Locus 4936

Sequence ID 2R_DroMel_CAF1
Location 16,100,167 – 16,100,303
Length 136
Max. P 0.997123
window7910 window7911 window7912 window7913

overview

Window 0

Location 16,100,167 – 16,100,269
Length 102
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 67.42
Mean single sequence MFE -23.95
Consensus MFE -12.17
Energy contribution -13.12
Covariance contribution 0.95
Combinations/Pair 1.28
Mean z-score -2.76
Structure conservation index 0.51
SVM decision value 2.80
SVM RNA-class probability 0.997123
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16100167 102 + 20766785
UC------CUACGCAGGU----------AACUUUCUCGAAGUACUUAGUACCAGAAACGUGUACUUU-ACAUAAAC-AUAAAAAAUAACACUUUGCUGAUACCAGGCACUUGGGAAAAUC
.(------((....))).----------...((((((.((((.(((.(((.(((....((((.....-........-..........))))....))).))).))).))))))))))... ( -18.00)
>DroSec_CAF1 22074 99 + 1
UA------CCCCGCAGGU----------AAGUUUCUCAAAGGGCUUGGUUCCAGAAACGUGUACUAU-ACAA--AC-AC-AAAAAUUACACCUAUCUGAUACCAGGCACUUCCGAAAAUC
((------((.....)))----------)..((((...(((.(((((((..((((...(((((....-....--..-..-......)))))...))))..))))))).)))..))))... ( -24.27)
>DroSim_CAF1 22156 96 + 1
UA------CCCCGCAGGU----------AAGUUUCUCAAAGGGCUUGGUUCCAAAAAAGGGUACUAU-ACAA------C-AAAAAUUACACCUCUCUGAAACCAGGCACUUGCGAAAAUC
..------...(((((((----------......((....))((((((((.((....((((((....-....------.-......))).)))...)).)))))))))))))))...... ( -23.06)
>DroEre_CAF1 24050 99 + 1
UU------CUCCGUAGUC----------AUGUUUCUCAAAGUACCUAGUACCAGUAACGUGUACUUU-ACCCAA---AU-AAAAAUUACACCUUGCUGAUACUAUGCACUUGGGAAAAUC
..------..........----------...((((((((.((.(.(((((.((((((.(((((.(((-......---..-..))).))))).)))))).))))).).))))))))))... ( -24.80)
>DroYak_CAF1 21775 99 + 1
UC------CUCCGUAGUU----------AGGUUUCUCGAAGUACGUAGUACCAGUAACGUGUACUUU-AACCAA---AC-AAAAAUUACACCUUGCUGAUACUAAGCACUUGGGAAAAUC
.(------((........----------)))((((((.((((.(.(((((.((((((.(((((.(((-......---..-..))).))))).)))))).))))).).))))))))))... ( -25.30)
>DroAna_CAF1 22081 119 + 1
UAAAAUAUUCACACACUUAAUUCAGAAGAAUUGUUUCAAAAUACAUAGAGUCGGAACCGUGUACUUGUGCGAGAAUAAG-ACAAGAUACACGAUGCCGGUUCUAAGAAAUUAUGAACAAC
.......((((......((((((....))))))............((((..(((...(((((((((((.(........)-))))).))))))...)))..))))........)))).... ( -28.30)
>consensus
UA______CCCCGCAGGU__________AAGUUUCUCAAAGUACUUAGUACCAGAAACGUGUACUUU_ACAAAA___AC_AAAAAUUACACCUUGCUGAUACCAGGCACUUGGGAAAAUC
...............................((((...((((.(.(((((.((((((.(((((.......................))))).)))))).))))).).))))..))))... (-12.17 = -13.12 +   0.95)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,100,167 – 16,100,269
Length 102
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 67.42
Mean single sequence MFE -29.88
Consensus MFE -20.18
Energy contribution -20.07
Covariance contribution -0.10
Combinations/Pair 1.40
Mean z-score -2.76
Structure conservation index 0.68
SVM decision value 2.33
SVM RNA-class probability 0.992425
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16100167 102 - 20766785
GAUUUUCCCAAGUGCCUGGUAUCAGCAAAGUGUUAUUUUUUAU-GUUUAUGU-AAAGUACACGUUUCUGGUACUAAGUACUUCGAGAAAGUU----------ACCUGCGUAG------GA
((((((((.((((((.(((((((((....((((....((((((-......))-)))).))))....))))))))).)))))).).)))))))----------.(((....))------). ( -31.40)
>DroSec_CAF1 22074 99 - 1
GAUUUUCGGAAGUGCCUGGUAUCAGAUAGGUGUAAUUUUU-GU-GU--UUGU-AUAGUACACGUUUCUGGAACCAAGCCCUUUGAGAAACUU----------ACCUGCGGGG------UA
..((((((((.(.((.((((.(((((.(.(((((....((-((-(.--...)-))))))))).).))))).)))).))).))))))))...(----------(((.....))------)) ( -27.90)
>DroSim_CAF1 22156 96 - 1
GAUUUUCGCAAGUGCCUGGUUUCAGAGAGGUGUAAUUUUU-G------UUGU-AUAGUACCCUUUUUUGGAACCAAGCCCUUUGAGAAACUU----------ACCUGCGGGG------UA
..((((((.(((.((.((((((((((((((.(((......-.------....-....))).)))))))))))))).)).)))))))))...(----------(((.....))------)) ( -28.46)
>DroEre_CAF1 24050 99 - 1
GAUUUUCCCAAGUGCAUAGUAUCAGCAAGGUGUAAUUUUU-AU---UUGGGU-AAAGUACACGUUACUGGUACUAGGUACUUUGAGAAACAU----------GACUACGGAG------AA
..(((((..((((((.(((((((((.((.(((((...(((-((---....))-))).))))).)).))))))))).)))))).)))))....----------..(....)..------.. ( -29.80)
>DroYak_CAF1 21775 99 - 1
GAUUUUCCCAAGUGCUUAGUAUCAGCAAGGUGUAAUUUUU-GU---UUGGUU-AAAGUACACGUUACUGGUACUACGUACUUCGAGAAACCU----------AACUACGGAG------GA
...(((((.((((((.(((((((((.((.(((((...(((-(.---.....)-))).))))).)).))))))))).)))))).).))))(((----------..(....)))------). ( -30.90)
>DroAna_CAF1 22081 119 - 1
GUUGUUCAUAAUUUCUUAGAACCGGCAUCGUGUAUCUUGU-CUUAUUCUCGCACAAGUACACGGUUCCGACUCUAUGUAUUUUGAAACAAUUCUUCUGAAUUAAGUGUGUGAAUAUUUUA
..((((((((......((((..(((.((((((((.(((((-(........).))))))))))))).)))..)))).............(((((....))))).....))))))))..... ( -30.80)
>consensus
GAUUUUCCCAAGUGCCUAGUAUCAGCAAGGUGUAAUUUUU_GU___UUUUGU_AAAGUACACGUUUCUGGUACUAAGUACUUUGAGAAACUU__________AACUGCGGAG______UA
..(((((...(((((.(((((((((.((.(((((.((((..............))))))))).)).))))))))).)))))..)))))................................ (-20.18 = -20.07 +  -0.10)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,100,191 – 16,100,303
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 65.59
Mean single sequence MFE -21.00
Consensus MFE -10.38
Energy contribution -10.63
Covariance contribution 0.25
Combinations/Pair 1.38
Mean z-score -1.48
Structure conservation index 0.49
SVM decision value 0.39
SVM RNA-class probability 0.715068
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16100191 112 + 20766785
GUACUUAGUACCAGAAACGUGUACUUU-ACAUAAAC-AUAAAAAAUAACACUUUGCUGAUACCAGGCACUUGGGAAAAUCAUGUCU------AGAUUUGUCAACAUUUUAAAUGGCUUAC
(((...((((((......).))))).)-))......-.............((..((((((.((((....))))....)))).))..------))....((((..........)))).... ( -13.40)
>DroSec_CAF1 22098 109 + 1
GGGCUUGGUUCCAGAAACGUGUACUAU-ACAA--AC-AC-AAAAAUUACACCUAUCUGAUACCAGGCACUUCCGAAAAUCAUGUCU------AGAUUCCUCAACAUUUUAAUUGCCUUAC
(((((((((..((((...(((((....-....--..-..-......)))))...))))..))))))).............((((..------((....))..))))........)).... ( -21.87)
>DroSim_CAF1 22180 106 + 1
GGGCUUGGUUCCAAAAAAGGGUACUAU-ACAA------C-AAAAAUUACACCUCUCUGAAACCAGGCACUUGCGAAAAUCAUGUCU------AGAUUCCUCAACAUUUUAAUUGCCUUAC
..((((((((.((....((((((....-....------.-......))).)))...)).))))))))....((((.....((((..------((....))..)))).....))))..... ( -19.26)
>DroEre_CAF1 24074 102 + 1
GUACCUAGUACCAGUAACGUGUACUUU-ACCCAA---AU-AAAAAUUACACCUUGCUGAUACUAUGCACUUGGGAAAAUCAG-------------GUUCUAGACAUCUUAACUUAUUUAC
(((..(((((.((((((.(((((.(((-......---..-..))).))))).)))))).))))))))((((((.....))))-------------))....................... ( -20.30)
>DroYak_CAF1 21799 110 + 1
GUACGUAGUACCAGUAACGUGUACUUU-AACCAA---AC-AAAAAUUACACCUUGCUGAUACUAAGCACUUGGGAAAAUCAGAUCC-----AAGAGUCCUGGACAUCGGAAGCCACUUAC
.....(((((.((((((.(((((.(((-......---..-..))).))))).)))))).))))).((.((((((.........)))-----)))..(((........))).))....... ( -24.30)
>DroAna_CAF1 22121 113 + 1
AUACAUAGAGUCGGAACCGUGUACUUGUGCGAGAAUAAG-ACAAGAUACACGAUGCCGGUUCUAAGAAAUUAUGAACAACUUUUUUUUUCUUUAAUUCCAAGA------AAUCACUUUAC
.....(((((((((...(((((((((((.(........)-))))).))))))...)))(((((((....))).)))).........((((((.......))))------))..)))))). ( -26.90)
>consensus
GUACUUAGUACCAGAAACGUGUACUUU_ACAAAA___AC_AAAAAUUACACCUUGCUGAUACCAGGCACUUGGGAAAAUCAUGUCU______AGAUUCCUCAACAUUUUAAUUGCCUUAC
.....(((((.((((((.(((((.......................))))).)))))).)))))........................................................ (-10.38 = -10.63 +   0.25)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,100,191 – 16,100,303
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 65.59
Mean single sequence MFE -26.06
Consensus MFE -16.41
Energy contribution -16.11
Covariance contribution -0.30
Combinations/Pair 1.46
Mean z-score -1.30
Structure conservation index 0.63
SVM decision value 0.69
SVM RNA-class probability 0.824420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16100191 112 - 20766785
GUAAGCCAUUUAAAAUGUUGACAAAUCU------AGACAUGAUUUUCCCAAGUGCCUGGUAUCAGCAAAGUGUUAUUUUUUAU-GUUUAUGU-AAAGUACACGUUUCUGGUACUAAGUAC
.................(((..(((((.------......)))))...)))((((.(((((((((....((((....((((((-......))-)))).))))....))))))))).)))) ( -22.80)
>DroSec_CAF1 22098 109 - 1
GUAAGGCAAUUAAAAUGUUGAGGAAUCU------AGACAUGAUUUUCGGAAGUGCCUGGUAUCAGAUAGGUGUAAUUUUU-GU-GU--UUGU-AUAGUACACGUUUCUGGAACCAAGCCC
...(((((......(((((.((....))------.)))))......(....))))))(((.(((((.(.(((((....((-((-(.--...)-))))))))).).))))).)))...... ( -25.90)
>DroSim_CAF1 22180 106 - 1
GUAAGGCAAUUAAAAUGUUGAGGAAUCU------AGACAUGAUUUUCGCAAGUGCCUGGUUUCAGAGAGGUGUAAUUUUU-G------UUGU-AUAGUACCCUUUUUUGGAACCAAGCCC
...(((((......(((((.((....))------.)))))......(....))))))(((((((((((((.(((......-.------....-....))).)))))))))))))...... ( -26.66)
>DroEre_CAF1 24074 102 - 1
GUAAAUAAGUUAAGAUGUCUAGAAC-------------CUGAUUUUCCCAAGUGCAUAGUAUCAGCAAGGUGUAAUUUUU-AU---UUGGGU-AAAGUACACGUUACUGGUACUAGGUAC
.............((.(((......-------------..)))..))....((((.(((((((((.((.(((((...(((-((---....))-))).))))).)).))))))))).)))) ( -24.80)
>DroYak_CAF1 21799 110 - 1
GUAAGUGGCUUCCGAUGUCCAGGACUCUU-----GGAUCUGAUUUUCCCAAGUGCUUAGUAUCAGCAAGGUGUAAUUUUU-GU---UUGGUU-AAAGUACACGUUACUGGUACUACGUAC
.....(((........(((((((...)))-----)))).........))).((((.(((((((((.((.(((((...(((-(.---.....)-))).))))).)).))))))))).)))) ( -30.73)
>DroAna_CAF1 22121 113 - 1
GUAAAGUGAUU------UCUUGGAAUUAAAGAAAAAAAAAGUUGUUCAUAAUUUCUUAGAACCGGCAUCGUGUAUCUUGU-CUUAUUCUCGCACAAGUACACGGUUCCGACUCUAUGUAU
.........((------((((.......))))))......................((((..(((.((((((((.(((((-(........).))))))))))))).)))..))))..... ( -25.50)
>consensus
GUAAGGCAAUUAAAAUGUCGAGGAAUCU______AGACAUGAUUUUCCCAAGUGCCUAGUAUCAGCAAGGUGUAAUUUUU_GU___UUUUGU_AAAGUACACGUUUCUGGUACUAAGUAC
...................................................((((.(((((((((.((.(((((.((((..............))))))))).)).))))))))).)))) (-16.41 = -16.11 +  -0.30)

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 11:32:43 2006