Locus 3083

Sequence ID X_DroMel_CAF1
Location 8,231,921 – 8,232,085
Length 164
Max. P 0.993205
window5041 window5042 window5043

overview

Window 1

Location 8,231,921 – 8,232,022
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 88.12
Mean single sequence MFE -38.43
Consensus MFE -28.73
Energy contribution -30.54
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -2.03
Structure conservation index 0.75
SVM decision value 0.71
SVM RNA-class probability 0.828941
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8231921 101 + 22224390
UCCCGCACCGGAUUCCUGGUCGGAUCCUUCCGCAAAAGCAAAGCGAAACGGGAGCGCCAGAGCCGAUCGAUGCGCAAAAGCAAGGACUCCAAAGAGGAGUC
(((((((((((....))))).(((....)))))....((...)).....))))((((..((.....))...)))).........((((((.....)))))) ( -33.20)
>DroSec_CAF1 132824 101 + 1
UCCCGCACCGAGUUCCUGGUCGGAUCCUUGCGCAAAAACAAAGCGAAGCGGGAGCGCCAGAGCCGCUCGAUGCGCAAAAGCAGGGACUCCAAAGAGGAGUC
(((((((.(((((.(((((.((..((((..(((.........)))....)))).)))))).)..))))).)))((....)).))))((((.....)))).. ( -38.70)
>DroEre_CAF1 121934 101 + 1
UCCCGCACCGAGAUCCUGGUCGGAUCCUUGCGCAAGAGCAAGGCGAAGCGGGAGCGCAAAAGCCGUUCGAUGCGCAAGUGCAUGGACUCCAAAGAGGAGUC
....((((...(((((.....))))).(((((((.((((..(((...(((....)))....)))))))..)))))))))))...((((((.....)))))) ( -44.20)
>DroYak_CAF1 122994 101 + 1
UCCCGCACCGAGAUCCUGGUCGGUUCCUUGCGCAAGAGCAAGGCGAGGCGGGAGCGCAAAAGUCGUUCGAUGCGCAAAAGCAGCGACUCCAAAGAGGACAA
((((((..((.(((....)))....((((((......))))))))..))))))........(((..(((.(((......))).)))(((....)))))).. ( -37.60)
>consensus
UCCCGCACCGAGAUCCUGGUCGGAUCCUUGCGCAAAAGCAAAGCGAAGCGGGAGCGCAAAAGCCGUUCGAUGCGCAAAAGCAGGGACUCCAAAGAGGAGUC
((((((.((((........))))..((((((......))))))....))))))((((..............)))).........((((((.....)))))) (-28.73 = -30.54 +   1.81)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,231,921 – 8,232,022
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 88.12
Mean single sequence MFE -38.93
Consensus MFE -32.97
Energy contribution -33.35
Covariance contribution 0.38
Combinations/Pair 1.13
Mean z-score -1.65
Structure conservation index 0.85
SVM decision value 0.50
SVM RNA-class probability 0.761776
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8231921 101 - 22224390
GACUCCUCUUUGGAGUCCUUGCUUUUGCGCAUCGAUCGGCUCUGGCGCUCCCGUUUCGCUUUGCUUUUGCGGAAGGAUCCGACCAGGAAUCCGGUGCGGGA
((((((.....)))))).........((((...((.....))..))))((((((.((..(((((....))))).((((((.....)).)))))).)))))) ( -37.20)
>DroSec_CAF1 132824 101 - 1
GACUCCUCUUUGGAGUCCCUGCUUUUGCGCAUCGAGCGGCUCUGGCGCUCCCGCUUCGCUUUGUUUUUGCGCAAGGAUCCGACCAGGAACUCGGUGCGGGA
((((((.....))))))((((((((((((((.(((((((....((((....)))))))).)))....)))))))))..((((........)))).))))). ( -41.10)
>DroEre_CAF1 121934 101 - 1
GACUCCUCUUUGGAGUCCAUGCACUUGCGCAUCGAACGGCUUUUGCGCUCCCGCUUCGCCUUGCUCUUGCGCAAGGAUCCGACCAGGAUCUCGGUGCGGGA
((((((.....)))))).........(((((............)))))((((((.(((.(((((......)))))(((((.....))))).))).)))))) ( -42.70)
>DroYak_CAF1 122994 101 - 1
UUGUCCUCUUUGGAGUCGCUGCUUUUGCGCAUCGAACGACUUUUGCGCUCCCGCCUCGCCUUGCUCUUGCGCAAGGAACCGACCAGGAUCUCGGUGCGGGA
..((((((....)))(((.(((......))).)))..)))........((((((....((((((......)))))).(((((........))))))))))) ( -34.70)
>consensus
GACUCCUCUUUGGAGUCCCUGCUUUUGCGCAUCGAACGGCUCUGGCGCUCCCGCUUCGCCUUGCUCUUGCGCAAGGAUCCGACCAGGAACUCGGUGCGGGA
((((((.....)))))).........((((...((.....))..))))((((((.(((((((((......)))))).(((.....)))...))).)))))) (-32.97 = -33.35 +   0.38)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,231,982 – 8,232,085
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.67
Mean single sequence MFE -39.68
Consensus MFE -20.98
Energy contribution -22.46
Covariance contribution 1.48
Combinations/Pair 1.32
Mean z-score -2.30
Structure conservation index 0.53
SVM decision value 2.38
SVM RNA-class probability 0.993205
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8231982 103 + 22224390
GCCGAUCGAUGCGCAAAAGCAAGGACUCCAAAGAGGAGUCUCAUCU---GGUCGAUAUGGGCAUGUUCAGUGGCCGUUCCAUGAGCAUGCCACCCCGUC-----CAUCUGC---------
((.(((.((((.((....))..(((((((.....))))))))))).---((.((.....((((((((((.(((.....)))))))))))))....)).)-----)))).))--------- ( -39.90)
>DroSec_CAF1 132885 103 + 1
GCCGCUCGAUGCGCAAAAGCAGGGACUCCAAAGAGGAGUCCCAUCU---GGUGGACAUGGGCAUGUUCAGUGGCCGUUCCAUGAGCAUGCCAUCCCGUC-----CAUCCGC---------
((.((.....))))....((.((((((((.....))))))))....---(((((((...((((((((((.(((.....))))))))))))).....)))-----)))).))--------- ( -50.00)
>DroEre_CAF1 121995 103 + 1
GCCGUUCGAUGCGCAAGUGCAUGGACUCCAAAGAGGAGUCCCAUCU---GAUGGACAUGGGCAUGUUCAGCGGCCGAUCCAUGAGCAUGCCACCCCGUC-----CAUCCGC---------
.......((((.((....))..(((((((.....))))))))))).---(((((((...((((((((((..((.....)).)))))))))).....)))-----))))...--------- ( -45.70)
>DroWil_CAF1 131861 109 + 1
-UUAAAUGAUUUGGAAAUAC-------CGCAAGAUGAUAAUGAUAA---UGGCGAUAUGACAUUGUUUAGUGGUCGCUCAAUGAGUUUGCCACCAAGGCCCCUGCAUUCGGCGCUAAAAC
-........(((((....((-------(((.....(((((((...(---((....)))..)))))))..)))))((((.((((.....(((.....))).....)))).))))))))).. ( -23.00)
>DroYak_CAF1 123055 106 + 1
GUCGUUCGAUGCGCAAAAGCAGCGACUCCAAAGAGGACAACCACCUGCUGGUGGACAUGGGCAUGUUCAGUGGCCGCUCCAUGAGCAUGCCACCCCGAC-----CAUCUGC---------
(((((....(((......)))))))).....(((((....(((((....))))).....((((((((((.(((.....))))))))))))).......)-----).)))..--------- ( -39.80)
>consensus
GCCGAUCGAUGCGCAAAAGCAGGGACUCCAAAGAGGAGUCCCAUCU___GGUGGACAUGGGCAUGUUCAGUGGCCGCUCCAUGAGCAUGCCACCCCGUC_____CAUCCGC_________
.......((((............((((((.....))))))(((((....))))).....((((((((((.(((.....))))))))))))).............))))............ (-20.98 = -22.46 +   1.48)

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 10:50:33 2006