......)))....(((((((.......))))))).....)).)))))((((((....))).))).....---.. ( -25.90)
>DroYak_CAF1 17010 115 - 1
AAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCAGCAACUCGGUUCGGCUUCAUCAUCUAUAUAGAGAUGACUACCUGGCCAUUUCCAGAUUUAUCUAUGAUUUAA---UG
...((((((((.......))))).(((((.........))))).....(((..((..(((((.(((....))))))))...))..)))....)))..................---.. ( -29.10)
>consensus
AAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGGCAUCAUCAUGUAUAUAGAGAUGCCUACUUGGCCGUUUCCACAUUUAUCUAUGAUUUAA___UA
((((((.((..(((......((((((..(......)..))))))......)))((((((.((.........))))))))....)).)))))).......................... (-23.14 = -23.74 +   0.60) 

alignment

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secondary structure

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dotplot

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Window 3

Location 660,662 – 660,754
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 94.02
Mean single sequence MFE -22.49
Consensus MFE -19.98
Energy contribution -20.22
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -2.02
Structure conservation index 0.89
SVM decision value 2.62
SVM RNA-class probability 0.995849
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 660662 92 + 23771897
GCAUCUCUAUAUACAUGAUGAUGCCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUGCAAUGCCCAUUUAGGACUCGGCCCCU
.((((...........))))..(((((.((.((((((............))))))(((......)))............))..))))).... ( -23.50)
>DroSec_CAF1 16435 92 + 1
GCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCGUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUUAGGACUCGGCCCCU
.((((...........))))..(((((.((.((((((............))))))(((((.......))))).......))..))))).... ( -22.50)
>DroSim_CAF1 16361 92 + 1
GCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCGUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUUAGGACUCGGCCCCU
.((((...........))))..(((((.((.((((((............))))))(((((.......))))).......))..))))).... ( -22.50)
>DroEre_CAF1 16736 92 + 1
UCAUCUCUAUAUAUAAAAUGAUGGCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUUAGGACUCGGCCCCU
(((((..............)))))(((.((.((((((............))))))(((((.......))))).......))..)))...... ( -17.04)
>DroYak_CAF1 17047 92 + 1
UCAUCUCUAUAUAGAUGAUGAAGCCGAACCGAGUUGCUGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUUAGGACUCGGCCCCU
((((((((....))).))))).(((((.((.(((((((..........)))))))(((((.......))))).......))..))))).... ( -26.90)
>consensus
GCAUCUCUAUAUACACGAUGAUGCCGAACCAAGCUGCAGCAUCAAUAAAGCAGCUGCAUUUAAUUUCAAUGCCCAUUUAGGACUCGGCCCCU
.((((...........))))..(((((.((.((((((............))))))(((((.......))))).......))..))))).... (-19.98 = -20.22 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 4

Location 660,662 – 660,754
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 94.02
Mean single sequence MFE -29.52
Consensus MFE -24.44
Energy contribution -24.92
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -2.37
Structure conservation index 0.83
SVM decision value 2.24
SVM RNA-class probability 0.990940
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 660662 92 - 23771897
AGGGGCCGAGUCCUAAAUGGGCAUUGCAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGGCAUCAUCAUGUAUAUAGAGAUGC
..(((((((((((.....))))..((((......))))(((((............)))))))))))).(((((.((.........))))))) ( -28.70)
>DroSec_CAF1 16435 92 - 1
AGGGGCCGAGUCCUAAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGACGCUGCAGCUUGGUUCGGCAUCAUCGUGUAUAUAGAGAUGC
..(((((((((((.....))))............((((((..(......)..))))))..))))))).(((((.((.........))))))) ( -28.90)
>DroSim_CAF1 16361 92 - 1
AGGGGCCGAGUCCUAAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGACGCUGCAGCUUGGUUCGGCAUCAUCGUGUAUAUAGAGAUGC
..(((((((((((.....))))............((((((..(......)..))))))..))))))).(((((.((.........))))))) ( -28.90)
>DroEre_CAF1 16736 92 - 1
AGGGGCCGAGUCCUAAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGCCAUCAUUUUAUAUAUAGAGAUGA
..(((((((((((.....))))............((((((............))))))..)))))))....(((((((.......))))))) ( -25.80)
>DroYak_CAF1 17047 92 - 1
AGGGGCCGAGUCCUAAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCAGCAACUCGGUUCGGCUUCAUCAUCUAUAUAGAGAUGA
.(((((((((.((.......(((((.......))))).(((((.........))))).....))))))))))).((((((......)))))) ( -35.30)
>consensus
AGGGGCCGAGUCCUAAAUGGGCAUUGAAAUUAAAUGCAGCUGCUUUAUUGAUGCUGCAGCUUGGUUCGGCAUCAUCAUGUAUAUAGAGAUGC
..(((((((((((.....))))............((((((..(......)..))))))..))))))).(((((.((.........))))))) (-24.44 = -24.92 +   0.48) 

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 09:37:18 2006