Locus 508

Sequence ID 3R_DroMel_CAF1
Location 1,898,741 – 1,898,859
Length 118
Max. P 0.880889
window813 window814 window815 window816

overview

Window 3

Location 1,898,741 – 1,898,831
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 77.56
Mean single sequence MFE -30.07
Consensus MFE -17.00
Energy contribution -16.69
Covariance contribution -0.30
Combinations/Pair 1.29
Mean z-score -2.00
Structure conservation index 0.57
SVM decision value 0.84
SVM RNA-class probability 0.864397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1898741 90 + 27905053
GGCA----ACUGGCAUCGGGAGGCGUUGGCCAUAAACGAUGGCAACGACCACGCCUCCAUUCACAUGGGG-CAAAAAAUUGCCUAAUUUAUAAAG-
((((----((((....)))..(((((((.((((.....))))))))).))..(((.((((....))))))-)......)))))............- ( -29.80)
>DroPse_CAF1 44412 87 + 1
CGUACGAUACU---------GGGCGUUGCUAAUAAAUGAUGGCAGCGGGCACGCCCCCAUUCACAUGAGGACACGAGAUUGCCUAAUUUAUUUAUG
((((.((((.(---------(((((((((((........)))))))(((....)))........................)))))...)))))))) ( -20.30)
>DroSec_CAF1 57016 90 + 1
GGCA----ACUGGCAUCGGGGGGCGUUGGCCAUAAACGAUGCCAGCGACCACGCCCCCAUUCACAUGAGG-CAGCAAAUUGCCUAAUUUAUAAAG-
((((----((((((((((...(((....))).....))))))))).......(((..(((....))).))-)......)))))............- ( -32.70)
>DroSim_CAF1 57839 90 + 1
GGCA----ACUGGCAUCGGGGGGCGUUGGCCAUAAACGAUGGCAGCGACCACGCCCCCAUUCACAUGAGG-CAGCAAAUUGCCUAAUUUAUAAAG-
((((----(...((....((((((((..(((((.....))))).......)))))))).(((....))).-..))...)))))............- ( -33.10)
>DroEre_CAF1 59109 90 + 1
GGUC----ACUGGCAUCGGGGGGCGUGAGCCCUAAACGACGGCAGCGACCACGCCCCCAUUCACAUGGGA-CGGCAAAUGGCCUAAUUUAUAAAG-
((((----.(((.(.(((.(((((....)))))...))).).))).))))..((((((((....))))).-.)))....................- ( -40.70)
>DroPer_CAF1 44806 87 + 1
CGUACGAUACU---------GGGCGUUGCUAAUAAAUGAUGGCAGCGGGCACGCCCCCAUUCACAUGAGGACAUGCGAUUGCCUAAUUUAUUUAUG
((((.((((.(---------(((((((((((........)))))))(((....)))....((.((((....)))).))..)))))...)))))))) ( -23.80)
>consensus
GGCA____ACUGGCAUCGGGGGGCGUUGGCCAUAAACGAUGGCAGCGACCACGCCCCCAUUCACAUGAGG_CAGCAAAUUGCCUAAUUUAUAAAG_
((((..............((((((((.((...................)))))))))).(((....)))..........))))............. (-17.00 = -16.69 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 4

Location 1,898,741 – 1,898,831
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 77.56
Mean single sequence MFE -30.68
Consensus MFE -16.69
Energy contribution -17.19
Covariance contribution 0.50
Combinations/Pair 1.25
Mean z-score -2.05
Structure conservation index 0.54
SVM decision value 0.80
SVM RNA-class probability 0.853207
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1898741 90 - 27905053
-CUUUAUAAAUUAGGCAAUUUUUUG-CCCCAUGUGAAUGGAGGCGUGGUCGUUGCCAUCGUUUAUGGCCAACGCCUCCCGAUGCCAGU----UGCC
-............(((((((.((..-(.....)..)).((((((((((((((.((....))..)))))).)))))))).......)))----)))) ( -30.90)
>DroPse_CAF1 44412 87 - 1
CAUAAAUAAAUUAGGCAAUCUCGUGUCCUCAUGUGAAUGGGGGCGUGCCCGCUGCCAUCAUUUAUUAGCAACGCCC---------AGUAUCGUACG
....(((((((..((((....(((((((((((....))))))))))).....))))...)))))))..........---------........... ( -20.30)
>DroSec_CAF1 57016 90 - 1
-CUUUAUAAAUUAGGCAAUUUGCUG-CCUCAUGUGAAUGGGGGCGUGGUCGCUGGCAUCGUUUAUGGCCAACGCCCCCCGAUGCCAGU----UGCC
-............(((((((.((..-..((....))..(((((((((((((..(((...)))..))))).))))))))....)).)))----)))) ( -34.40)
>DroSim_CAF1 57839 90 - 1
-CUUUAUAAAUUAGGCAAUUUGCUG-CCUCAUGUGAAUGGGGGCGUGGUCGCUGCCAUCGUUUAUGGCCAACGCCCCCCGAUGCCAGU----UGCC
-............(((((((.((..-..((....))..(((((((((((((..((....))...))))).))))))))....)).)))----)))) ( -33.60)
>DroEre_CAF1 59109 90 - 1
-CUUUAUAAAUUAGGCCAUUUGCCG-UCCCAUGUGAAUGGGGGCGUGGUCGCUGCCGUCGUUUAGGGCUCACGCCCCCCGAUGCCAGU----GACC
-............(((.....)))(-((((((....)).)))))..((((((((.(((((....((((....))))..))))).))))----)))) ( -37.60)
>DroPer_CAF1 44806 87 - 1
CAUAAAUAAAUUAGGCAAUCGCAUGUCCUCAUGUGAAUGGGGGCGUGCCCGCUGCCAUCAUUUAUUAGCAACGCCC---------AGUAUCGUACG
....(((((((..((((...((((((((((((....))))))))))))....))))...)))))))..........---------........... ( -27.30)
>consensus
_CUUUAUAAAUUAGGCAAUUUGCUG_CCUCAUGUGAAUGGGGGCGUGGUCGCUGCCAUCGUUUAUGGCCAACGCCCCCCGAUGCCAGU____UACC
.............((((......)).))..........((((((((((((...............)))).)))))))).................. (-16.69 = -17.19 +   0.50)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,898,756 – 1,898,859
Length 103
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 76.97
Mean single sequence MFE -31.45
Consensus MFE -20.01
Energy contribution -20.20
Covariance contribution 0.19
Combinations/Pair 1.17
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value 0.91
SVM RNA-class probability 0.880889
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1898756 103 + 27905053
GAGGCGUUGGCCAUAAACGAUGGCAACGACCACGCCUCCAUUCACAUGGGGCAAAAAAUUGCCUAAUUUAUAAAGUAG-------GGUCGGUAGAUUUAACAUUAAACAU
(((((((..(((((.....))))).......))))))).......(((((((((....))))))..........((..-------((((....))))..))......))) ( -28.30)
>DroSec_CAF1 57031 92 + 1
GGGGCGUUGGCCAUAAACGAUGCCAGCGACCACGCCCCCAUUCACAUGAGGCAGCAAAUUGCCUAAUUUAUAAAGUAGAAGAUG-GGUCGGUA-----------------
..(((((((((.((.....))))))))).))..(((((((((......((((((....))))))..(((((...))))).))))-))..))).----------------- ( -28.80)
>DroSim_CAF1 57854 92 + 1
GGGGCGUUGGCCAUAAACGAUGGCAGCGACCACGCCCCCAUUCACAUGAGGCAGCAAAUUGCCUAAUUUAUAAAGUAGAAGACG-GCUCGGUA-----------------
(((((((..(((((.....))))).......)))))))..........((((((....))))))....(((..(((........-)))..)))----------------- ( -26.40)
>DroEre_CAF1 59124 107 + 1
GGGGCGUGAGCCCUAAACGACGGCAGCGACCACGCCCCCAUUCACAUGGGACGGCAAAUGGCCUAAUUUAUAAAGUGGCAGAUAUGGUCGGUACCG-UAGC--GAAACAU
(((((....)))))...((((((.(.((((((.((((((((....)))))..))).....(((.............))).....)))))).).)))-)..)--)...... ( -42.32)
>consensus
GGGGCGUUGGCCAUAAACGAUGGCAGCGACCACGCCCCCAUUCACAUGAGGCAGCAAAUUGCCUAAUUUAUAAAGUAGAAGAUG_GGUCGGUA_________________
(((((((..(((((.....))))).......)))))))..........((((((....)))))).............................................. (-20.01 = -20.20 +   0.19)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,898,756 – 1,898,859
Length 103
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 76.97
Mean single sequence MFE -31.13
Consensus MFE -21.73
Energy contribution -22.22
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -1.74
Structure conservation index 0.70
SVM decision value 0.70
SVM RNA-class probability 0.826578
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1898756 103 - 27905053
AUGUUUAAUGUUAAAUCUACCGACC-------CUACUUUAUAAAUUAGGCAAUUUUUUGCCCCAUGUGAAUGGAGGCGUGGUCGUUGCCAUCGUUUAUGGCCAACGCCUC
.........................-------...............(((((....)))))((((....))))((((((((((((.((....))..)))))).)))))). ( -26.80)
>DroSec_CAF1 57031 92 - 1
-----------------UACCGACC-CAUCUUCUACUUUAUAAAUUAGGCAAUUUGCUGCCUCAUGUGAAUGGGGGCGUGGUCGCUGGCAUCGUUUAUGGCCAACGCCCC
-----------------........-..........((((((....(((((......)))))..))))))..((((((((((((..(((...)))..))))).))))))) ( -27.90)
>DroSim_CAF1 57854 92 - 1
-----------------UACCGAGC-CGUCUUCUACUUUAUAAAUUAGGCAAUUUGCUGCCUCAUGUGAAUGGGGGCGUGGUCGCUGCCAUCGUUUAUGGCCAACGCCCC
-----------------........-..........((((((....(((((......)))))..))))))..((((((((((((..((....))...))))).))))))) ( -27.10)
>DroEre_CAF1 59124 107 - 1
AUGUUUC--GCUA-CGGUACCGACCAUAUCUGCCACUUUAUAAAUUAGGCCAUUUGCCGUCCCAUGUGAAUGGGGGCGUGGUCGCUGCCGUCGUUUAGGGCUCACGCCCC
.......--((.(-(((((.(((((((....(((.............(((.....)))..(((((....))))))))))))))).)))))).))...((((....)))). ( -42.70)
>consensus
_________________UACCGACC_CAUCUUCUACUUUAUAAAUUAGGCAAUUUGCUGCCCCAUGUGAAUGGGGGCGUGGUCGCUGCCAUCGUUUAUGGCCAACGCCCC
....................................((((((....(((((......)))))..))))))..((((((((((((..((....))...))))).))))))) (-21.73 = -22.22 +   0.50)

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 09:44:52 2006