Locus 860

Sequence ID 2R_DroMel_CAF1
Location 4,017,010 – 4,017,266
Length 256
Max. P 0.968939
window1487 window1488 window1489 window1490

overview

Window 7

Location 4,017,010 – 4,017,109
Length 99
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 83.95
Mean single sequence MFE -23.15
Consensus MFE -22.63
Energy contribution -21.97
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -0.72
Structure conservation index 0.98
SVM decision value 0.95
SVM RNA-class probability 0.887681
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4017010 99 - 20766785
AAUGCCAAUUUGUUUUAUGGGCGACAAGUUAAGCUUGCCUUUGCUUUGCUUUGAUGUUGAUUUUUAUAUUAUGAUGUCGGAGCGCCCAU--------------GCCCCA-------UCCU
...............((((((((.((((.....)))).)........((((((((((((((......)))..)))))))))))))))))--------------).....-------.... ( -25.20)
>DroSim_CAF1 1924 109 - 1
AAUGCCAAUUUGUUUUAUGGGCGACAAGUUAAGCUUGCCUUUGCUUUGCUUUGAUGUUGAUUUUUAUAUUAUGAUGUUGGAGCGCCCAUCCCC--------AUGCCCCCUGUU---UCCC
................(((((((.((((.....)))).)........((((..((((((((......)))..)))))..))))))))))....--------............---.... ( -22.40)
>DroYak_CAF1 1706 120 - 1
AAUGCCAAUUUGUUUUAUGGGUGACAAGUUGAGCUUGCCUUUGCUUUGCUUUGAUGUUGAUUUUUAUAUUAUGAUGUCGGAGCGCCCAUCCCCUAUCCCCCAUCCCCCAUCUCCCAUCCU
................(((((.((.((((.((((........)))).))))((((((........)))))).((((..(((..............)))..)))).....)).)))))... ( -21.84)
>consensus
AAUGCCAAUUUGUUUUAUGGGCGACAAGUUAAGCUUGCCUUUGCUUUGCUUUGAUGUUGAUUUUUAUAUUAUGAUGUCGGAGCGCCCAUCCCC________AUGCCCCAU_U____UCCU
................((((((........((((........)))).((((((((((((((......)))..)))))))))))))))))............................... (-22.63 = -21.97 +  -0.66)

alignment

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secondary structure

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Window 8

Location 4,017,029 – 4,017,149
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -23.73
Consensus MFE -21.83
Energy contribution -22.50
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.68
Structure conservation index 0.92
SVM decision value 1.63
SVM RNA-class probability 0.968939
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4017029 120 + 20766785
CCGACAUCAUAAUAUAAAAAUCAACAUCAAAGCAAAGCAAAGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAA
..(((((((((((((((((((....................((((((.....))))))(((.((.......)).)))))))))).))))))(((.....)))..)))))).......... ( -26.10)
>DroSim_CAF1 1953 120 + 1
CCAACAUCAUAAUAUAAAAAUCAACAUCAAAGCAAAGCAAAGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAA
...((((((((((((((((((....................((((((.....))))))(((.((.......)).)))))))))).))))))(((.....)))..)))))........... ( -21.60)
>DroYak_CAF1 1746 120 + 1
CCGACAUCAUAAUAUAAAAAUCAACAUCAAAGCAAAGCAAAGGCAAGCUCAACUUGUCACCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAA
..(((((((((((((((((((....................((((((.....))))))..(((..........))).))))))).))))))(((.....)))..)))))).......... ( -23.50)
>consensus
CCGACAUCAUAAUAUAAAAAUCAACAUCAAAGCAAAGCAAAGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAA
..(((((((((((((((((((....................((((((.....))))))(((.((.......)).)))))))))).))))))(((.....)))..)))))).......... (-21.83 = -22.50 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,017,069 – 4,017,186
Length 117
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 98.86
Mean single sequence MFE -27.94
Consensus MFE -27.94
Energy contribution -27.94
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 1.00
SVM decision value 0.69
SVM RNA-class probability 0.822634
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4017069 117 + 20766785
AGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAACCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCG
.((((((.....))))))................(((.............((((.....))))(((((..............)))))....((((..((....))))))....))). ( -27.94)
>DroSim_CAF1 1993 117 + 1
AGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAACCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCG
.((((((.....))))))................(((.............((((.....))))(((((..............)))))....((((..((....))))))....))). ( -27.94)
>DroYak_CAF1 1786 117 + 1
AGGCAAGCUCAACUUGUCACCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAACCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCG
.((((((.....))))))................(((.............((((.....))))(((((..............)))))....((((..((....))))))....))). ( -27.94)
>consensus
AGGCAAGCUUAACUUGUCGCCCAUAAAACAAAUUGGCAUUUUUAUUAUUAUGACAAACAGUCAGGAUGUCACACAGUCAACCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCG
.((((((.....))))))................(((.............((((.....))))(((((..............)))))....((((..((....))))))....))). (-27.94 = -27.94 +  -0.00)

alignment

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secondary structure

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Window 0

Location 4,017,149 – 4,017,266
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 96.24
Mean single sequence MFE -36.24
Consensus MFE -31.56
Energy contribution -31.32
Covariance contribution -0.24
Combinations/Pair 1.10
Mean z-score -1.40
Structure conservation index 0.87
SVM decision value 0.42
SVM RNA-class probability 0.731066
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4017149 117 + 20766785
CCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCGGAAAAGCGGCGACGGGCCACAAUGAGCUACGCUUAUCUUUUGAAAGCAGCUAAACCGCUUUUGAUUAUGUGGAAGUUGUU
(((.((.....((((..((....))))))....((((......)))))).)))(((((((((((...))))))...(..(((((.........)))))..)...)))))........ ( -35.50)
>DroSec_CAF1 21 117 + 1
CCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCGGAAAAGCGGCGACGGGCCACAAUGAGCUACGCUUAUCUUUUGAAAGCAGCUAAACUGCUUUUGAUUAUGUGGAAGUUGUU
(((.((.....((((..((....))))))....((((......)))))).)))(((((((((((...))))))...(..(((((((.....)))))))..)...)))))........ ( -40.10)
>DroSim_CAF1 2073 117 + 1
CCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCGGAAAAGCGGCGACGGGCCACAAUGAGCUACGCUUAUCUUUUGAAAGCAGCUAAACCGCUUUUGAUUAUGUGGAAGUUGUU
(((.((.....((((..((....))))))....((((......)))))).)))(((((((((((...))))))...(..(((((.........)))))..)...)))))........ ( -35.50)
>DroEre_CAF1 19 116 + 1
CCCAUCCAAGAGCUCGU-GGAGAUUAAGGAAAACCCGGAAAAGCGGCGACGGGCCACAAUGAGCCACGCUUAUCUUUUGAAAGCAGCUAAAGCGCUUUUGAUUAUGUGGAAGUUGUU
.((.((((.(....).)-)))......((.....))))......((((((...(((((((((((...))))))...(..(((((.((....)))))))..)...)))))..)))))) ( -32.00)
>DroYak_CAF1 1866 117 + 1
CCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCGGAAAAGCGGCGACGGGCCGCAAUGAGCCACGCUUAUCUUUUGAAAGCAGCUAAAGCGCUUUUGAUUAUGUGGAAGUUGUU
(((.((.....((((..((....))))))....((((......)))))).)))(((((((((((...))))))...(..(((((.((....)))))))..)...)))))........ ( -38.10)
>consensus
CCCAUCCAAGACCUCGCAGGAGACUGAGGAAAAGCCGGAAAAGCGGCGACGGGCCACAAUGAGCUACGCUUAUCUUUUGAAAGCAGCUAAACCGCUUUUGAUUAUGUGGAAGUUGUU
(((.(((..(....).(((....))).)))...((((......))))...)))(((((((((((...))))))...(..(((((.........)))))..)...)))))........ (-31.56 = -31.32 +  -0.24)

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 09:49:09 2006