Locus 6623

Sequence ID X_DroMel_CAF1
Location 16,512,119 – 16,512,284
Length 165
Max. P 0.999990
window10818 window10819 window10820 window10821 window10822

overview

Window 8

Location 16,512,119 – 16,512,231
Length 112
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 73.21
Mean single sequence MFE -27.27
Consensus MFE -17.34
Energy contribution -16.57
Covariance contribution -0.77
Combinations/Pair 1.22
Mean z-score -3.44
Structure conservation index 0.64
SVM decision value 5.56
SVM RNA-class probability 0.999990
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16512119 112 + 22224390
AAUAAAUUAUUGUAGUUGAGAGAACGUUUUAAAAUGCUA-UAAUAGGUUGCCAUAAUUACCAUAUAGAAACUUAAGAACUUUUGGUGUUCCAAAGGUUCGAAAUGGAACAUUU
......(((((((((((((((.....)))))....))))-))))))(((.((((..........(((....))).((((((((((....))))))))))...))))))).... ( -23.40)
>DroSec_CAF1 8782 108 + 1
AAUAUAUUAC-----UUCUGGGAACGUUUUAAAAUGCUAAUGAUGGGUUGCCAUAAUUACCAUAUAGAAACUAAAGGACUUUUGGUGUUCCAAAGGUCCGAACUGGAACGUUU
..........-----......((((((((((..(((.((((.((((....)))).)))).)))............((((((((((....))))))))))....)))))))))) ( -30.50)
>DroEre_CAF1 8766 95 + 1
AAUAUAUCAAU--AG-------------UUCAAGUGGUA-UAAUAGGU-ACCAUAAUUCCCAUAUA-AAACUAUAGGACUUUUGGUAUCCCAGAGGUCCAAAAAUGAACAUUU
...........--.(-------------((((.((((((-(.....))-)))))............-........((((((((((....)))))))))).....))))).... ( -27.90)
>consensus
AAUAUAUUAAU__AGUU__G_GAACGUUUUAAAAUGCUA_UAAUAGGUUGCCAUAAUUACCAUAUAGAAACUAAAGGACUUUUGGUGUUCCAAAGGUCCGAAAUGGAACAUUU
...............................(((((.........(((..........)))..............((((((((((....)))))))))).........))))) (-17.34 = -16.57 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,512,119 – 16,512,231
Length 112
Sequences 3
Columns 113
Reading direction reverse
Mean pairwise identity 73.21
Mean single sequence MFE -21.40
Consensus MFE -11.88
Energy contribution -12.43
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -2.31
Structure conservation index 0.55
SVM decision value 1.88
SVM RNA-class probability 0.981078
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16512119 112 - 22224390
AAAUGUUCCAUUUCGAACCUUUGGAACACCAAAAGUUCUUAAGUUUCUAUAUGGUAAUUAUGGCAACCUAUUA-UAGCAUUUUAAAACGUUCUCUCAACUACAAUAAUUUAUU
.((((((.......((((.(((((....))))).))))(((((...(((((.(((..........)))...))-)))...)))))))))))...................... ( -16.00)
>DroSec_CAF1 8782 108 - 1
AAACGUUCCAGUUCGGACCUUUGGAACACCAAAAGUCCUUUAGUUUCUAUAUGGUAAUUAUGGCAACCCAUCAUUAGCAUUUUAAAACGUUCCCAGAA-----GUAAUAUAUU
.........(.(((((((.(((((....))))).))))....((((..(.(((.((((.((((....)))).)))).))).)..)))).......)))-----.)........ ( -22.80)
>DroEre_CAF1 8766 95 - 1
AAAUGUUCAUUUUUGGACCUCUGGGAUACCAAAAGUCCUAUAGUUU-UAUAUGGGAAUUAUGGU-ACCUAUUA-UACCACUUGAA-------------CU--AUUGAUAUAUU
....(((((....(((.....((((.(((((.((.(((((((....-..))))))).)).))))-)))))...-..)))..))))-------------).--........... ( -25.40)
>consensus
AAAUGUUCCAUUUCGGACCUUUGGAACACCAAAAGUCCUUUAGUUUCUAUAUGGUAAUUAUGGCAACCUAUUA_UAGCAUUUUAAAACGUUC_C__AACU__AAUAAUAUAUU
..............((((.(((((....))))).))))....(((.(((((.......))))).))).............................................. (-11.88 = -12.43 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,512,156 – 16,512,260
Length 104
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 77.38
Mean single sequence MFE -23.13
Consensus MFE -16.12
Energy contribution -15.57
Covariance contribution -0.55
Combinations/Pair 1.19
Mean z-score -2.43
Structure conservation index 0.70
SVM decision value 2.60
SVM RNA-class probability 0.995640
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16512156 104 + 22224390
UA-UAAUAGGUUGCCAUAAUUACCAUAUAGAAACUUAAGAACUUUUGGUGUUCCAAAGGUUCGAAAUGGAACAUUUUUAUUU-----------AACUAAUAUCUUGAAAGCGAAAA
..-.......((((........................((((((((((....)))))))))).(((((((.....)))))))-----------................))))... ( -17.20)
>DroSec_CAF1 8814 116 + 1
UAAUGAUGGGUUGCCAUAAUUACCAUAUAGAAACUAAAGGACUUUUGGUGUUCCAAAGGUCCGAACUGGAACGUUUUUAUAUUUUUAUCAUGGAACUUAUAUCUCGAAAGCGAAAA
.....(((((((.((((.((....((((((((((....((((((((((....))))))))))(........)))))))))))....)).))))))))))).((.(....).))... ( -33.20)
>DroEre_CAF1 8788 100 + 1
UA-UAAUAGGU-ACCAUAAUUCCCAUAUA-AAACUAUAGGACUUUUGGUAUCCCAGAGGUCCAAAAAUGAACAUUUUAAUUC-----------AACUU-UAUCUCGAAACCGAA-A
..-.....(((-.................-........((((((((((....)))))))))).....((((........)))-----------)....-.........)))...-. ( -19.00)
>consensus
UA_UAAUAGGUUGCCAUAAUUACCAUAUAGAAACUAAAGGACUUUUGGUGUUCCAAAGGUCCGAAAUGGAACAUUUUUAUUU___________AACUUAUAUCUCGAAAGCGAAAA
........(((..........)))..............((((((((((....)))))))))).........................................(((....)))... (-16.12 = -15.57 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,512,191 – 16,512,284
Length 93
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 69.37
Mean single sequence MFE -23.50
Consensus MFE -15.82
Energy contribution -14.93
Covariance contribution -0.88
Combinations/Pair 1.23
Mean z-score -2.37
Structure conservation index 0.67
SVM decision value 5.00
SVM RNA-class probability 0.999968
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16512191 93 + 22224390
AAGAACUUUUGGUGUUCCAAAGGUUCGAAAUGGAACAUUUUUAUUU-----------AACUAAUAUCUUGAAAGCGAAAAAAGCAAAAGAUUUUU-GA---------------UAAGUGU
..((((((((((....))))))))))((((((...))))))(((((-----------(.(....(((((....((.......))..)))))....-).---------------)))))). ( -20.10)
>DroSec_CAF1 8850 105 + 1
AAGGACUUUUGGUGUUCCAAAGGUCCGAACUGGAACGUUUUUAUAUUUUUAUCAUGGAACUUAUAUCUCGAAAGCGAAAAAAGUAAAAGAUUUUUGGA---------------UAAGUGU
..((((((((((....))))))))))...(..(((.((((((.(((((((.((..(((.......)))(....).)).))))))))))))))))..).---------------....... ( -24.80)
>DroEre_CAF1 8821 106 + 1
UAGGACUUUUGGUAUCCCAGAGGUCCAAAAAUGAACAUUUUAAUUC-----------AACUU-UAUCUCGAAACCGAA-AAUGCAAUAGAUUUUU-GAUUUUUGUUUAGUUUCUGAGUUU
..((((((((((....)))))))))).....((((........)))-----------)....-...((((((((((((-(((.(((.......))-))))))))....))))).)))... ( -25.60)
>consensus
AAGGACUUUUGGUGUUCCAAAGGUCCGAAAUGGAACAUUUUUAUUU___________AACUUAUAUCUCGAAAGCGAAAAAAGCAAAAGAUUUUU_GA_______________UAAGUGU
..((((((((((....)))))))))).........................................(((....)))........................................... (-15.82 = -14.93 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,512,191 – 16,512,284
Length 93
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 69.37
Mean single sequence MFE -16.03
Consensus MFE -10.43
Energy contribution -10.77
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -1.63
Structure conservation index 0.65
SVM decision value 2.04
SVM RNA-class probability 0.986518
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16512191 93 - 22224390
ACACUUA---------------UC-AAAAAUCUUUUGCUUUUUUCGCUUUCAAGAUAUUAGUU-----------AAAUAAAAAUGUUCCAUUUCGAACCUUUGGAACACCAAAAGUUCUU
..((((.---------------..-....(((((..((.......))....))))).......-----------.........(((((((...........)))))))....)))).... ( -11.70)
>DroSec_CAF1 8850 105 - 1
ACACUUA---------------UCCAAAAAUCUUUUACUUUUUUCGCUUUCGAGAUAUAAGUUCCAUGAUAAAAAUAUAAAAACGUUCCAGUUCGGACCUUUGGAACACCAAAAGUCCUU
.......---------------.......(((....((((.(((((....)))))...)))).....)))........................((((.(((((....))))).)))).. ( -16.90)
>DroEre_CAF1 8821 106 - 1
AAACUCAGAAACUAAACAAAAAUC-AAAAAUCUAUUGCAUU-UUCGGUUUCGAGAUA-AAGUU-----------GAAUUAAAAUGUUCAUUUUUGGACCUCUGGGAUACCAAAAGUCCUA
...(((.((((((.....((((((-((.......))).)))-)).)))))))))..(-(((.(-----------((((......))))).))))((((...(((....)))...)))).. ( -19.50)
>consensus
ACACUUA_______________UC_AAAAAUCUUUUGCUUUUUUCGCUUUCGAGAUAUAAGUU___________AAAUAAAAAUGUUCCAUUUCGGACCUUUGGAACACCAAAAGUCCUU
....................................((((...((........))...))))................................((((.(((((....))))).)))).. (-10.43 = -10.77 +   0.34)

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 12:18:35 2006