Locus 3004

Sequence ID 2R_DroMel_CAF1
Location 10,361,492 – 10,361,707
Length 215
Max. P 0.844228
window4959 window4960 window4961

overview

Window 9

Location 10,361,492 – 10,361,597
Length 105
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 75.76
Mean single sequence MFE -46.09
Consensus MFE -24.24
Energy contribution -21.80
Covariance contribution -2.44
Combinations/Pair 1.50
Mean z-score -1.94
Structure conservation index 0.53
SVM decision value 0.76
SVM RNA-class probability 0.844228
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10361492 105 + 20766785
GGUGGUGCAGGUG---CUCAUUGGGUGGCGGUGGAGGCGGUUGCUGGUGGGCAGCAUGAAGGGCCUGAGCGGCCUCCACAUGCUUGCGUUGCUCGCUUUGCUGUUGCU
(((((.((....)---)))))).((..((((..(((.(((..((....(.((((((((..(((((.....)))))...))))).))).).))))))))..))))..)) ( -42.20)
>DroVir_CAF1 96415 99 + 1
GAUGAUGCAAAUGCUGCUCAUUGGGCGGCGG---UGGCGGCUGCUGAUGGGCGGCAUGCUGCUGCUGGUGGGCAGCCUCAAGCUUGCGCUGUUCGCUUUGCU------
..(((.((...(((((((.....))))))).---..))(((((((.((.((((((.....)))))).)).))))))))))(((..(((.....)))...)))------ ( -49.00)
>DroGri_CAF1 104225 99 + 1
GAUGAUGCAAAUGCUGCUCAUUUGACGGCGG---CGGCGGCUGCUGGUGGGCAGCAUGCUGCUGCUGAUGCGCCGCCUCCAGUUUACGCUGUUCGUUCUGCU------
(((((.(((.....)))))))).((((((((---.((((((.((..((.((((((.....)))))).)))))))))).)).(....))))))).........------ ( -41.90)
>DroSec_CAF1 80341 105 + 1
GGUGGUGCAGAUG---CUCAUUGGGUGGCGGUGGAGGCGGUUGCUGGUGGGCAGCAUGAAGAGCCUGAGCGGCCUCCACAUGCUUGCGUUGCUCGCUCUGCUGUUGCU
(((..((((((.(---(.....(((..(((((((((((.((((((....)))))).......((....)).)))))))).......)))..)))))))))).)..))) ( -42.11)
>DroSim_CAF1 76369 105 + 1
GGUGAUGCAGGUG---CUCAUUGGGUGGCGGUGGAGGAGGUUGCUGGUGGGCAGCAUGAAGGGCCUGUGCAGCCUCCACAUGCUUGCGUUGCUCGCUCUGCUGUUGCU
(((((.((....)---)))))).((..((((..(((((((((((..(..(((..(.....).)))..))))))))))........(((.....)))))..))))..)) ( -45.10)
>DroMoj_CAF1 110020 99 + 1
GAUGAUGCAAGUGCUGCUCAUUGGGUGGCGG---CGGGGGCUGCUGGUGAGCGGCGUGCUGCUGCUGAUGGGCAGCCUCCAGCUUGCGCUGCUCACUCUGCU------
(((((.(((.....))))))))(((((((((---(((((((((((.((.((((((.....)))))).)).)))))))))).(....)))))).)))))....------ ( -56.20)
>consensus
GAUGAUGCAAAUG___CUCAUUGGGUGGCGG___AGGCGGCUGCUGGUGGGCAGCAUGAAGCGCCUGAGCGGCCGCCACAAGCUUGCGCUGCUCGCUCUGCU______
......(((((((.....))))((((((((.........((((((....)))))).....(((.((....)).)))..........))))))))....)))....... (-24.24 = -21.80 +  -2.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,361,492 – 10,361,597
Length 105
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 75.76
Mean single sequence MFE -33.15
Consensus MFE -15.96
Energy contribution -15.63
Covariance contribution -0.33
Combinations/Pair 1.32
Mean z-score -1.88
Structure conservation index 0.48
SVM decision value 0.25
SVM RNA-class probability 0.652606
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10361492 105 - 20766785
AGCAACAGCAAAGCGAGCAACGCAAGCAUGUGGAGGCCGCUCAGGCCCUUCAUGCUGCCCACCAGCAACCGCCUCCACCGCCACCCAAUGAG---CACCUGCACCACC
.(((...((...(((.....)))..((..((((((((.((....))......(((((.....)))))...)))))))).))..........)---)...)))...... ( -32.20)
>DroVir_CAF1 96415 99 - 1
------AGCAAAGCGAACAGCGCAAGCUUGAGGCUGCCCACCAGCAGCAGCAUGCCGCCCAUCAGCAGCCGCCA---CCGCCGCCCAAUGAGCAGCAUUUGCAUCAUC
------.(((((((....(((....)))...((((((......((.((.....)).))......))))))))..---..((.((.......)).)).)))))...... ( -31.60)
>DroGri_CAF1 104225 99 - 1
------AGCAGAACGAACAGCGUAAACUGGAGGCGGCGCAUCAGCAGCAGCAUGCUGCCCACCAGCAGCCGCCG---CCGCCGUCAAAUGAGCAGCAUUUGCAUCAUC
------.((((((((.....)))....((..((((((((....)).((.((.(((((.....))))))).)).)---)))))..))...........)))))...... ( -34.90)
>DroSec_CAF1 80341 105 - 1
AGCAACAGCAGAGCGAGCAACGCAAGCAUGUGGAGGCCGCUCAGGCUCUUCAUGCUGCCCACCAGCAACCGCCUCCACCGCCACCCAAUGAG---CAUCUGCACCACC
.......((((((((.....)))..((..((((((((.((....))......(((((.....)))))...)))))))).))...........---..)))))...... ( -35.10)
>DroSim_CAF1 76369 105 - 1
AGCAACAGCAGAGCGAGCAACGCAAGCAUGUGGAGGCUGCACAGGCCCUUCAUGCUGCCCACCAGCAACCUCCUCCACCGCCACCCAAUGAG---CACCUGCAUCACC
.......((((.(((.....)))..((..(((((((..((....))......(((((.....)))))....))))))).))...........---...))))...... ( -28.40)
>DroMoj_CAF1 110020 99 - 1
------AGCAGAGUGAGCAGCGCAAGCUGGAGGCUGCCCAUCAGCAGCAGCACGCCGCUCACCAGCAGCCCCCG---CCGCCACCCAAUGAGCAGCACUUGCAUCAUC
------.(((.((((.(((((....)))((.((((((.....(((.((.....)).))).....)))))).)))---).((((.....)).))..)))))))...... ( -36.70)
>consensus
______AGCAGAGCGAGCAACGCAAGCAUGAGGAGGCCCAUCAGCAGCAGCAUGCUGCCCACCAGCAACCGCCU___CCGCCACCCAAUGAG___CACCUGCAUCACC
.......((((.(((.....)))........((.(((......((....)).(((((.....)))))............))).)).............))))...... (-15.96 = -15.63 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,361,597 – 10,361,707
Length 110
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 81.27
Mean single sequence MFE -38.58
Consensus MFE -22.21
Energy contribution -24.05
Covariance contribution 1.84
Combinations/Pair 1.27
Mean z-score -1.83
Structure conservation index 0.58
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10361597 110 - 20766785
AUCUGCAGGCGCAGUUGCUGUGCCCAUUCAUACCUCCCAGCAGCUGCCUCUUUUCCAACUUCAGAAGAAGUACGAGGAGAACAGCGUGGAGAAGGUUCAUCAGCAGCAAC
..((((.(((((((...))))))).......((((((((...((((..(((((((..(((((....)))))..))))))).)))).))).).))))......)))).... ( -39.20)
>DroSec_CAF1 80446 110 - 1
AUCUGCAGGCGCAGUUGUUGUGCCCAUUCAUGCCUCCCAGCAGCUGCCUCUUUUCCAGCUUCAGAAGAAGUACGAGGAGAACAGCGUGGAGAAGGUUCAUCAGCAGCAAC
..((((.(((((((...))))))).......((((((((...((((..(((((((..(((((....)))))..))))))).)))).))).).))))......)))).... ( -37.80)
>DroSim_CAF1 76474 110 - 1
AUCUGCAGGCGCAGUUGCUGUGCCCAUUCAUGCCUCCCAGCAGCUGCCUCUUUUCCAACUUCAGAAGAAGUACGAAGAGACCAGCGUGGAGAAGGUUCAUCAGCAGCAAC
..((((.(((((((...))))))).......((((((((...((((..(((((((..(((((....)))))..))))))).)))).))).).))))......)))).... ( -39.10)
>DroEre_CAF1 78107 110 - 1
GUCUGCAGGGGCAGUUGCUGUGCCCAUCCAUGCCUCCCAGCAGCUGCCUCUUUUCCAGCUUCAGAAGAAGUACGAGGAGAACACCGUGGAGAAGGUUCAUCAGCAGCAAC
(.((((..((((((((((((.((........))....))))))))))))(((((((((((((....)))))....((......)).))))))))........)))))... ( -42.50)
>DroAna_CAF1 80440 106 - 1
AGGUGCUGGAUCCGUUUCUGUUCCUCUACACGGUUCUCAGCAGCUACCGAUCUUCCAGUUGCAAAAGAAGUACGAGGAGAGUGCCGUGGACAAAGUCCACCAGCAG----
.((..(((((......))).(((((((((....((((..((((((...........))))))...))))))).))))))))..))((((((...))))))......---- ( -32.20)
>DroPer_CAF1 85985 106 - 1
-UCUGCCGCCUCG---GCCGUGUCCCUACACGUCCCCCAGCAGCUGCCGCUCUUCCAGCUUCAGAAGAAGUACGAGGAGAGCGCCGCCGAGAAGGCUCACCAGCAGCAGC
-.((((.((((((---(((((((....))))).............(.(((((((((.(((((....)))))..).)))))))).)))))))..((....)).)).)))). ( -40.70)
>consensus
AUCUGCAGGCGCAGUUGCUGUGCCCAUUCAUGCCUCCCAGCAGCUGCCUCUUUUCCAGCUUCAGAAGAAGUACGAGGAGAACACCGUGGAGAAGGUUCAUCAGCAGCAAC
..((((..((((((((((((.................)))))))))).(((((((..(((((....)))))..)))))))...))(((((.....)))))..)))).... (-22.21 = -24.05 +   1.84)

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 10:45:03 2006