Locus 8278

Sequence ID 3R_DroMel_CAF1
Location 22,142,169 – 22,142,369
Length 200
Max. P 0.999543
window13349 window13350 window13351 window13352

overview

Window 9

Location 22,142,169 – 22,142,289
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.00
Mean single sequence MFE -40.33
Consensus MFE -37.74
Energy contribution -37.22
Covariance contribution -0.52
Combinations/Pair 1.11
Mean z-score -2.41
Structure conservation index 0.94
SVM decision value 3.70
SVM RNA-class probability 0.999543
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22142169 120 + 27905053
UGGCACUUUGUGCGCGAAUUUAUUCUUUCUUUUGCCCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCUGGGGUUUAGCUACGGCAUUUGGCCAUUUAAGAGG
..(((.((((((((((((............)))))..)).))))).))).(((((......(((((((((..((.........))..)).....((....))...)))))))...))))) ( -39.20)
>DroSec_CAF1 72564 120 + 1
UGGCACUUUGUGUGCGAAUUUAUUCUUUCUUUUGCCCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCUGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGG
..(((.((((((((((((............)))))..)).))))).))).(((((......(((((((((..((.........))..))....(((....)))..)))))))...))))) ( -38.30)
>DroSim_CAF1 65571 120 + 1
UGGCACUUUGUGCGCGAAUUUAUUCUUUCUUUUGCCCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGG
..(((.((((((((((((............)))))..)).))))).))).(((((......(((((((((((((.........))))))....(((....)))..)))))))...))))) ( -41.40)
>DroEre_CAF1 67830 120 + 1
UGGCACUUUGUGCGCGAAUUUAUUCUUUCUUUUGCUCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAGGAGG
..(((.((((((((((((............)))))..)).))))).))).(((((......(((((((((((((.........))))))....(((....)))..)))))))...))))) ( -41.40)
>DroYak_CAF1 65139 120 + 1
UGGCACUUUGUGCGCGAAUUUAUUCCUUCUUUAGCUCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGG
..(((.((((((.((((..................)))))))))).))).(((((......(((((((((((((.........))))))....(((....)))..)))))))...))))) ( -41.37)
>consensus
UGGCACUUUGUGCGCGAAUUUAUUCUUUCUUUUGCCCGCUGCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGG
..(((.((((((((((((............)))))..)).))))).))).(((((......(((((((...(((...)))...((((..((...))..))))...)))))))...))))) (-37.74 = -37.22 +  -0.52)

alignment

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secondary structure

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Window 0

Location 22,142,169 – 22,142,289
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.00
Mean single sequence MFE -31.66
Consensus MFE -28.63
Energy contribution -28.79
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.39
Structure conservation index 0.90
SVM decision value 0.64
SVM RNA-class probability 0.807017
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22142169 120 - 27905053
CCUCUUAAAUGGCCAAAUGCCGUAGCUAAACCCCAGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGGGCAAAAGAAAGAAUAAAUUCGCGCACAAAGUGCCA
(((((...(((((((...(((((.(((.......)))....)))..))....)))))))......))))).((..(((((.....))))).....(((....)))))((((...)))).. ( -30.70)
>DroSec_CAF1 72564 120 - 1
CCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCAGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGGGCAAAAGAAAGAAUAAAUUCGCACACAAAGUGCCA
..((((..(((((.....)))))......((((.......((..(((((....)).)))..)).....(.(((.....))).)))))..))))............((((.....)))).. ( -29.70)
>DroSim_CAF1 65571 120 - 1
CCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGGGCAAAAGAAAGAAUAAAUUCGCGCACAAAGUGCCA
(((((...((((((...(((((..((...))..)))))...((........))))))))......))))).((..(((((.....))))).....(((....)))))((((...)))).. ( -32.90)
>DroEre_CAF1 67830 120 - 1
CCUCCUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGAGCAAAAGAAAGAAUAAAUUCGCGCACAAAGUGCCA
........((((((...(((((..((...))..)))))...((........)))))))).........((..(....(((.(((((................))))))))....)..)). ( -32.09)
>DroYak_CAF1 65139 120 - 1
CCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGAGCUAAAGAAGGAAUAAAUUCGCGCACAAAGUGCCA
(((((...((((((...(((((..((...))..)))))...((........))))))))......))))).(((.((((..(((((................)))))...)))).))).. ( -32.89)
>consensus
CCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAAGACGAUGCCAAGUGGCCAUAAUCACAGAGGUGCAAUUUGCAGCGGGCAAAAGAAAGAAUAAAUUCGCGCACAAAGUGCCA
(((((...(((((((..((.(((..(...((....))...)...))).))..)))))))......))))).(((.((((..(((((................)))))...)))).))).. (-28.63 = -28.79 +   0.16)

alignment

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secondary structure

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Window 1

Location 22,142,209 – 22,142,329
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.67
Mean single sequence MFE -43.10
Consensus MFE -41.24
Energy contribution -40.52
Covariance contribution -0.72
Combinations/Pair 1.12
Mean z-score -2.07
Structure conservation index 0.96
SVM decision value 3.03
SVM RNA-class probability 0.998206
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22142209 120 + 27905053
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCUGGGGUUUAGCUACGGCAUUUGGCCAUUUAAGAGGUGUUCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((((..((.........))..)).....((....))...)))))))...))))))))....((((.((..(.((....)))...)).))))... ( -41.00)
>DroSec_CAF1 72604 120 + 1
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCUGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGGUGUUCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((((..((.........))..))....(((....)))..)))))))...))))))))....((((.((..(.((....)))...)).))))... ( -41.50)
>DroSim_CAF1 65611 120 + 1
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGGUGUUCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((((((((.........))))))....(((....)))..)))))))...))))))))....((((.((..(.((....)))...)).))))... ( -43.20)
>DroEre_CAF1 67870 120 + 1
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAGGAGGUGCGCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((((((((.........))))))....(((....)))..)))))))...))))))))....((((.((..(.((....)))...)).))))... ( -46.00)
>DroYak_CAF1 65179 120 + 1
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGGUGUGCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((((((((.........))))))....(((....)))..)))))))...))))))))....((((.((..(.((....)))...)).))))... ( -43.80)
>consensus
GCAAAUUGCACCUCUGUGAUUAUGGCCACUUGGCAUCGUCUUCGCCGGGGCUUUGCUACGGCAUUUGGCCAUUUAAGAGGUGUUCCCGGGAUGGUGGCUCUAAUGACAUUCUUUCCCCCA
.......((((((((......(((((((...(((...)))...((((..((...))..))))...)))))))...))))))))....((((.((..(.((....)))...)).))))... (-41.24 = -40.52 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,142,249 – 22,142,369
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -38.32
Consensus MFE -33.10
Energy contribution -32.94
Covariance contribution -0.16
Combinations/Pair 1.10
Mean z-score -1.36
Structure conservation index 0.86
SVM decision value 0.34
SVM RNA-class probability 0.697427
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22142249 120 - 27905053
CGGGCAUGGCUCCUAAUGAACAGUGUCUAGUGCACAUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGAACACCUCUUAAAUGGCCAAAUGCCGUAGCUAAACCCCAGCGAA
.(..(((........)))..).((((.....)))).(((((((((...((.(((.((((.(.((((.......((.....)).......))))).)))).)))..))...))))))))). ( -37.24)
>DroSec_CAF1 72644 120 - 1
CAGGCAUGACUCCUAAUAAACAGUGUCUAGUGCAUUUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGAACACCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCAGCGAA
...(((((((..............)))..))))..((((((((((........((((((((((...((.....))......))))..))))))....(((....)))...)))))))))) ( -34.44)
>DroSim_CAF1 65651 120 - 1
CGGGCAUGGCUCCUAAUGAACAGUGUCUAGUGCAUUUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGAACACCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAA
..((..((((((.((((((.((.(.(((((((.....))))))).)......)))))))))))))))).(((((((............(((((.....))))).((...))))))).)). ( -39.10)
>DroEre_CAF1 67910 120 - 1
CGGGCUUGGCUCCUAAUGAACAAUGUCUAGUGCAUUUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGCGCACCUCCUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAA
..((..((((((.((((((....(.(((((((.....))))))).)........)))))))))))))).(((((((.((.....(((...(((.....))).)))....))))))).)). ( -39.80)
>DroYak_CAF1 65219 120 - 1
CGGGCAUGGCUCCUAAUGAACAGUGUCUAGUGCAUUUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGCACACCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAA
((((..((((((.((((((.((.(.(((((((.....))))))).)......))))))))))))))....))))(((.((.........)))))...(((((..((...))..))))).. ( -41.00)
>consensus
CGGGCAUGGCUCCUAAUGAACAGUGUCUAGUGCAUUUCGCUGGGGGAAAGAAUGUCAUUAGAGCCACCAUCCCGGGAACACCUCUUAAAUGGCCAAAUGCCGUAGCAAAGCCCCGGCGAA
.((((((...((.....))...))))))........(((((((((......(((.((((.(.((((.......((.....)).......))))).)))).))).......))))))))). (-33.10 = -32.94 +  -0.16)

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 13:07:42 2006