Locus 7571

Sequence ID 3L_DroMel_CAF1
Location 20,352,393 – 20,352,544
Length 151
Max. P 0.941464
window12295 window12296 window12297

overview

Window 5

Location 20,352,393 – 20,352,504
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.52
Mean single sequence MFE -28.57
Consensus MFE -17.31
Energy contribution -16.87
Covariance contribution -0.44
Combinations/Pair 1.16
Mean z-score -1.40
Structure conservation index 0.61
SVM decision value 0.86
SVM RNA-class probability 0.869186
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20352393 111 + 23771897
UUGGGCUCAACUGAUCCUCGCUGUCGCGUUGCCCCGCCGG---------CAACAAAAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACCUAUCUUCCACCA
...((((............((....))((((((.....))---------)))).....))))..(((....(((((((((....))))))))).....)))................... ( -35.10)
>DroEre_CAF1 21572 111 + 1
UUGGGCUCAACUGAUCCUCGCUGUCGCGUUACGCCGCCGG---------CAACACCAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACUUAUCUGCCACCA
...(((((....)).....((((..(((......))).((---------(((((((........)))))..(((((((((....)))))))))))))...)))).........))).... ( -35.70)
>DroWil_CAF1 28844 105 + 1
CCAGGAUCCACUGAUCCCCGUUGUC---------CUCAAGAAUCAAGAACUACUCUCAAACCAAGAUGCUAUCCUGGUUCAACCGACCCAGAAUGC------GCCACAUAUCUUCCAUCA
...(((((....)))))........---------.....((...((((.....(((.......))).(((((.((((.((....)).)))).))).------))......))))...)). ( -14.90)
>consensus
UUGGGCUCAACUGAUCCUCGCUGUCGCGUU_C_CCGCCGG_________CAACACAAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACAUAUCUUCCACCA
...((.((....)).))...............................................((((...(((((((((....))))))))).((......))...........)))). (-17.31 = -16.87 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,352,393 – 20,352,504
Length 111
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 67.52
Mean single sequence MFE -37.97
Consensus MFE -21.78
Energy contribution -22.23
Covariance contribution 0.45
Combinations/Pair 1.19
Mean z-score -1.56
Structure conservation index 0.57
SVM decision value 0.99
SVM RNA-class probability 0.896009
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20352393 111 - 23771897
UGGUGGAAGAUAGGUAGCUGGUUGACAUUCCGGAUCCCUUGAUCCGGAAAAACACCUUGGCUUUUUUGUUG---------CCGGCGGGGCAACGCGACAGCGAGGAUCAGUUGAGCCCAA
............((((((((((.....(((((((((....))))))))).....(((((.((.((.(((((---------((.....))))))).)).))))))))))))))..)))... ( -41.20)
>DroEre_CAF1 21572 111 - 1
UGGUGGCAGAUAAGUAGCUGGUUGACAUUCCGGAUCCCUUGAUCCGGAAAAACACCUUGGCUUUGGUGUUG---------CCGGCGGCGUAACGCGACAGCGAGGAUCAGUUGAGCCCAA
..(.(((......((.((((((.....(((((((((....))))))))).((((((........)))))))---------))))).))....(((....)))............)))).. ( -42.00)
>DroWil_CAF1 28844 105 - 1
UGAUGGAAGAUAUGUGGC------GCAUUCUGGGUCGGUUGAACCAGGAUAGCAUCUUGGUUUGAGAGUAGUUCUUGAUUCUUGAG---------GACAACGGGGAUCAGUGGAUCCUGG
.(((...(((.(((....------.))))))..)))..(..(((((((((...)))))))))..)..((.(((((..(...)..))---------))).)).((((((....)))))).. ( -30.70)
>consensus
UGGUGGAAGAUAAGUAGCUGGUUGACAUUCCGGAUCCCUUGAUCCGGAAAAACACCUUGGCUUUAGUGUUG_________CCGGCGG_G_AACGCGACAGCGAGGAUCAGUUGAGCCCAA
.((((........((.........)).(((((((((....)))))))))...))))..((((.....................(((......)))..((((........))))))))... (-21.78 = -22.23 +   0.45)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,352,433 – 20,352,544
Length 111
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 67.24
Mean single sequence MFE -25.21
Consensus MFE -17.45
Energy contribution -15.23
Covariance contribution -2.21
Combinations/Pair 1.33
Mean z-score -1.23
Structure conservation index 0.69
SVM decision value 1.32
SVM RNA-class probability 0.941464
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20352433 111 + 23771897
---------CAACAAAAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACCUAUCUUCCACCAACAACGAGGAGAUCUUCGACCAAGCCGCGUUGCUAUCCCG
---------((((.....(((...(((....(((((((((....))))))))).....))).)))...................(((((....)))))..........))))........ ( -28.90)
>DroEre_CAF1 21612 111 + 1
---------CAACACCAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACUUAUCUGCCACCAACCACAAGGAGGUCUUCGCCCAAGCCGCGUUGCUAUCCAG
---------.((((((........)))))).(((((((((....))))))))).(.(((((.(((........(((.((........)).))).........))).).)))))....... ( -31.03)
>DroWil_CAF1 28875 114 + 1
AAUCAAGAACUACUCUCAAACCAAGAUGCUAUCCUGGUUCAACCGACCCAGAAUGC------GCCACAUAUCUUCCAUCAACCACAAGACUACCGGUAACUAAACCAAGAUGUUACCCUG
......................((((((((((.((((.((....)).)))).))).------)).....)))))....................((((((...........))))))... ( -15.70)
>consensus
_________CAACACAAAAGCCAAGGUGUUUUUCCGGAUCAAGGGAUCCGGAAUGUCAACCAGCUACAUAUCUUCCACCAACCACAAGGAGAUCUUCGACCAAGCCGCGUUGCUAUCCAG
..................(((...((((...(((((((((....))))))))).((......))...........)))).........(((...)))..............)))...... (-17.45 = -15.23 +  -2.21)

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 12:50:27 2006