Locus 6742

Sequence ID X_DroMel_CAF1
Location 16,759,569 – 16,759,724
Length 155
Max. P 0.827375
window11025 window11026 window11027 window11028

overview

Window 5

Location 16,759,569 – 16,759,689
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.82
Mean single sequence MFE -30.15
Consensus MFE -23.89
Energy contribution -23.95
Covariance contribution 0.06
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.79
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16759569 120 + 22224390
UGCUAUAAAGCAUUCGGUUUAAGGUUUUCCACUGCCACACGAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAAAAAGUCUA
((((....)))).....((((((..(((...(((.(((..(((.((((..........)))).)))....((((((..(....)..))))))))).)))..)))..))))))........ ( -28.30)
>DroSec_CAF1 46414 119 + 1
UGCCAUAAAGCAUUCGGUUUAAGGUUUUCCACUGCCACACGAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUA
(((......)))...((((((((..(((...(((.(((..(((.((((..........)))).)))....((((((..(....)..))))))))).)))..)))..))))))-))..... ( -30.80)
>DroSim_CAF1 44354 119 + 1
UGCUAUAAAGCAUUCGGUUUAAGGUUUUCCACUGCCACACGAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUA
((((....))))...((((((((..(((...(((.(((..(((.((((..........)))).)))....((((((..(....)..))))))))).)))..)))..))))))-))..... ( -32.20)
>DroYak_CAF1 38523 119 + 1
UGCUAUAAAGCAUUCGGUUUAAGGUUUUCCACUGCCACACAAAUAAUACUAUAGAUUUUAUUUCUCAAUUGCGGAAACUGCGACAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUA
((((....))))...((((((((..(((...(((.(((..((((((...........)))))).......((((((.(((...)))))))))))).)))..)))..))))))-))..... ( -29.30)
>consensus
UGCUAUAAAGCAUUCGGUUUAAGGUUUUCCACUGCCACACGAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA_UCUUGUA
(((......))).....((((((..(((...(((.(((..((((((...........)))))).......((((((..(....)..))))))))).)))..)))..))))))........ (-23.89 = -23.95 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 16,759,569 – 16,759,689
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.82
Mean single sequence MFE -28.18
Consensus MFE -25.77
Energy contribution -25.65
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -1.62
Structure conservation index 0.91
SVM decision value 0.28
SVM RNA-class probability 0.667027
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16759569 120 - 22224390
UAGACUUUUUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUCGUGUGGCAGUGGAAAACCUUAAACCGAAUGCUUUAUAGCA
........((((((...(((((((.((((((((......((((...)))).(((....)))................))))))))....))))))).)))))).....((((....)))) ( -28.10)
>DroSec_CAF1 46414 119 - 1
UACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUCGUGUGGCAGUGGAAAACCUUAAACCGAAUGCUUUAUGGCA
.....(.-((((((...(((((((.((((((((......((((...)))).(((....)))................))))))))....))))))).)))))).)...((((....)))) ( -28.70)
>DroSim_CAF1 44354 119 - 1
UACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUCGUGUGGCAGUGGAAAACCUUAAACCGAAUGCUUUAUAGCA
.....(.-((((((...(((((((.((((((((......((((...)))).(((....)))................))))))))....))))))).)))))).)...((((....)))) ( -28.70)
>DroYak_CAF1 38523 119 - 1
UACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUGUCGCAGUUUCCGCAAUUGAGAAAUAAAAUCUAUAGUAUUAUUUGUGUGGCAGUGGAAAACCUUAAACCGAAUGCUUUAUAGCA
.....(.-((((((...(((((((.((((((((((((...))).)))))).....(.((((((.((.....)).)))))).))))....))))))).)))))).)...((((....)))) ( -27.20)
>consensus
UACAAGA_UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUCGUGUGGCAGUGGAAAACCUUAAACCGAAUGCUUUAUAGCA
........((((((...(((((((.((((((((......((((...)))).(((....)))................))))))))....))))))).)))))).....((((....)))) (-25.77 = -25.65 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,759,609 – 16,759,724
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.52
Mean single sequence MFE -28.38
Consensus MFE -19.52
Energy contribution -20.52
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.15
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.827375
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16759609 115 + 22224390
GAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAAAAAGUCUAUAAAAAUAAUACGUUUCGAUUCGAUUCGAAAC-----GAU
.........((((((((((.((((((...(((((((..(....)..))))))).....))))))........)))))))))).........((((((((......)))))))-----).. ( -33.70)
>DroSec_CAF1 46454 109 + 1
GAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUAUAAAAAUAAUACGUUUCGA-----UUCGAAAC-----GAU
.....((((...((((((..((((((...(((((((..(....)..))))))).....)))))).....)))-))).))))..........(((((((.-----..))))))-----).. ( -30.40)
>DroSim_CAF1 44394 109 + 1
GAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUAUAAAAAUAAUACGUUUCGA-----UUCGAAAC-----GAU
.....((((...((((((..((((((...(((((((..(....)..))))))).....)))))).....)))-))).))))..........(((((((.-----..))))))-----).. ( -30.40)
>DroYak_CAF1 38563 114 + 1
AAAUAAUACUAUAGAUUUUAUUUCUCAAUUGCGGAAACUGCGACAGUUCCGCGUGUCGGAAAAAGUCUUAAA-UCUUGUAUAAAAAUAAUUCGUUUCGA-----UUCAAUUCAAUUAAAU
.....((((...((((((..(((((....(((((((.(((...))))))))))....))))).......)))-))).))))................((-----......))........ ( -19.00)
>consensus
GAAUAAUACUAUAGAUUUUAUUUUUCAAUUGCGGAAACCGCGAGAGUUCCGCGUGUCGGAAAAAGUCUUAAA_UCUUGUAUAAAAAUAAUACGUUUCGA_____UUCGAAAC_____GAU
............(((((((.(((..((...((((((..(....)..)))))).))..))).)))))))........................(((((((......)))))))........ (-19.52 = -20.52 +   1.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,759,609 – 16,759,724
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.52
Mean single sequence MFE -21.32
Consensus MFE -18.08
Energy contribution -18.45
Covariance contribution 0.37
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.85
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16759609 115 - 22224390
AUC-----GUUUCGAAUCGAAUCGAAACGUAUUAUUUUUAUAGACUUUUUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUC
..(-----(((((((......))))))))........(((((((.((((((((......(((((.....))))).....((((...))))..)))))))).....)))))))........ ( -26.00)
>DroSec_CAF1 46454 109 - 1
AUC-----GUUUCGAA-----UCGAAACGUAUUAUUUUUAUACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUC
..(-----((((((..-----.)))))))..........((((.(((-(((........(((((.....))))).....((((...))))............))))))...))))..... ( -20.80)
>DroSim_CAF1 44394 109 - 1
AUC-----GUUUCGAA-----UCGAAACGUAUUAUUUUUAUACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUC
..(-----((((((..-----.)))))))..........((((.(((-(((........(((((.....))))).....((((...))))............))))))...))))..... ( -20.80)
>DroYak_CAF1 38563 114 - 1
AUUUAAUUGAAUUGAA-----UCGAAACGAAUUAUUUUUAUACAAGA-UUUAAGACUUUUUCCGACACGCGGAACUGUCGCAGUUUCCGCAAUUGAGAAAUAAAAUCUAUAGUAUUAUUU
.((((((((..(((((-----((......((......))......))-)))))(((...(((((.....)))))..)))..........))))))))....................... ( -17.70)
>consensus
AUC_____GUUUCGAA_____UCGAAACGUAUUAUUUUUAUACAAGA_UUUAAGACUUUUUCCGACACGCGGAACUCUCGCGGUUUCCGCAAUUGAAAAAUAAAAUCUAUAGUAUUAUUC
........(((((((......)))))))...((((((((....................(((((.....))))).....((((...)))).....))))))))................. (-18.08 = -18.45 +   0.37)

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 12:21:41 2006